Starting phenix.real_space_refine on Thu Jan 15 17:17:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pxf_13701/01_2026/7pxf_13701.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pxf_13701/01_2026/7pxf_13701.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pxf_13701/01_2026/7pxf_13701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pxf_13701/01_2026/7pxf_13701.map" model { file = "/net/cci-nas-00/data/ceres_data/7pxf_13701/01_2026/7pxf_13701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pxf_13701/01_2026/7pxf_13701.cif" } resolution = 2.68 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= 0.000 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 3 8.98 5 Mg 4 5.21 5 S 192 5.16 5 C 18192 2.51 5 N 4592 2.21 5 O 5116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28099 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 885, 7023 Classifications: {'peptide': 885} Link IDs: {'PTRANS': 32, 'TRANS': 852} Chain breaks: 5 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' K': 3, ' MG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Restraints were copied for chains: B, C, D Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" K K A1202 " occ=0.25 residue: pdb=" K K A1203 " occ=0.25 residue: pdb=" K K A1204 " occ=0.10 Time building chain proxies: 7.77, per 1000 atoms: 0.28 Number of scatterers: 28099 At special positions: 0 Unit cell: (150.5, 150.5, 133, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 3 19.00 S 192 16.00 Mg 4 11.99 O 5116 8.00 N 4592 7.00 C 18192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.70 Conformation dependent library (CDL) restraints added in 1.3 seconds 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6696 Finding SS restraints... Secondary structure from input PDB file: 184 helices and 24 sheets defined 54.6% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 48 through 67 removed outlier: 3.599A pdb=" N GLY A 63 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU A 64 " --> pdb=" O PHE A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 75 removed outlier: 3.688A pdb=" N PHE A 73 " --> pdb=" O TRP A 70 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA A 74 " --> pdb=" O ARG A 71 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE A 75 " --> pdb=" O ALA A 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 70 through 75' Processing helix chain 'A' and resid 107 through 119 removed outlier: 3.524A pdb=" N ALA A 111 " --> pdb=" O PHE A 107 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS A 112 " --> pdb=" O MET A 108 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 149 removed outlier: 3.582A pdb=" N LEU A 132 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 146 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP A 147 " --> pdb=" O ILE A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 177 removed outlier: 3.907A pdb=" N LEU A 169 " --> pdb=" O GLN A 165 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL A 177 " --> pdb=" O ILE A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 185 removed outlier: 3.606A pdb=" N ILE A 181 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG A 182 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA A 185 " --> pdb=" O ILE A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 194 removed outlier: 3.728A pdb=" N LEU A 194 " --> pdb=" O TRP A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 203 removed outlier: 3.743A pdb=" N ASP A 201 " --> pdb=" O TYR A 197 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE A 203 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 214 removed outlier: 3.581A pdb=" N SER A 208 " --> pdb=" O THR A 204 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A 209 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER A 211 " --> pdb=" O PRO A 207 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR A 213 " --> pdb=" O PHE A 209 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU A 214 " --> pdb=" O VAL A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 230 Processing helix chain 'A' and resid 231 through 239 Processing helix chain 'A' and resid 244 through 274 Processing helix chain 'A' and resid 287 through 300 removed outlier: 3.661A pdb=" N TYR A 293 " --> pdb=" O TRP A 289 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL A 297 " --> pdb=" O TYR A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 342 removed outlier: 3.652A pdb=" N CYS A 332 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 333 " --> pdb=" O PHE A 329 " (cutoff:3.500A) Proline residue: A 334 - end of helix removed outlier: 4.473A pdb=" N ASP A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU A 339 " --> pdb=" O GLU A 335 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR A 342 " --> pdb=" O ASP A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 378 removed outlier: 4.308A pdb=" N HIS A 372 " --> pdb=" O GLU A 368 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 373 " --> pdb=" O SER A 369 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP A 376 " --> pdb=" O HIS A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 408 removed outlier: 4.066A pdb=" N LEU A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 428 Processing helix chain 'A' and resid 429 through 433 Processing helix chain 'A' and resid 446 through 465 Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 479 through 485 removed outlier: 4.013A pdb=" N LEU A 483 " --> pdb=" O ASN A 479 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 484 " --> pdb=" O LYS A 480 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN A 485 " --> pdb=" O ALA A 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 479 through 485' Processing helix chain 'A' and resid 500 through 514 removed outlier: 3.560A pdb=" N LEU A 513 " --> pdb=" O ALA A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 525 Processing helix chain 'A' and resid 537 through 548 Processing helix chain 'A' and resid 557 through 561 removed outlier: 3.553A pdb=" N ILE A 561 " --> pdb=" O PRO A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 575 Processing helix chain 'A' and resid 617 through 626 removed outlier: 4.091A pdb=" N VAL A 621 " --> pdb=" O SER A 617 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG A 623 " --> pdb=" O ASP A 619 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA A 624 " --> pdb=" O GLU A 620 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N TRP A 625 " --> pdb=" O VAL A 621 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE A 626 " --> pdb=" O LYS A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 796 No H-bonds generated for 'chain 'A' and resid 794 through 796' Processing helix chain 'A' and resid 800 through 807 Processing helix chain 'A' and resid 828 through 836 Proline residue: A 834 - end of helix Processing helix chain 'A' and resid 853 through 859 removed outlier: 3.566A pdb=" N ARG A 859 " --> pdb=" O ASP A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 865 removed outlier: 3.755A pdb=" N MET A 863 " --> pdb=" O GLU A 860 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN A 865 " --> pdb=" O LYS A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 887 removed outlier: 3.682A pdb=" N LEU A 883 " --> pdb=" O SER A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 891 Processing helix chain 'A' and resid 907 through 911 removed outlier: 4.341A pdb=" N ASP A 911 " --> pdb=" O THR A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 924 Processing helix chain 'A' and resid 960 through 964 Processing helix chain 'A' and resid 975 through 979 Processing helix chain 'A' and resid 990 through 993 Processing helix chain 'A' and resid 994 through 999 Processing helix chain 'A' and resid 1005 through 1018 removed outlier: 3.969A pdb=" N ASP A1009 " --> pdb=" O VAL A1005 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET A1012 " --> pdb=" O LEU A1008 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER A1013 " --> pdb=" O ASP A1009 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A1014 " --> pdb=" O SER A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1030 removed outlier: 4.353A pdb=" N THR A1023 " --> pdb=" O GLN A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1042 removed outlier: 3.938A pdb=" N GLU A1038 " --> pdb=" O THR A1034 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU A1039 " --> pdb=" O PRO A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1061 Processing helix chain 'A' and resid 1073 through 1079 removed outlier: 4.154A pdb=" N GLN A1077 " --> pdb=" O PRO A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1095 Processing helix chain 'B' and resid 48 through 67 removed outlier: 3.599A pdb=" N GLY B 63 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU B 64 " --> pdb=" O PHE B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 removed outlier: 3.688A pdb=" N PHE B 73 " --> pdb=" O TRP B 70 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA B 74 " --> pdb=" O ARG B 71 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE B 75 " --> pdb=" O ALA B 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 70 through 75' Processing helix chain 'B' and resid 107 through 119 removed outlier: 3.524A pdb=" N ALA B 111 " --> pdb=" O PHE B 107 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS B 112 " --> pdb=" O MET B 108 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY B 116 " --> pdb=" O LYS B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 149 removed outlier: 3.581A pdb=" N LEU B 132 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B 133 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE B 134 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER B 137 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL B 146 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP B 147 " --> pdb=" O ILE B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 177 removed outlier: 3.908A pdb=" N LEU B 169 " --> pdb=" O GLN B 165 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL B 177 " --> pdb=" O ILE B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 185 removed outlier: 3.606A pdb=" N ILE B 181 " --> pdb=" O VAL B 177 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG B 182 " --> pdb=" O TYR B 178 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA B 185 " --> pdb=" O ILE B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 194 removed outlier: 3.729A pdb=" N LEU B 194 " --> pdb=" O TRP B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 203 removed outlier: 3.744A pdb=" N ASP B 201 " --> pdb=" O TYR B 197 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE B 203 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 removed outlier: 3.582A pdb=" N SER B 208 " --> pdb=" O THR B 204 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE B 209 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER B 211 " --> pdb=" O PRO B 207 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR B 213 " --> pdb=" O PHE B 209 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU B 214 " --> pdb=" O VAL B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 230 Processing helix chain 'B' and resid 231 through 239 Processing helix chain 'B' and resid 244 through 274 Processing helix chain 'B' and resid 287 through 300 removed outlier: 3.661A pdb=" N TYR B 293 " --> pdb=" O TRP B 289 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL B 297 " --> pdb=" O TYR B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 342 removed outlier: 3.652A pdb=" N CYS B 332 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE B 333 " --> pdb=" O PHE B 329 " (cutoff:3.500A) Proline residue: B 334 - end of helix removed outlier: 4.473A pdb=" N ASP B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU B 339 " --> pdb=" O GLU B 335 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE B 340 " --> pdb=" O ILE B 336 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR B 342 " --> pdb=" O ASP B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 378 removed outlier: 4.307A pdb=" N HIS B 372 " --> pdb=" O GLU B 368 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE B 373 " --> pdb=" O SER B 369 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP B 376 " --> pdb=" O HIS B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 408 removed outlier: 4.066A pdb=" N LEU B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 428 Processing helix chain 'B' and resid 429 through 433 Processing helix chain 'B' and resid 446 through 465 Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 479 through 485 removed outlier: 4.013A pdb=" N LEU B 483 " --> pdb=" O ASN B 479 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 484 " --> pdb=" O LYS B 480 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN B 485 " --> pdb=" O ALA B 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 479 through 485' Processing helix chain 'B' and resid 500 through 514 removed outlier: 3.560A pdb=" N LEU B 513 " --> pdb=" O ALA B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 525 Processing helix chain 'B' and resid 537 through 548 Processing helix chain 'B' and resid 557 through 561 removed outlier: 3.553A pdb=" N ILE B 561 " --> pdb=" O PRO B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 575 Processing helix chain 'B' and resid 617 through 626 removed outlier: 4.091A pdb=" N VAL B 621 " --> pdb=" O SER B 617 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG B 623 " --> pdb=" O ASP B 619 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA B 624 " --> pdb=" O GLU B 620 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N TRP B 625 " --> pdb=" O VAL B 621 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE B 626 " --> pdb=" O LYS B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 796 No H-bonds generated for 'chain 'B' and resid 794 through 796' Processing helix chain 'B' and resid 800 through 807 Processing helix chain 'B' and resid 828 through 836 Proline residue: B 834 - end of helix Processing helix chain 'B' and resid 853 through 859 removed outlier: 3.567A pdb=" N ARG B 859 " --> pdb=" O ASP B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 865 removed outlier: 3.754A pdb=" N MET B 863 " --> pdb=" O GLU B 860 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN B 865 " --> pdb=" O LYS B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 887 removed outlier: 3.682A pdb=" N LEU B 883 " --> pdb=" O SER B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 891 Processing helix chain 'B' and resid 907 through 911 removed outlier: 4.341A pdb=" N ASP B 911 " --> pdb=" O THR B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 924 Processing helix chain 'B' and resid 960 through 964 Processing helix chain 'B' and resid 975 through 979 Processing helix chain 'B' and resid 990 through 993 Processing helix chain 'B' and resid 994 through 999 Processing helix chain 'B' and resid 1005 through 1018 removed outlier: 3.968A pdb=" N ASP B1009 " --> pdb=" O VAL B1005 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET B1012 " --> pdb=" O LEU B1008 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER B1013 " --> pdb=" O ASP B1009 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR B1014 " --> pdb=" O SER B1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 1019 through 1030 removed outlier: 4.353A pdb=" N THR B1023 " --> pdb=" O GLN B1019 " (cutoff:3.500A) Processing helix chain 'B' and resid 1034 through 1042 removed outlier: 3.939A pdb=" N GLU B1038 " --> pdb=" O THR B1034 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU B1039 " --> pdb=" O PRO B1035 " (cutoff:3.500A) Processing helix chain 'B' and resid 1056 through 1061 Processing helix chain 'B' and resid 1073 through 1079 removed outlier: 4.155A pdb=" N GLN B1077 " --> pdb=" O PRO B1074 " (cutoff:3.500A) Processing helix chain 'B' and resid 1083 through 1095 Processing helix chain 'C' and resid 48 through 67 removed outlier: 3.600A pdb=" N GLY C 63 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU C 64 " --> pdb=" O PHE C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 75 removed outlier: 3.687A pdb=" N PHE C 73 " --> pdb=" O TRP C 70 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA C 74 " --> pdb=" O ARG C 71 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE C 75 " --> pdb=" O ALA C 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 70 through 75' Processing helix chain 'C' and resid 107 through 119 removed outlier: 3.524A pdb=" N ALA C 111 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS C 112 " --> pdb=" O MET C 108 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 149 removed outlier: 3.581A pdb=" N LEU C 132 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL C 133 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE C 134 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER C 137 " --> pdb=" O VAL C 133 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL C 146 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP C 147 " --> pdb=" O ILE C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 177 removed outlier: 3.907A pdb=" N LEU C 169 " --> pdb=" O GLN C 165 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE C 174 " --> pdb=" O ALA C 170 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL C 177 " --> pdb=" O ILE C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 185 removed outlier: 3.607A pdb=" N ILE C 181 " --> pdb=" O VAL C 177 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG C 182 " --> pdb=" O TYR C 178 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA C 185 " --> pdb=" O ILE C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 194 removed outlier: 3.729A pdb=" N LEU C 194 " --> pdb=" O TRP C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 203 removed outlier: 3.743A pdb=" N ASP C 201 " --> pdb=" O TYR C 197 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE C 203 " --> pdb=" O PHE C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 214 removed outlier: 3.582A pdb=" N SER C 208 " --> pdb=" O THR C 204 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE C 209 " --> pdb=" O ILE C 205 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER C 211 " --> pdb=" O PRO C 207 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR C 213 " --> pdb=" O PHE C 209 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU C 214 " --> pdb=" O VAL C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 230 Processing helix chain 'C' and resid 231 through 239 Processing helix chain 'C' and resid 244 through 274 Processing helix chain 'C' and resid 287 through 300 removed outlier: 3.660A pdb=" N TYR C 293 " --> pdb=" O TRP C 289 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL C 297 " --> pdb=" O TYR C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 342 removed outlier: 3.652A pdb=" N CYS C 332 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE C 333 " --> pdb=" O PHE C 329 " (cutoff:3.500A) Proline residue: C 334 - end of helix removed outlier: 4.473A pdb=" N ASP C 338 " --> pdb=" O PRO C 334 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU C 339 " --> pdb=" O GLU C 335 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE C 340 " --> pdb=" O ILE C 336 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR C 342 " --> pdb=" O ASP C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 378 removed outlier: 4.307A pdb=" N HIS C 372 " --> pdb=" O GLU C 368 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE C 373 " --> pdb=" O SER C 369 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP C 376 " --> pdb=" O HIS C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 408 removed outlier: 4.067A pdb=" N LEU C 404 " --> pdb=" O GLU C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 428 Processing helix chain 'C' and resid 429 through 433 Processing helix chain 'C' and resid 446 through 465 Processing helix chain 'C' and resid 476 through 478 No H-bonds generated for 'chain 'C' and resid 476 through 478' Processing helix chain 'C' and resid 479 through 485 removed outlier: 4.013A pdb=" N LEU C 483 " --> pdb=" O ASN C 479 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU C 484 " --> pdb=" O LYS C 480 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN C 485 " --> pdb=" O ALA C 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 479 through 485' Processing helix chain 'C' and resid 500 through 514 removed outlier: 3.560A pdb=" N LEU C 513 " --> pdb=" O ALA C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 525 Processing helix chain 'C' and resid 537 through 548 Processing helix chain 'C' and resid 557 through 561 removed outlier: 3.554A pdb=" N ILE C 561 " --> pdb=" O PRO C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 575 Processing helix chain 'C' and resid 617 through 626 removed outlier: 4.092A pdb=" N VAL C 621 " --> pdb=" O SER C 617 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG C 623 " --> pdb=" O ASP C 619 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA C 624 " --> pdb=" O GLU C 620 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N TRP C 625 " --> pdb=" O VAL C 621 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE C 626 " --> pdb=" O LYS C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 794 through 796 No H-bonds generated for 'chain 'C' and resid 794 through 796' Processing helix chain 'C' and resid 800 through 807 Processing helix chain 'C' and resid 828 through 836 Proline residue: C 834 - end of helix Processing helix chain 'C' and resid 853 through 859 removed outlier: 3.567A pdb=" N ARG C 859 " --> pdb=" O ASP C 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 860 through 865 removed outlier: 3.755A pdb=" N MET C 863 " --> pdb=" O GLU C 860 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN C 865 " --> pdb=" O LYS C 862 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 887 removed outlier: 3.683A pdb=" N LEU C 883 " --> pdb=" O SER C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 888 through 891 Processing helix chain 'C' and resid 907 through 911 removed outlier: 4.341A pdb=" N ASP C 911 " --> pdb=" O THR C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 924 Processing helix chain 'C' and resid 960 through 964 Processing helix chain 'C' and resid 975 through 979 Processing helix chain 'C' and resid 990 through 993 Processing helix chain 'C' and resid 994 through 999 Processing helix chain 'C' and resid 1005 through 1018 removed outlier: 3.967A pdb=" N ASP C1009 " --> pdb=" O VAL C1005 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET C1012 " --> pdb=" O LEU C1008 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER C1013 " --> pdb=" O ASP C1009 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR C1014 " --> pdb=" O SER C1010 " (cutoff:3.500A) Processing helix chain 'C' and resid 1019 through 1030 removed outlier: 4.353A pdb=" N THR C1023 " --> pdb=" O GLN C1019 " (cutoff:3.500A) Processing helix chain 'C' and resid 1034 through 1042 removed outlier: 3.938A pdb=" N GLU C1038 " --> pdb=" O THR C1034 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU C1039 " --> pdb=" O PRO C1035 " (cutoff:3.500A) Processing helix chain 'C' and resid 1056 through 1061 Processing helix chain 'C' and resid 1073 through 1079 removed outlier: 4.154A pdb=" N GLN C1077 " --> pdb=" O PRO C1074 " (cutoff:3.500A) Processing helix chain 'C' and resid 1083 through 1095 Processing helix chain 'D' and resid 48 through 67 removed outlier: 3.599A pdb=" N GLY D 63 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU D 64 " --> pdb=" O PHE D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 75 removed outlier: 3.688A pdb=" N PHE D 73 " --> pdb=" O TRP D 70 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA D 74 " --> pdb=" O ARG D 71 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE D 75 " --> pdb=" O ALA D 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 70 through 75' Processing helix chain 'D' and resid 107 through 119 removed outlier: 3.525A pdb=" N ALA D 111 " --> pdb=" O PHE D 107 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS D 112 " --> pdb=" O MET D 108 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP D 113 " --> pdb=" O THR D 109 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY D 116 " --> pdb=" O LYS D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 149 removed outlier: 3.582A pdb=" N LEU D 132 " --> pdb=" O ILE D 128 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL D 133 " --> pdb=" O LEU D 129 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE D 134 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU D 136 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER D 137 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL D 146 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP D 147 " --> pdb=" O ILE D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 177 removed outlier: 3.907A pdb=" N LEU D 169 " --> pdb=" O GLN D 165 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL D 177 " --> pdb=" O ILE D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 185 removed outlier: 3.606A pdb=" N ILE D 181 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG D 182 " --> pdb=" O TYR D 178 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA D 185 " --> pdb=" O ILE D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 194 removed outlier: 3.729A pdb=" N LEU D 194 " --> pdb=" O TRP D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 203 removed outlier: 3.744A pdb=" N ASP D 201 " --> pdb=" O TYR D 197 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE D 203 " --> pdb=" O PHE D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 214 removed outlier: 3.582A pdb=" N SER D 208 " --> pdb=" O THR D 204 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE D 209 " --> pdb=" O ILE D 205 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER D 211 " --> pdb=" O PRO D 207 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR D 213 " --> pdb=" O PHE D 209 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU D 214 " --> pdb=" O VAL D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 230 Processing helix chain 'D' and resid 231 through 239 Processing helix chain 'D' and resid 244 through 274 Processing helix chain 'D' and resid 287 through 300 removed outlier: 3.660A pdb=" N TYR D 293 " --> pdb=" O TRP D 289 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL D 297 " --> pdb=" O TYR D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 342 removed outlier: 3.653A pdb=" N CYS D 332 " --> pdb=" O ILE D 328 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE D 333 " --> pdb=" O PHE D 329 " (cutoff:3.500A) Proline residue: D 334 - end of helix removed outlier: 4.473A pdb=" N ASP D 338 " --> pdb=" O PRO D 334 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU D 339 " --> pdb=" O GLU D 335 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE D 340 " --> pdb=" O ILE D 336 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR D 342 " --> pdb=" O ASP D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 378 removed outlier: 4.308A pdb=" N HIS D 372 " --> pdb=" O GLU D 368 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE D 373 " --> pdb=" O SER D 369 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP D 376 " --> pdb=" O HIS D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 408 removed outlier: 4.066A pdb=" N LEU D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 428 Processing helix chain 'D' and resid 429 through 433 Processing helix chain 'D' and resid 446 through 465 Processing helix chain 'D' and resid 476 through 478 No H-bonds generated for 'chain 'D' and resid 476 through 478' Processing helix chain 'D' and resid 479 through 485 removed outlier: 4.013A pdb=" N LEU D 483 " --> pdb=" O ASN D 479 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU D 484 " --> pdb=" O LYS D 480 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN D 485 " --> pdb=" O ALA D 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 479 through 485' Processing helix chain 'D' and resid 500 through 514 removed outlier: 3.560A pdb=" N LEU D 513 " --> pdb=" O ALA D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 525 Processing helix chain 'D' and resid 537 through 548 Processing helix chain 'D' and resid 557 through 561 removed outlier: 3.553A pdb=" N ILE D 561 " --> pdb=" O PRO D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 575 Processing helix chain 'D' and resid 617 through 626 removed outlier: 4.092A pdb=" N VAL D 621 " --> pdb=" O SER D 617 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG D 623 " --> pdb=" O ASP D 619 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA D 624 " --> pdb=" O GLU D 620 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N TRP D 625 " --> pdb=" O VAL D 621 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE D 626 " --> pdb=" O LYS D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 794 through 796 No H-bonds generated for 'chain 'D' and resid 794 through 796' Processing helix chain 'D' and resid 800 through 807 Processing helix chain 'D' and resid 828 through 836 Proline residue: D 834 - end of helix Processing helix chain 'D' and resid 853 through 859 removed outlier: 3.566A pdb=" N ARG D 859 " --> pdb=" O ASP D 855 " (cutoff:3.500A) Processing helix chain 'D' and resid 860 through 865 removed outlier: 3.754A pdb=" N MET D 863 " --> pdb=" O GLU D 860 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN D 865 " --> pdb=" O LYS D 862 " (cutoff:3.500A) Processing helix chain 'D' and resid 879 through 887 removed outlier: 3.682A pdb=" N LEU D 883 " --> pdb=" O SER D 879 " (cutoff:3.500A) Processing helix chain 'D' and resid 888 through 891 Processing helix chain 'D' and resid 907 through 911 removed outlier: 4.342A pdb=" N ASP D 911 " --> pdb=" O THR D 908 " (cutoff:3.500A) Processing helix chain 'D' and resid 912 through 924 Processing helix chain 'D' and resid 960 through 964 Processing helix chain 'D' and resid 975 through 979 Processing helix chain 'D' and resid 990 through 993 Processing helix chain 'D' and resid 994 through 999 Processing helix chain 'D' and resid 1005 through 1018 removed outlier: 3.968A pdb=" N ASP D1009 " --> pdb=" O VAL D1005 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET D1012 " --> pdb=" O LEU D1008 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER D1013 " --> pdb=" O ASP D1009 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR D1014 " --> pdb=" O SER D1010 " (cutoff:3.500A) Processing helix chain 'D' and resid 1019 through 1030 removed outlier: 4.353A pdb=" N THR D1023 " --> pdb=" O GLN D1019 " (cutoff:3.500A) Processing helix chain 'D' and resid 1034 through 1042 removed outlier: 3.938A pdb=" N GLU D1038 " --> pdb=" O THR D1034 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU D1039 " --> pdb=" O PRO D1035 " (cutoff:3.500A) Processing helix chain 'D' and resid 1056 through 1061 Processing helix chain 'D' and resid 1073 through 1079 removed outlier: 4.154A pdb=" N GLN D1077 " --> pdb=" O PRO D1074 " (cutoff:3.500A) Processing helix chain 'D' and resid 1083 through 1095 Processing sheet with id=AA1, first strand: chain 'A' and resid 154 through 156 Processing sheet with id=AA2, first strand: chain 'A' and resid 412 through 416 removed outlier: 6.389A pdb=" N VAL A 389 " --> pdb=" O GLU A 413 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N PHE A 415 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N PHE A 391 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY A 363 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N HIS A 358 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N LEU A 437 " --> pdb=" O HIS A 358 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL A 360 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N LEU A 439 " --> pdb=" O VAL A 360 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N CYS A 362 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL A 470 " --> pdb=" O ASP A 496 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ILE A 498 " --> pdb=" O VAL A 470 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE A 472 " --> pdb=" O ILE A 498 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 550 through 555 removed outlier: 4.791A pdb=" N GLN A 610 " --> pdb=" O GLU A 584 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA A 582 " --> pdb=" O PHE A 612 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE A 614 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LEU A 580 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 597 " --> pdb=" O ILE A 583 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 780 through 781 removed outlier: 4.406A pdb=" N TYR A 780 " --> pdb=" O GLY A1050 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 798 through 799 removed outlier: 3.999A pdb=" N ASN A 874 " --> pdb=" O LEU A 799 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL A 848 " --> pdb=" O SER A 871 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N LEU A 873 " --> pdb=" O VAL A 848 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE A 850 " --> pdb=" O LEU A 873 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N CYS A 894 " --> pdb=" O ILE A 967 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N GLU A 969 " --> pdb=" O CYS A 894 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ILE A 896 " --> pdb=" O GLU A 969 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1064 through 1069 removed outlier: 6.588A pdb=" N GLN A1135 " --> pdb=" O LEU A1102 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU A1102 " --> pdb=" O GLN A1135 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE A1137 " --> pdb=" O ILE A1100 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 154 through 156 Processing sheet with id=AA8, first strand: chain 'B' and resid 412 through 416 removed outlier: 6.388A pdb=" N VAL B 389 " --> pdb=" O GLU B 413 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N PHE B 415 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N PHE B 391 " --> pdb=" O PHE B 415 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY B 363 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N HIS B 358 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N LEU B 437 " --> pdb=" O HIS B 358 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL B 360 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N LEU B 439 " --> pdb=" O VAL B 360 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N CYS B 362 " --> pdb=" O LEU B 439 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL B 470 " --> pdb=" O ASP B 496 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ILE B 498 " --> pdb=" O VAL B 470 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE B 472 " --> pdb=" O ILE B 498 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 550 through 555 removed outlier: 4.791A pdb=" N GLN B 610 " --> pdb=" O GLU B 584 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA B 582 " --> pdb=" O PHE B 612 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE B 614 " --> pdb=" O LEU B 580 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LEU B 580 " --> pdb=" O ILE B 614 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B 597 " --> pdb=" O ILE B 583 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 780 through 781 removed outlier: 4.406A pdb=" N TYR B 780 " --> pdb=" O GLY B1050 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 798 through 799 removed outlier: 3.999A pdb=" N ASN B 874 " --> pdb=" O LEU B 799 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL B 848 " --> pdb=" O SER B 871 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N LEU B 873 " --> pdb=" O VAL B 848 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE B 850 " --> pdb=" O LEU B 873 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N CYS B 894 " --> pdb=" O ILE B 967 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N GLU B 969 " --> pdb=" O CYS B 894 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE B 896 " --> pdb=" O GLU B 969 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 1064 through 1069 removed outlier: 6.588A pdb=" N GLN B1135 " --> pdb=" O LEU B1102 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU B1102 " --> pdb=" O GLN B1135 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE B1137 " --> pdb=" O ILE B1100 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 154 through 156 Processing sheet with id=AB5, first strand: chain 'C' and resid 412 through 416 removed outlier: 6.389A pdb=" N VAL C 389 " --> pdb=" O GLU C 413 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N PHE C 415 " --> pdb=" O VAL C 389 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N PHE C 391 " --> pdb=" O PHE C 415 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY C 363 " --> pdb=" O LEU C 392 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N HIS C 358 " --> pdb=" O ALA C 435 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N LEU C 437 " --> pdb=" O HIS C 358 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL C 360 " --> pdb=" O LEU C 437 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU C 439 " --> pdb=" O VAL C 360 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N CYS C 362 " --> pdb=" O LEU C 439 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL C 470 " --> pdb=" O ASP C 496 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ILE C 498 " --> pdb=" O VAL C 470 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE C 472 " --> pdb=" O ILE C 498 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 550 through 555 removed outlier: 4.790A pdb=" N GLN C 610 " --> pdb=" O GLU C 584 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA C 582 " --> pdb=" O PHE C 612 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE C 614 " --> pdb=" O LEU C 580 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LEU C 580 " --> pdb=" O ILE C 614 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER C 597 " --> pdb=" O ILE C 583 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 780 through 781 removed outlier: 4.406A pdb=" N TYR C 780 " --> pdb=" O GLY C1050 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 798 through 799 removed outlier: 4.000A pdb=" N ASN C 874 " --> pdb=" O LEU C 799 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL C 848 " --> pdb=" O SER C 871 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N LEU C 873 " --> pdb=" O VAL C 848 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE C 850 " --> pdb=" O LEU C 873 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N CYS C 894 " --> pdb=" O ILE C 967 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N GLU C 969 " --> pdb=" O CYS C 894 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE C 896 " --> pdb=" O GLU C 969 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 1064 through 1069 removed outlier: 6.588A pdb=" N GLN C1135 " --> pdb=" O LEU C1102 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU C1102 " --> pdb=" O GLN C1135 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE C1137 " --> pdb=" O ILE C1100 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 154 through 156 Processing sheet with id=AC2, first strand: chain 'D' and resid 412 through 416 removed outlier: 6.389A pdb=" N VAL D 389 " --> pdb=" O GLU D 413 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N PHE D 415 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N PHE D 391 " --> pdb=" O PHE D 415 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY D 363 " --> pdb=" O LEU D 392 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N HIS D 358 " --> pdb=" O ALA D 435 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N LEU D 437 " --> pdb=" O HIS D 358 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL D 360 " --> pdb=" O LEU D 437 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU D 439 " --> pdb=" O VAL D 360 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N CYS D 362 " --> pdb=" O LEU D 439 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL D 470 " --> pdb=" O ASP D 496 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ILE D 498 " --> pdb=" O VAL D 470 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE D 472 " --> pdb=" O ILE D 498 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 550 through 555 removed outlier: 4.790A pdb=" N GLN D 610 " --> pdb=" O GLU D 584 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA D 582 " --> pdb=" O PHE D 612 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE D 614 " --> pdb=" O LEU D 580 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LEU D 580 " --> pdb=" O ILE D 614 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER D 597 " --> pdb=" O ILE D 583 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 780 through 781 removed outlier: 4.406A pdb=" N TYR D 780 " --> pdb=" O GLY D1050 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 798 through 799 removed outlier: 3.999A pdb=" N ASN D 874 " --> pdb=" O LEU D 799 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL D 848 " --> pdb=" O SER D 871 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N LEU D 873 " --> pdb=" O VAL D 848 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE D 850 " --> pdb=" O LEU D 873 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N CYS D 894 " --> pdb=" O ILE D 967 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N GLU D 969 " --> pdb=" O CYS D 894 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE D 896 " --> pdb=" O GLU D 969 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 1064 through 1069 removed outlier: 6.589A pdb=" N GLN D1135 " --> pdb=" O LEU D1102 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU D1102 " --> pdb=" O GLN D1135 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE D1137 " --> pdb=" O ILE D1100 " (cutoff:3.500A) 1148 hydrogen bonds defined for protein. 3108 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.27 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8901 1.34 - 1.46: 6432 1.46 - 1.58: 13095 1.58 - 1.69: 0 1.69 - 1.81: 296 Bond restraints: 28724 Sorted by residual: bond pdb=" CB MET C 521 " pdb=" CG MET C 521 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.91e-01 bond pdb=" CB MET A 521 " pdb=" CG MET A 521 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.77e-01 bond pdb=" CB MET D 521 " pdb=" CG MET D 521 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.49e-01 bond pdb=" CB MET B 521 " pdb=" CG MET B 521 " ideal model delta sigma weight residual 1.520 1.493 0.027 3.00e-02 1.11e+03 8.34e-01 bond pdb=" CA ILE B 333 " pdb=" CB ILE B 333 " ideal model delta sigma weight residual 1.539 1.535 0.004 5.40e-03 3.43e+04 6.48e-01 ... (remaining 28719 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 38244 1.29 - 2.59: 549 2.59 - 3.88: 139 3.88 - 5.17: 28 5.17 - 6.47: 12 Bond angle restraints: 38972 Sorted by residual: angle pdb=" N ASP C 384 " pdb=" CA ASP C 384 " pdb=" C ASP C 384 " ideal model delta sigma weight residual 108.63 113.35 -4.72 1.60e+00 3.91e-01 8.72e+00 angle pdb=" N ASP A 384 " pdb=" CA ASP A 384 " pdb=" C ASP A 384 " ideal model delta sigma weight residual 108.63 113.35 -4.72 1.60e+00 3.91e-01 8.71e+00 angle pdb=" N ASP B 384 " pdb=" CA ASP B 384 " pdb=" C ASP B 384 " ideal model delta sigma weight residual 108.63 113.35 -4.72 1.60e+00 3.91e-01 8.70e+00 angle pdb=" N ASP D 384 " pdb=" CA ASP D 384 " pdb=" C ASP D 384 " ideal model delta sigma weight residual 108.63 113.34 -4.71 1.60e+00 3.91e-01 8.68e+00 angle pdb=" N VAL B 177 " pdb=" CA VAL B 177 " pdb=" C VAL B 177 " ideal model delta sigma weight residual 113.16 109.75 3.41 1.49e+00 4.50e-01 5.25e+00 ... (remaining 38967 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.85: 15374 15.85 - 31.70: 1283 31.70 - 47.56: 239 47.56 - 63.41: 84 63.41 - 79.26: 36 Dihedral angle restraints: 17016 sinusoidal: 6676 harmonic: 10340 Sorted by residual: dihedral pdb=" CA GLU A 383 " pdb=" C GLU A 383 " pdb=" N ASP A 384 " pdb=" CA ASP A 384 " ideal model delta harmonic sigma weight residual 180.00 -160.31 -19.69 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA GLU D 383 " pdb=" C GLU D 383 " pdb=" N ASP D 384 " pdb=" CA ASP D 384 " ideal model delta harmonic sigma weight residual -180.00 -160.31 -19.69 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA GLU C 383 " pdb=" C GLU C 383 " pdb=" N ASP C 384 " pdb=" CA ASP C 384 " ideal model delta harmonic sigma weight residual 180.00 -160.31 -19.69 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 17013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2716 0.028 - 0.055: 1129 0.055 - 0.083: 348 0.083 - 0.110: 235 0.110 - 0.138: 44 Chirality restraints: 4472 Sorted by residual: chirality pdb=" CA PRO B 987 " pdb=" N PRO B 987 " pdb=" C PRO B 987 " pdb=" CB PRO B 987 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA PRO C 987 " pdb=" N PRO C 987 " pdb=" C PRO C 987 " pdb=" CB PRO C 987 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CA PRO A 987 " pdb=" N PRO A 987 " pdb=" C PRO A 987 " pdb=" CB PRO A 987 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.50e-01 ... (remaining 4469 not shown) Planarity restraints: 4904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 206 " -0.043 5.00e-02 4.00e+02 6.52e-02 6.80e+00 pdb=" N PRO B 207 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 207 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 207 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 206 " -0.043 5.00e-02 4.00e+02 6.51e-02 6.78e+00 pdb=" N PRO D 207 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO D 207 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 207 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 206 " 0.043 5.00e-02 4.00e+02 6.50e-02 6.77e+00 pdb=" N PRO A 207 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 207 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 207 " 0.037 5.00e-02 4.00e+02 ... (remaining 4901 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.78: 5962 2.78 - 3.37: 30745 3.37 - 3.96: 52221 3.96 - 4.55: 73207 4.55 - 5.14: 106362 Nonbonded interactions: 268497 Sorted by model distance: nonbonded pdb=" OE1 GLU D 550 " pdb=" OH TYR D 552 " model vdw 2.188 3.040 nonbonded pdb=" OE1 GLU B 550 " pdb=" OH TYR B 552 " model vdw 2.188 3.040 nonbonded pdb=" OE1 GLU C 550 " pdb=" OH TYR C 552 " model vdw 2.188 3.040 nonbonded pdb=" OE1 GLU A 550 " pdb=" OH TYR A 552 " model vdw 2.189 3.040 nonbonded pdb=" OG SER B 557 " pdb=" O ALA B 624 " model vdw 2.238 3.040 ... (remaining 268492 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 44 through 1201) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.10 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: 7.890 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: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 29.660 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.040 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:7.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 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 0.028 28724 Z= 0.096 Angle : 0.446 6.466 38972 Z= 0.237 Chirality : 0.039 0.138 4472 Planarity : 0.003 0.065 4904 Dihedral : 12.989 79.259 10320 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.65 % Allowed : 0.13 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.14), residues: 3492 helix: -0.32 (0.13), residues: 1560 sheet: 1.26 (0.26), residues: 440 loop : -0.26 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1106 TYR 0.016 0.001 TYR A 197 PHE 0.017 0.001 PHE C 626 TRP 0.008 0.001 TRP D 625 HIS 0.002 0.000 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.00206 (28724) covalent geometry : angle 0.44629 (38972) hydrogen bonds : bond 0.27289 ( 1148) hydrogen bonds : angle 7.81092 ( 3108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 524 time to evaluate : 0.841 Fit side-chains REVERT: A 176 MET cc_start: 0.7401 (ppp) cc_final: 0.7191 (ppp) REVERT: A 196 MET cc_start: 0.6233 (OUTLIER) cc_final: 0.5118 (pmm) REVERT: B 176 MET cc_start: 0.7492 (ppp) cc_final: 0.7227 (ppp) REVERT: B 196 MET cc_start: 0.6040 (OUTLIER) cc_final: 0.5086 (pmm) REVERT: B 272 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8452 (mm-30) REVERT: B 882 ASP cc_start: 0.7878 (m-30) cc_final: 0.7577 (m-30) REVERT: C 176 MET cc_start: 0.7383 (ppp) cc_final: 0.7148 (ppp) REVERT: C 196 MET cc_start: 0.6203 (OUTLIER) cc_final: 0.5088 (pmm) REVERT: D 176 MET cc_start: 0.7489 (ppp) cc_final: 0.7248 (ppp) REVERT: D 196 MET cc_start: 0.6190 (OUTLIER) cc_final: 0.5112 (pmm) REVERT: D 272 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8482 (mm-30) outliers start: 20 outliers final: 9 residues processed: 527 average time/residue: 0.6597 time to fit residues: 403.2132 Evaluate side-chains 396 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 383 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 806 MET Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 806 MET Chi-restraints excluded: chain D residue 822 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.0370 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.0000 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 0.8980 overall best weight: 0.5062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 ASN A 610 GLN A 839 ASN A1135 GLN B 479 ASN B 610 GLN B 839 ASN B1135 GLN C 567 GLN C 610 GLN C 839 ASN D 479 ASN D 567 GLN D 610 GLN D 839 ASN D1135 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.187054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.120321 restraints weight = 35175.218| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.49 r_work: 0.3206 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 28724 Z= 0.121 Angle : 0.516 7.310 38972 Z= 0.272 Chirality : 0.041 0.146 4472 Planarity : 0.004 0.069 4904 Dihedral : 4.677 55.231 3840 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.49 % Allowed : 10.43 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.14), residues: 3492 helix: 0.11 (0.13), residues: 1604 sheet: 1.04 (0.26), residues: 440 loop : -0.01 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1048 TYR 0.013 0.001 TYR D 293 PHE 0.015 0.001 PHE A 626 TRP 0.009 0.001 TRP C 289 HIS 0.004 0.001 HIS B 847 Details of bonding type rmsd covalent geometry : bond 0.00256 (28724) covalent geometry : angle 0.51596 (38972) hydrogen bonds : bond 0.04999 ( 1148) hydrogen bonds : angle 5.09276 ( 3108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 427 time to evaluate : 0.983 Fit side-chains REVERT: A 196 MET cc_start: 0.5776 (OUTLIER) cc_final: 0.5143 (pmm) REVERT: A 271 LEU cc_start: 0.8140 (mm) cc_final: 0.7937 (mm) REVERT: A 406 LYS cc_start: 0.8618 (mmmm) cc_final: 0.8391 (mtmt) REVERT: A 806 MET cc_start: 0.7366 (ptt) cc_final: 0.7115 (ptt) REVERT: B 196 MET cc_start: 0.5267 (OUTLIER) cc_final: 0.4372 (ttp) REVERT: B 357 ARG cc_start: 0.8036 (mtm180) cc_final: 0.7747 (mtp180) REVERT: B 406 LYS cc_start: 0.8648 (mmmm) cc_final: 0.8364 (mttp) REVERT: B 595 LYS cc_start: 0.8702 (tppt) cc_final: 0.8444 (tppt) REVERT: B 882 ASP cc_start: 0.8693 (m-30) cc_final: 0.8439 (m-30) REVERT: C 196 MET cc_start: 0.5557 (OUTLIER) cc_final: 0.4542 (ttp) REVERT: C 394 ARG cc_start: 0.8809 (ttp80) cc_final: 0.8567 (ttp80) REVERT: C 406 LYS cc_start: 0.8629 (mmmm) cc_final: 0.8343 (mttp) REVERT: D 196 MET cc_start: 0.5567 (OUTLIER) cc_final: 0.4587 (ttp) REVERT: D 550 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8083 (mt-10) REVERT: D 561 ILE cc_start: 0.8922 (tt) cc_final: 0.8542 (mp) REVERT: D 844 GLU cc_start: 0.8750 (pt0) cc_final: 0.8417 (pt0) REVERT: D 972 ASN cc_start: 0.8597 (t0) cc_final: 0.8275 (m-40) outliers start: 46 outliers final: 22 residues processed: 453 average time/residue: 0.5939 time to fit residues: 320.4032 Evaluate side-chains 410 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 384 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 496 ASP Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 488 SER Chi-restraints excluded: chain D residue 557 SER Chi-restraints excluded: chain D residue 1120 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 131 optimal weight: 0.6980 chunk 340 optimal weight: 0.6980 chunk 349 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 302 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 190 optimal weight: 0.0870 chunk 164 optimal weight: 1.9990 chunk 181 optimal weight: 8.9990 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN A 839 ASN A 920 ASN B 610 GLN B 839 ASN C 610 GLN C 839 ASN C 920 ASN D 610 GLN D 839 ASN D 920 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.182105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.114371 restraints weight = 35025.828| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.48 r_work: 0.3136 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28724 Z= 0.147 Angle : 0.499 7.100 38972 Z= 0.261 Chirality : 0.041 0.148 4472 Planarity : 0.004 0.069 4904 Dihedral : 4.503 54.352 3829 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.26 % Allowed : 11.82 % Favored : 85.92 % 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: 0.35 (0.14), residues: 3492 helix: 0.32 (0.13), residues: 1608 sheet: 0.98 (0.26), residues: 436 loop : 0.09 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D1048 TYR 0.017 0.001 TYR C1095 PHE 0.020 0.001 PHE B 317 TRP 0.008 0.001 TRP D 289 HIS 0.005 0.001 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.00340 (28724) covalent geometry : angle 0.49936 (38972) hydrogen bonds : bond 0.04449 ( 1148) hydrogen bonds : angle 4.68821 ( 3108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 412 time to evaluate : 1.053 Fit side-chains REVERT: A 196 MET cc_start: 0.5661 (OUTLIER) cc_final: 0.4630 (ttp) REVERT: A 394 ARG cc_start: 0.8805 (ttp80) cc_final: 0.8553 (ttp80) REVERT: A 620 GLU cc_start: 0.8242 (mp0) cc_final: 0.8017 (mp0) REVERT: A 802 ASN cc_start: 0.8957 (m-40) cc_final: 0.8738 (m-40) REVERT: A 854 VAL cc_start: 0.9080 (m) cc_final: 0.8792 (t) REVERT: B 196 MET cc_start: 0.5150 (OUTLIER) cc_final: 0.4262 (ttp) REVERT: B 394 ARG cc_start: 0.8808 (ttp80) cc_final: 0.8538 (ttp80) REVERT: B 550 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8204 (mt-10) REVERT: B 1093 LYS cc_start: 0.8970 (mtmt) cc_final: 0.8736 (mtpp) REVERT: C 176 MET cc_start: 0.7478 (ppp) cc_final: 0.7226 (ppp) REVERT: C 196 MET cc_start: 0.5537 (OUTLIER) cc_final: 0.4530 (ttp) REVERT: C 394 ARG cc_start: 0.8804 (ttp80) cc_final: 0.8576 (ttp80) REVERT: C 620 GLU cc_start: 0.8244 (mp0) cc_final: 0.8001 (mp0) REVERT: C 972 ASN cc_start: 0.8648 (t0) cc_final: 0.8395 (m-40) REVERT: C 980 ASP cc_start: 0.8516 (t70) cc_final: 0.8291 (t70) REVERT: D 196 MET cc_start: 0.5305 (OUTLIER) cc_final: 0.4366 (ttp) REVERT: D 550 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8143 (mt-10) REVERT: D 561 ILE cc_start: 0.8953 (tt) cc_final: 0.8656 (mp) REVERT: D 620 GLU cc_start: 0.8241 (mp0) cc_final: 0.7995 (mp0) REVERT: D 980 ASP cc_start: 0.8525 (t70) cc_final: 0.8286 (t70) outliers start: 70 outliers final: 25 residues processed: 461 average time/residue: 0.6025 time to fit residues: 326.2417 Evaluate side-chains 429 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 400 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1013 SER Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 1013 SER Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 496 ASP Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 1012 MET Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain C residue 1120 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 488 SER Chi-restraints excluded: chain D residue 496 ASP Chi-restraints excluded: chain D residue 557 SER Chi-restraints excluded: chain D residue 1013 SER Chi-restraints excluded: chain D residue 1120 VAL Chi-restraints excluded: chain D residue 1133 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 201 optimal weight: 3.9990 chunk 186 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 348 optimal weight: 0.7980 chunk 233 optimal weight: 3.9990 chunk 339 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN ** A 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 920 ASN B 610 GLN ** B 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 479 ASN C 610 GLN ** C 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 GLN ** D 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.183345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.115590 restraints weight = 34737.340| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.47 r_work: 0.3129 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 28724 Z= 0.124 Angle : 0.472 8.348 38972 Z= 0.247 Chirality : 0.041 0.142 4472 Planarity : 0.004 0.068 4904 Dihedral : 4.267 52.367 3816 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.26 % Allowed : 13.57 % Favored : 84.17 % 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: 0.44 (0.14), residues: 3492 helix: 0.40 (0.13), residues: 1608 sheet: 0.91 (0.26), residues: 436 loop : 0.17 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 407 TYR 0.016 0.001 TYR D1095 PHE 0.019 0.001 PHE C 317 TRP 0.007 0.001 TRP D 289 HIS 0.003 0.000 HIS C 269 Details of bonding type rmsd covalent geometry : bond 0.00285 (28724) covalent geometry : angle 0.47214 (38972) hydrogen bonds : bond 0.03600 ( 1148) hydrogen bonds : angle 4.46851 ( 3108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 421 time to evaluate : 1.012 Fit side-chains REVERT: A 196 MET cc_start: 0.5483 (OUTLIER) cc_final: 0.4493 (ttp) REVERT: A 271 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7841 (mm) REVERT: A 394 ARG cc_start: 0.8820 (ttp80) cc_final: 0.8579 (ttp80) REVERT: A 550 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8247 (mt-10) REVERT: A 620 GLU cc_start: 0.8290 (mp0) cc_final: 0.8048 (mp0) REVERT: A 854 VAL cc_start: 0.9056 (m) cc_final: 0.8757 (t) REVERT: A 1011 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8613 (mp) REVERT: B 196 MET cc_start: 0.5138 (OUTLIER) cc_final: 0.4255 (ttp) REVERT: B 394 ARG cc_start: 0.8808 (ttp80) cc_final: 0.8530 (ttp80) REVERT: B 550 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8162 (mt-10) REVERT: B 561 ILE cc_start: 0.8932 (tt) cc_final: 0.8648 (mp) REVERT: B 620 GLU cc_start: 0.8111 (mp0) cc_final: 0.7770 (mp0) REVERT: B 854 VAL cc_start: 0.8950 (m) cc_final: 0.8699 (t) REVERT: B 1011 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8589 (mp) REVERT: B 1093 LYS cc_start: 0.8974 (mtmt) cc_final: 0.8744 (mtpp) REVERT: C 196 MET cc_start: 0.5325 (OUTLIER) cc_final: 0.4430 (ttp) REVERT: C 394 ARG cc_start: 0.8808 (ttp80) cc_final: 0.8571 (ttp80) REVERT: C 550 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8229 (mt-10) REVERT: C 620 GLU cc_start: 0.8282 (mp0) cc_final: 0.8030 (mp0) REVERT: C 844 GLU cc_start: 0.8804 (pt0) cc_final: 0.8513 (pt0) REVERT: C 980 ASP cc_start: 0.8485 (t70) cc_final: 0.8228 (t70) REVERT: D 196 MET cc_start: 0.5156 (OUTLIER) cc_final: 0.4275 (ttp) REVERT: D 550 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8231 (mt-10) REVERT: D 561 ILE cc_start: 0.8952 (tt) cc_final: 0.8743 (mp) REVERT: D 620 GLU cc_start: 0.8292 (mp0) cc_final: 0.7950 (mp0) REVERT: D 844 GLU cc_start: 0.8799 (pt0) cc_final: 0.8457 (pt0) REVERT: D 980 ASP cc_start: 0.8475 (t70) cc_final: 0.8209 (t70) REVERT: D 983 ASP cc_start: 0.6569 (p0) cc_final: 0.6286 (p0) outliers start: 70 outliers final: 26 residues processed: 468 average time/residue: 0.6060 time to fit residues: 333.3088 Evaluate side-chains 436 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 403 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1012 MET Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 1011 LEU Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 496 ASP Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 1012 MET Chi-restraints excluded: chain C residue 1120 VAL Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 488 SER Chi-restraints excluded: chain D residue 557 SER Chi-restraints excluded: chain D residue 1120 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 138 optimal weight: 3.9990 chunk 326 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 135 optimal weight: 0.8980 chunk 315 optimal weight: 0.5980 chunk 242 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 610 GLN ** A 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 GLN B 610 GLN ** B 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 920 ASN C 165 GLN C 610 GLN ** C 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 GLN ** D 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 920 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.180368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.112156 restraints weight = 34832.705| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.48 r_work: 0.3070 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 28724 Z= 0.190 Angle : 0.530 7.318 38972 Z= 0.275 Chirality : 0.043 0.139 4472 Planarity : 0.004 0.067 4904 Dihedral : 4.408 50.400 3816 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.45 % Allowed : 14.44 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.14), residues: 3492 helix: 0.36 (0.13), residues: 1584 sheet: 0.83 (0.26), residues: 424 loop : 0.32 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1048 TYR 0.020 0.001 TYR C1095 PHE 0.022 0.001 PHE B 317 TRP 0.009 0.001 TRP A 218 HIS 0.004 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00456 (28724) covalent geometry : angle 0.52979 (38972) hydrogen bonds : bond 0.04163 ( 1148) hydrogen bonds : angle 4.56415 ( 3108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 419 time to evaluate : 1.031 Fit side-chains REVERT: A 196 MET cc_start: 0.5402 (OUTLIER) cc_final: 0.4461 (ttp) REVERT: A 271 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7842 (mm) REVERT: A 394 ARG cc_start: 0.8862 (ttp80) cc_final: 0.8655 (ttp80) REVERT: A 550 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8271 (OUTLIER) REVERT: A 561 ILE cc_start: 0.8822 (tt) cc_final: 0.8558 (mt) REVERT: A 584 GLU cc_start: 0.8580 (mm-30) cc_final: 0.7695 (pp20) REVERT: A 620 GLU cc_start: 0.8359 (mp0) cc_final: 0.8125 (mp0) REVERT: A 913 GLU cc_start: 0.8640 (mp0) cc_final: 0.8301 (mp0) REVERT: B 176 MET cc_start: 0.7256 (ppp) cc_final: 0.7003 (ppp) REVERT: B 196 MET cc_start: 0.5053 (OUTLIER) cc_final: 0.4173 (ttp) REVERT: B 230 MET cc_start: 0.7547 (mtp) cc_final: 0.7304 (mtt) REVERT: B 394 ARG cc_start: 0.8872 (ttp80) cc_final: 0.8634 (ttp80) REVERT: B 550 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8227 (mt-10) REVERT: B 561 ILE cc_start: 0.8967 (tt) cc_final: 0.8732 (mp) REVERT: B 620 GLU cc_start: 0.8244 (mp0) cc_final: 0.8000 (mp0) REVERT: B 874 ASN cc_start: 0.8715 (t0) cc_final: 0.8459 (t0) REVERT: B 1093 LYS cc_start: 0.8995 (mtmt) cc_final: 0.8782 (mtpp) REVERT: C 176 MET cc_start: 0.7540 (ppp) cc_final: 0.7280 (OUTLIER) REVERT: C 196 MET cc_start: 0.5264 (OUTLIER) cc_final: 0.4313 (ttp) REVERT: C 271 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7908 (mm) REVERT: C 394 ARG cc_start: 0.8851 (ttp80) cc_final: 0.8649 (ttp80) REVERT: C 550 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8347 (mt-10) REVERT: C 561 ILE cc_start: 0.8803 (tt) cc_final: 0.8488 (mp) REVERT: C 584 GLU cc_start: 0.8509 (mm-30) cc_final: 0.7679 (pp20) REVERT: C 620 GLU cc_start: 0.8340 (mp0) cc_final: 0.8096 (mp0) REVERT: C 844 GLU cc_start: 0.8783 (pt0) cc_final: 0.8459 (pt0) REVERT: C 913 GLU cc_start: 0.8636 (mp0) cc_final: 0.8292 (mp0) REVERT: D 196 MET cc_start: 0.5165 (OUTLIER) cc_final: 0.4271 (ttp) REVERT: D 550 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8268 (mt-10) REVERT: D 561 ILE cc_start: 0.8988 (tt) cc_final: 0.8753 (mp) REVERT: D 844 GLU cc_start: 0.8767 (pt0) cc_final: 0.8411 (pt0) REVERT: D 913 GLU cc_start: 0.8609 (mp0) cc_final: 0.8279 (mp0) REVERT: D 1140 MET cc_start: 0.9035 (mtm) cc_final: 0.8831 (mtp) outliers start: 76 outliers final: 30 residues processed: 473 average time/residue: 0.6274 time to fit residues: 347.0493 Evaluate side-chains 418 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 384 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 1013 SER Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 1013 SER Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 496 ASP Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 1012 MET Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain C residue 1120 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 488 SER Chi-restraints excluded: chain D residue 496 ASP Chi-restraints excluded: chain D residue 557 SER Chi-restraints excluded: chain D residue 1013 SER Chi-restraints excluded: chain D residue 1120 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 34 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 131 optimal weight: 0.6980 chunk 294 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 57 optimal weight: 0.0970 chunk 136 optimal weight: 2.9990 chunk 347 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN ** A 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 920 ASN B 610 GLN ** B 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 610 GLN ** C 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 920 ASN D 165 GLN D 610 GLN ** D 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.181674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.114159 restraints weight = 34864.060| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.48 r_work: 0.3108 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 28724 Z= 0.124 Angle : 0.502 8.538 38972 Z= 0.261 Chirality : 0.041 0.137 4472 Planarity : 0.004 0.067 4904 Dihedral : 4.288 48.715 3816 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.97 % Allowed : 16.09 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.14), residues: 3492 helix: 0.49 (0.13), residues: 1584 sheet: 0.82 (0.26), residues: 436 loop : 0.39 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 407 TYR 0.016 0.001 TYR D1095 PHE 0.020 0.001 PHE D 317 TRP 0.007 0.001 TRP D 289 HIS 0.003 0.000 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.00289 (28724) covalent geometry : angle 0.50219 (38972) hydrogen bonds : bond 0.03494 ( 1148) hydrogen bonds : angle 4.39659 ( 3108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 421 time to evaluate : 1.059 Fit side-chains REVERT: A 196 MET cc_start: 0.5376 (OUTLIER) cc_final: 0.4457 (ttp) REVERT: A 271 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7846 (mm) REVERT: A 394 ARG cc_start: 0.8856 (ttp80) cc_final: 0.8644 (ttp80) REVERT: A 550 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8297 (mt-10) REVERT: A 561 ILE cc_start: 0.8810 (tt) cc_final: 0.8580 (mp) REVERT: A 584 GLU cc_start: 0.8565 (mm-30) cc_final: 0.7719 (pp20) REVERT: A 620 GLU cc_start: 0.8329 (mp0) cc_final: 0.8129 (mp0) REVERT: A 913 GLU cc_start: 0.8586 (mp0) cc_final: 0.8248 (mp0) REVERT: B 196 MET cc_start: 0.5027 (OUTLIER) cc_final: 0.4159 (ttp) REVERT: B 230 MET cc_start: 0.7541 (mtp) cc_final: 0.7298 (mtt) REVERT: B 394 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8624 (ttp80) REVERT: B 550 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8181 (mt-10) REVERT: B 608 ASN cc_start: 0.8813 (m110) cc_final: 0.8609 (m110) REVERT: B 854 VAL cc_start: 0.8971 (m) cc_final: 0.8725 (t) REVERT: B 1093 LYS cc_start: 0.8976 (mtmt) cc_final: 0.8765 (mtpp) REVERT: C 176 MET cc_start: 0.7496 (ppp) cc_final: 0.7197 (OUTLIER) REVERT: C 193 MET cc_start: 0.6423 (mmm) cc_final: 0.6222 (mmm) REVERT: C 196 MET cc_start: 0.5181 (OUTLIER) cc_final: 0.4290 (ttp) REVERT: C 271 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7894 (mm) REVERT: C 550 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8297 (mt-10) REVERT: C 561 ILE cc_start: 0.8759 (tt) cc_final: 0.8508 (mp) REVERT: C 584 GLU cc_start: 0.8491 (mm-30) cc_final: 0.7671 (pp20) REVERT: C 620 GLU cc_start: 0.8294 (mp0) cc_final: 0.8088 (mp0) REVERT: C 844 GLU cc_start: 0.8754 (pt0) cc_final: 0.8479 (pt0) REVERT: C 913 GLU cc_start: 0.8600 (mp0) cc_final: 0.8252 (mp0) REVERT: C 1093 LYS cc_start: 0.8960 (mtmt) cc_final: 0.8718 (mtpp) REVERT: D 176 MET cc_start: 0.7504 (ppp) cc_final: 0.7094 (ppp) REVERT: D 196 MET cc_start: 0.5165 (OUTLIER) cc_final: 0.4280 (ttp) REVERT: D 550 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8238 (mt-10) REVERT: D 620 GLU cc_start: 0.8531 (mp0) cc_final: 0.8302 (mp0) REVERT: D 913 GLU cc_start: 0.8588 (mp0) cc_final: 0.8254 (mp0) REVERT: D 1011 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8655 (mp) outliers start: 61 outliers final: 29 residues processed: 463 average time/residue: 0.6159 time to fit residues: 334.4437 Evaluate side-chains 442 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 406 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 394 ARG Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 496 ASP Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain C residue 1120 VAL Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 488 SER Chi-restraints excluded: chain D residue 496 ASP Chi-restraints excluded: chain D residue 1011 LEU Chi-restraints excluded: chain D residue 1120 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 205 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 345 optimal weight: 3.9990 chunk 226 optimal weight: 4.9990 chunk 204 optimal weight: 0.9980 chunk 317 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 216 optimal weight: 0.7980 chunk 242 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN ** A 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 920 ASN B 610 GLN ** B 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 920 ASN C 610 GLN ** C 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 920 ASN D 610 GLN ** D 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 920 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.180651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.113258 restraints weight = 34737.896| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.44 r_work: 0.3088 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2956 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 28724 Z= 0.155 Angle : 0.513 9.348 38972 Z= 0.265 Chirality : 0.042 0.139 4472 Planarity : 0.004 0.065 4904 Dihedral : 4.295 46.965 3816 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.26 % Allowed : 16.54 % Favored : 81.20 % 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: 0.60 (0.14), residues: 3492 helix: 0.50 (0.13), residues: 1568 sheet: 0.80 (0.26), residues: 436 loop : 0.38 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D1048 TYR 0.017 0.001 TYR A1095 PHE 0.021 0.001 PHE A 317 TRP 0.008 0.001 TRP A 218 HIS 0.004 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00371 (28724) covalent geometry : angle 0.51290 (38972) hydrogen bonds : bond 0.03672 ( 1148) hydrogen bonds : angle 4.39373 ( 3108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 415 time to evaluate : 0.830 Fit side-chains REVERT: A 196 MET cc_start: 0.5379 (OUTLIER) cc_final: 0.4472 (ttp) REVERT: A 271 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7892 (mm) REVERT: A 394 ARG cc_start: 0.8864 (ttp80) cc_final: 0.8657 (ttp80) REVERT: A 550 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8304 (mt-10) REVERT: A 584 GLU cc_start: 0.8571 (mm-30) cc_final: 0.7735 (pp20) REVERT: A 844 GLU cc_start: 0.8820 (pt0) cc_final: 0.8500 (pt0) REVERT: A 913 GLU cc_start: 0.8593 (mp0) cc_final: 0.8237 (mp0) REVERT: B 196 MET cc_start: 0.4980 (OUTLIER) cc_final: 0.4125 (ttp) REVERT: B 230 MET cc_start: 0.7609 (mtp) cc_final: 0.7377 (mtt) REVERT: B 345 LYS cc_start: 0.7452 (ttpp) cc_final: 0.7219 (tptt) REVERT: B 394 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8676 (ttp80) REVERT: B 550 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8230 (mt-10) REVERT: B 608 ASN cc_start: 0.8836 (m110) cc_final: 0.8627 (m110) REVERT: B 620 GLU cc_start: 0.8526 (mp0) cc_final: 0.8216 (mp0) REVERT: B 874 ASN cc_start: 0.8689 (t0) cc_final: 0.8424 (t0) REVERT: B 913 GLU cc_start: 0.8654 (mp0) cc_final: 0.8245 (mp0) REVERT: B 1011 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8638 (mp) REVERT: B 1093 LYS cc_start: 0.8986 (mtmt) cc_final: 0.8779 (mtpp) REVERT: C 176 MET cc_start: 0.7492 (ppp) cc_final: 0.7190 (OUTLIER) REVERT: C 196 MET cc_start: 0.5220 (OUTLIER) cc_final: 0.4323 (ttp) REVERT: C 271 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7914 (mm) REVERT: C 550 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8303 (mt-10) REVERT: C 561 ILE cc_start: 0.8752 (tt) cc_final: 0.8542 (mp) REVERT: C 584 GLU cc_start: 0.8528 (mm-30) cc_final: 0.7693 (pp20) REVERT: C 844 GLU cc_start: 0.8753 (pt0) cc_final: 0.8458 (pt0) REVERT: C 913 GLU cc_start: 0.8613 (mp0) cc_final: 0.8255 (mp0) REVERT: C 1093 LYS cc_start: 0.8957 (mtmt) cc_final: 0.8732 (mtpp) REVERT: D 176 MET cc_start: 0.7537 (ppp) cc_final: 0.7095 (ppp) REVERT: D 196 MET cc_start: 0.5113 (OUTLIER) cc_final: 0.4236 (ttp) REVERT: D 345 LYS cc_start: 0.7476 (ttpp) cc_final: 0.7212 (tptt) REVERT: D 368 GLU cc_start: 0.8532 (pm20) cc_final: 0.8311 (pp20) REVERT: D 550 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8252 (mt-10) REVERT: D 844 GLU cc_start: 0.8801 (pt0) cc_final: 0.8511 (pt0) REVERT: D 913 GLU cc_start: 0.8579 (mp0) cc_final: 0.8285 (mp0) REVERT: D 1011 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8643 (mp) outliers start: 70 outliers final: 35 residues processed: 468 average time/residue: 0.6260 time to fit residues: 342.7689 Evaluate side-chains 445 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 402 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 1013 SER Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 394 ARG Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 1011 LEU Chi-restraints excluded: chain B residue 1013 SER Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 496 ASP Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain C residue 1120 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 488 SER Chi-restraints excluded: chain D residue 496 ASP Chi-restraints excluded: chain D residue 557 SER Chi-restraints excluded: chain D residue 1011 LEU Chi-restraints excluded: chain D residue 1013 SER Chi-restraints excluded: chain D residue 1120 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 325 optimal weight: 0.9990 chunk 326 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 197 optimal weight: 0.0050 chunk 185 optimal weight: 8.9990 chunk 207 optimal weight: 3.9990 chunk 223 optimal weight: 0.7980 chunk 153 optimal weight: 0.5980 chunk 182 optimal weight: 0.9990 chunk 310 optimal weight: 0.1980 chunk 38 optimal weight: 0.5980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN ** A 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 920 ASN B 610 GLN ** B 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 610 GLN ** C 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 920 ASN D 610 GLN ** D 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.182994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.116141 restraints weight = 34734.754| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.44 r_work: 0.3142 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 28724 Z= 0.101 Angle : 0.497 10.191 38972 Z= 0.256 Chirality : 0.040 0.137 4472 Planarity : 0.004 0.065 4904 Dihedral : 4.146 45.337 3816 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.65 % Allowed : 17.47 % Favored : 80.88 % 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: 0.52 (0.14), residues: 3492 helix: 0.47 (0.13), residues: 1636 sheet: 0.82 (0.26), residues: 440 loop : 0.24 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 407 TYR 0.016 0.001 TYR B1095 PHE 0.026 0.001 PHE A 317 TRP 0.007 0.001 TRP D 289 HIS 0.004 0.000 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00231 (28724) covalent geometry : angle 0.49718 (38972) hydrogen bonds : bond 0.03088 ( 1148) hydrogen bonds : angle 4.20666 ( 3108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 431 time to evaluate : 0.866 Fit side-chains REVERT: A 196 MET cc_start: 0.5350 (OUTLIER) cc_final: 0.4435 (ttp) REVERT: A 271 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7889 (mm) REVERT: A 345 LYS cc_start: 0.6737 (tptt) cc_final: 0.6533 (ttpm) REVERT: A 368 GLU cc_start: 0.8479 (pm20) cc_final: 0.8266 (pp20) REVERT: A 394 ARG cc_start: 0.8855 (ttp80) cc_final: 0.8648 (ttp80) REVERT: A 550 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8276 (mt-10) REVERT: A 584 GLU cc_start: 0.8518 (mm-30) cc_final: 0.7765 (pp20) REVERT: A 620 GLU cc_start: 0.8490 (mp0) cc_final: 0.8241 (mp0) REVERT: A 913 GLU cc_start: 0.8584 (mp0) cc_final: 0.8234 (mp0) REVERT: A 1011 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8595 (mp) REVERT: B 196 MET cc_start: 0.4851 (OUTLIER) cc_final: 0.4046 (ttp) REVERT: B 230 MET cc_start: 0.7576 (mtp) cc_final: 0.7328 (mtt) REVERT: B 394 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8646 (ttp80) REVERT: B 550 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8211 (mt-10) REVERT: B 608 ASN cc_start: 0.8785 (m110) cc_final: 0.8568 (m110) REVERT: B 620 GLU cc_start: 0.8483 (mp0) cc_final: 0.7945 (mp0) REVERT: B 844 GLU cc_start: 0.8796 (pt0) cc_final: 0.8485 (pt0) REVERT: B 854 VAL cc_start: 0.8964 (m) cc_final: 0.8732 (t) REVERT: B 874 ASN cc_start: 0.8605 (t0) cc_final: 0.8318 (t0) REVERT: B 1093 LYS cc_start: 0.8973 (mtmt) cc_final: 0.8772 (mtpp) REVERT: C 196 MET cc_start: 0.5229 (OUTLIER) cc_final: 0.4344 (ttp) REVERT: C 271 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7940 (mm) REVERT: C 550 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8274 (mt-10) REVERT: C 584 GLU cc_start: 0.8484 (mm-30) cc_final: 0.7698 (pp20) REVERT: C 620 GLU cc_start: 0.8486 (mp0) cc_final: 0.8237 (mp0) REVERT: C 913 GLU cc_start: 0.8576 (mp0) cc_final: 0.8225 (mp0) REVERT: C 1011 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8636 (mp) REVERT: C 1093 LYS cc_start: 0.8972 (mtmt) cc_final: 0.8758 (mtpp) REVERT: C 1140 MET cc_start: 0.8967 (mtp) cc_final: 0.8766 (mtm) REVERT: D 196 MET cc_start: 0.5051 (OUTLIER) cc_final: 0.4166 (ttp) REVERT: D 357 ARG cc_start: 0.8190 (mtm180) cc_final: 0.7961 (mtp180) REVERT: D 368 GLU cc_start: 0.8499 (pm20) cc_final: 0.8284 (pp20) REVERT: D 550 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8229 (mt-10) REVERT: D 913 GLU cc_start: 0.8567 (mp0) cc_final: 0.8227 (mp0) outliers start: 51 outliers final: 25 residues processed: 465 average time/residue: 0.6227 time to fit residues: 338.9242 Evaluate side-chains 451 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 417 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 394 ARG Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 1011 LEU Chi-restraints excluded: chain C residue 1120 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 488 SER Chi-restraints excluded: chain D residue 496 ASP Chi-restraints excluded: chain D residue 557 SER Chi-restraints excluded: chain D residue 1013 SER Chi-restraints excluded: chain D residue 1120 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 0.0060 chunk 47 optimal weight: 1.9990 chunk 190 optimal weight: 8.9990 chunk 244 optimal weight: 0.0470 chunk 236 optimal weight: 0.0070 chunk 97 optimal weight: 10.0000 chunk 38 optimal weight: 0.6980 chunk 179 optimal weight: 0.0970 chunk 311 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 overall best weight: 0.1710 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN ** A 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 GLN ** B 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 610 GLN ** C 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 GLN ** D 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 920 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.184465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.118218 restraints weight = 34641.427| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.45 r_work: 0.3170 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.083 28724 Z= 0.095 Angle : 0.500 10.515 38972 Z= 0.255 Chirality : 0.040 0.139 4472 Planarity : 0.004 0.065 4904 Dihedral : 4.016 43.830 3816 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.74 % Allowed : 17.86 % Favored : 80.39 % 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 (0.14), residues: 3492 helix: 0.55 (0.13), residues: 1636 sheet: 0.89 (0.26), residues: 440 loop : 0.29 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 407 TYR 0.016 0.001 TYR C1095 PHE 0.018 0.001 PHE B 317 TRP 0.008 0.001 TRP D 289 HIS 0.004 0.000 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00217 (28724) covalent geometry : angle 0.50030 (38972) hydrogen bonds : bond 0.02830 ( 1148) hydrogen bonds : angle 4.09819 ( 3108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 435 time to evaluate : 1.080 Fit side-chains REVERT: A 196 MET cc_start: 0.5349 (OUTLIER) cc_final: 0.4415 (ttp) REVERT: A 271 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7756 (mm) REVERT: A 357 ARG cc_start: 0.8197 (mtm180) cc_final: 0.7961 (mtp180) REVERT: A 368 GLU cc_start: 0.8515 (pm20) cc_final: 0.8272 (pp20) REVERT: A 394 ARG cc_start: 0.8843 (ttp80) cc_final: 0.8641 (ttp80) REVERT: A 550 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8259 (mt-10) REVERT: A 584 GLU cc_start: 0.8560 (mm-30) cc_final: 0.7820 (pp20) REVERT: A 620 GLU cc_start: 0.8498 (mp0) cc_final: 0.8227 (mp0) REVERT: A 801 ARG cc_start: 0.8400 (ttm170) cc_final: 0.8160 (ttm170) REVERT: A 913 GLU cc_start: 0.8586 (mp0) cc_final: 0.8245 (mp0) REVERT: B 196 MET cc_start: 0.4786 (OUTLIER) cc_final: 0.4071 (ttp) REVERT: B 230 MET cc_start: 0.7506 (mtp) cc_final: 0.7295 (mtt) REVERT: B 394 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8648 (ttp80) REVERT: B 608 ASN cc_start: 0.8791 (m110) cc_final: 0.8550 (m110) REVERT: B 620 GLU cc_start: 0.8476 (mp0) cc_final: 0.7783 (mp0) REVERT: B 854 VAL cc_start: 0.8941 (m) cc_final: 0.8738 (t) REVERT: B 874 ASN cc_start: 0.8507 (t0) cc_final: 0.8187 (t0) REVERT: B 1093 LYS cc_start: 0.8972 (mtmt) cc_final: 0.8756 (mtpp) REVERT: C 196 MET cc_start: 0.5149 (OUTLIER) cc_final: 0.4269 (ttp) REVERT: C 271 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7889 (mm) REVERT: C 368 GLU cc_start: 0.8520 (pm20) cc_final: 0.8251 (pp20) REVERT: C 550 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8227 (mt-10) REVERT: C 620 GLU cc_start: 0.8464 (mp0) cc_final: 0.8193 (mp0) REVERT: C 913 GLU cc_start: 0.8582 (mp0) cc_final: 0.8236 (mp0) REVERT: C 1093 LYS cc_start: 0.8967 (mtmt) cc_final: 0.8749 (mtpp) REVERT: D 176 MET cc_start: 0.7554 (ppp) cc_final: 0.7245 (ppp) REVERT: D 196 MET cc_start: 0.5115 (OUTLIER) cc_final: 0.4224 (ttp) REVERT: D 357 ARG cc_start: 0.8215 (mtm180) cc_final: 0.7992 (mtp180) REVERT: D 368 GLU cc_start: 0.8451 (pm20) cc_final: 0.8218 (pp20) REVERT: D 550 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8189 (mt-10) REVERT: D 620 GLU cc_start: 0.8467 (mp0) cc_final: 0.8203 (mp0) outliers start: 54 outliers final: 22 residues processed: 468 average time/residue: 0.6029 time to fit residues: 332.0008 Evaluate side-chains 445 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 416 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 563 ILE Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 394 ARG Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 1120 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 488 SER Chi-restraints excluded: chain D residue 557 SER Chi-restraints excluded: chain D residue 563 ILE Chi-restraints excluded: chain D residue 1120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 344 optimal weight: 0.7980 chunk 168 optimal weight: 0.9980 chunk 240 optimal weight: 0.9980 chunk 3 optimal weight: 0.0040 chunk 179 optimal weight: 0.9980 chunk 348 optimal weight: 0.6980 chunk 21 optimal weight: 0.0980 chunk 225 optimal weight: 0.0970 chunk 34 optimal weight: 1.9990 chunk 90 optimal weight: 0.0570 chunk 304 optimal weight: 0.7980 overall best weight: 0.1908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN ** A 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 920 ASN B 610 GLN ** B 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 920 ASN C 610 GLN ** C 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 920 ASN C1135 GLN D 610 GLN ** D 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 920 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.185234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.119250 restraints weight = 34562.014| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.45 r_work: 0.3182 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 28724 Z= 0.093 Angle : 0.504 12.259 38972 Z= 0.255 Chirality : 0.040 0.140 4472 Planarity : 0.004 0.065 4904 Dihedral : 3.938 42.651 3816 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.39 % Allowed : 18.41 % Favored : 80.20 % 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: 0.68 (0.14), residues: 3492 helix: 0.56 (0.13), residues: 1640 sheet: 0.95 (0.26), residues: 440 loop : 0.36 (0.17), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 407 TYR 0.015 0.001 TYR D1095 PHE 0.014 0.001 PHE D 317 TRP 0.008 0.001 TRP D 289 HIS 0.003 0.000 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00212 (28724) covalent geometry : angle 0.50400 (38972) hydrogen bonds : bond 0.02791 ( 1148) hydrogen bonds : angle 4.06572 ( 3108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6984 Ramachandran restraints generated. 3492 Oldfield, 0 Emsley, 3492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 453 time to evaluate : 1.075 Fit side-chains REVERT: A 196 MET cc_start: 0.5291 (OUTLIER) cc_final: 0.4371 (ttp) REVERT: A 271 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7908 (mm) REVERT: A 357 ARG cc_start: 0.8184 (mtm180) cc_final: 0.7952 (mtp180) REVERT: A 368 GLU cc_start: 0.8482 (pm20) cc_final: 0.8271 (pp20) REVERT: A 394 ARG cc_start: 0.8852 (ttp80) cc_final: 0.8594 (ttp80) REVERT: A 550 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8191 (mt-10) REVERT: A 584 GLU cc_start: 0.8601 (mm-30) cc_final: 0.7875 (pp20) REVERT: A 620 GLU cc_start: 0.8470 (mp0) cc_final: 0.7908 (mp0) REVERT: A 801 ARG cc_start: 0.8404 (ttm170) cc_final: 0.8176 (ttm170) REVERT: A 913 GLU cc_start: 0.8587 (mp0) cc_final: 0.8248 (mp0) REVERT: A 1011 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8574 (mp) REVERT: A 1093 LYS cc_start: 0.8903 (mtpt) cc_final: 0.8686 (mtpp) REVERT: B 196 MET cc_start: 0.4810 (OUTLIER) cc_final: 0.4094 (ttp) REVERT: B 230 MET cc_start: 0.7527 (mtp) cc_final: 0.7319 (mtt) REVERT: B 394 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8644 (ttp80) REVERT: B 620 GLU cc_start: 0.8443 (mp0) cc_final: 0.7801 (mp0) REVERT: B 874 ASN cc_start: 0.8462 (t0) cc_final: 0.8136 (t0) REVERT: B 1093 LYS cc_start: 0.8971 (mtmt) cc_final: 0.8752 (mtpp) REVERT: C 196 MET cc_start: 0.5129 (OUTLIER) cc_final: 0.4255 (ttp) REVERT: C 271 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7897 (mm) REVERT: C 368 GLU cc_start: 0.8502 (pm20) cc_final: 0.8237 (pp20) REVERT: C 550 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8197 (mt-10) REVERT: C 584 GLU cc_start: 0.8523 (mm-30) cc_final: 0.7704 (pp20) REVERT: C 620 GLU cc_start: 0.8468 (mp0) cc_final: 0.7902 (mp0) REVERT: C 913 GLU cc_start: 0.8581 (mp0) cc_final: 0.8237 (mp0) REVERT: C 1011 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8572 (mp) REVERT: C 1093 LYS cc_start: 0.8962 (mtmt) cc_final: 0.8739 (mtpp) REVERT: D 176 MET cc_start: 0.7540 (ppp) cc_final: 0.7217 (ppp) REVERT: D 196 MET cc_start: 0.5118 (OUTLIER) cc_final: 0.4253 (ttp) REVERT: D 357 ARG cc_start: 0.8166 (mtm180) cc_final: 0.7942 (mtp180) REVERT: D 368 GLU cc_start: 0.8457 (pm20) cc_final: 0.8246 (pp20) REVERT: D 550 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8198 (mt-10) REVERT: D 620 GLU cc_start: 0.8465 (mp0) cc_final: 0.8189 (mp0) REVERT: D 913 GLU cc_start: 0.8574 (mp0) cc_final: 0.8207 (mp0) outliers start: 43 outliers final: 19 residues processed: 475 average time/residue: 0.5931 time to fit residues: 332.5091 Evaluate side-chains 458 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 430 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1120 VAL Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 394 ARG Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 1011 LEU Chi-restraints excluded: chain C residue 1120 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 488 SER Chi-restraints excluded: chain D residue 557 SER Chi-restraints excluded: chain D residue 563 ILE Chi-restraints excluded: chain D residue 1120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 143 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 341 optimal weight: 0.8980 chunk 193 optimal weight: 0.9990 chunk 244 optimal weight: 1.9990 chunk 212 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 175 optimal weight: 0.7980 chunk 113 optimal weight: 7.9990 chunk 222 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN ** A 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 920 ASN B 610 GLN ** B 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 920 ASN C 610 GLN ** C 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 920 ASN D 610 GLN ** D 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.182615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.115812 restraints weight = 34706.391| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.44 r_work: 0.3134 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28724 Z= 0.127 Angle : 0.522 12.218 38972 Z= 0.264 Chirality : 0.041 0.139 4472 Planarity : 0.004 0.064 4904 Dihedral : 4.026 41.719 3816 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.68 % Allowed : 18.64 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.14), residues: 3492 helix: 0.61 (0.13), residues: 1608 sheet: 0.96 (0.26), residues: 440 loop : 0.34 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 407 TYR 0.015 0.001 TYR A1095 PHE 0.011 0.001 PHE B 174 TRP 0.009 0.001 TRP D 625 HIS 0.005 0.001 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.00303 (28724) covalent geometry : angle 0.52178 (38972) hydrogen bonds : bond 0.03206 ( 1148) hydrogen bonds : angle 4.16218 ( 3108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14823.91 seconds wall clock time: 251 minutes 32.31 seconds (15092.31 seconds total)