Starting phenix.real_space_refine on Fri Mar 6 04:17:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pxf_13701/03_2026/7pxf_13701.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pxf_13701/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7pxf_13701/03_2026/7pxf_13701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pxf_13701/03_2026/7pxf_13701.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pxf_13701/03_2026/7pxf_13701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pxf_13701/03_2026/7pxf_13701.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28099 Number of models: 1 Model: "" Number of chains: 8 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: "B" 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: "C" 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: "D" 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} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} 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: 6.28, per 1000 atoms: 0.22 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: 2.19 Conformation dependent library (CDL) restraints added in 1.2 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: 1.22 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: 5.72 Time building geometry restraints manager: 2.91 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: 6.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 24.870 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.260 ------------------------------------------------------------------------------- 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 : 1.048 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: 0.6870 time to fit residues: 419.3902 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 : 1.049 ------------------------------------------------------------------------------- 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 = 61)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.120263 restraints weight = 35175.217| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.50 r_work: 0.3206 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 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 = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 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 : 1.050 Fit side-chains REVERT: A 196 MET cc_start: 0.5770 (OUTLIER) cc_final: 0.5141 (pmm) REVERT: A 271 LEU cc_start: 0.8138 (mm) cc_final: 0.7935 (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: 0.5261 (OUTLIER) cc_final: 0.4368 (ttp) REVERT: B 357 ARG cc_start: 0.8038 (mtm180) cc_final: 0.7750 (mtp180) REVERT: B 406 LYS cc_start: 0.8649 (mmmm) cc_final: 0.8364 (mttp) REVERT: B 595 LYS cc_start: 0.8702 (tppt) cc_final: 0.8443 (tppt) REVERT: B 882 ASP cc_start: 0.8694 (m-30) cc_final: 0.8439 (m-30) REVERT: C 196 MET cc_start: 0.5553 (OUTLIER) cc_final: 0.4539 (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: 0.8342 (mttp) REVERT: D 196 MET cc_start: 0.5562 (OUTLIER) cc_final: 0.4582 (ttp) REVERT: D 550 GLU cc_start: 0.8478 (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: 0.8751 (pt0) cc_final: 0.8418 (pt0) REVERT: D 972 ASN cc_start: 0.8598 (t0) cc_final: 0.8275 (m-40) outliers start: 46 outliers final: 22 residues processed: 453 average time/residue: 0.5789 time to fit residues: 311.4058 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 : 1.255 ------------------------------------------------------------------------------- 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: 0.8980 chunk 349 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 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: 0.0770 chunk 164 optimal weight: 1.9990 chunk 181 optimal weight: 8.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- 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 = 0.4113 r_free = 0.4113 target = 0.182964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.115587 restraints weight = 35080.699| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.48 r_work: 0.3154 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28724 Z= 0.132 Angle : 0.486 7.171 38972 Z= 0.254 Chirality : 0.041 0.147 4472 Planarity : 0.004 0.069 4904 Dihedral : 4.464 54.513 3829 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.07 % Allowed : 11.76 % Favored : 86.18 % 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: 0.36 (0.14), residues: 3492 helix: 0.33 (0.13), residues: 1608 sheet: 1.01 (0.26), residues: 436 loop : 0.09 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D1048 TYR 0.016 0.001 TYR C1095 PHE 0.019 0.001 PHE C 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 0.00302 (28724) covalent geometry : angle 0.48598 (38972) hydrogen bonds : bond 0.04393 ( 1148) hydrogen bonds : angle 4.68962 ( 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 475 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 411 time to evaluate : 1.101 Fit side-chains REVERT: A 176 MET cc_start: 0.7410 (ppp) cc_final: 0.7174 (ppp) REVERT: A 196 MET cc_start: 0.5704 (OUTLIER) cc_final: 0.4646 (ttp) REVERT: A 394 ARG cc_start: 0.8783 (ttp80) cc_final: 0.8520 (ttp80) REVERT: A 620 GLU cc_start: 0.8247 (mp0) cc_final: 0.7991 (mp0) REVERT: A 802 ASN cc_start: 0.8949 (m-40) cc_final: 0.8697 (m-40) REVERT: A 854 VAL cc_start: 0.9071 (m) cc_final: 0.8792 (t) REVERT: B 176 MET cc_start: 0.7418 (ppp) cc_final: 0.7126 (ppp) REVERT: B 196 MET cc_start: 0.5164 (OUTLIER) cc_final: 0.4319 (ttm) REVERT: B 402 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8327 (mm-30) REVERT: B 550 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8147 (mt-10) REVERT: B 1093 LYS cc_start: 0.8960 (mtmt) cc_final: 0.8735 (mtpp) REVERT: C 176 MET cc_start: 0.7453 (ppp) cc_final: 0.7169 (ppp) REVERT: C 196 MET cc_start: 0.5567 (OUTLIER) cc_final: 0.4581 (ttp) REVERT: C 394 ARG cc_start: 0.8805 (ttp80) cc_final: 0.8563 (ttp80) REVERT: C 620 GLU cc_start: 0.8264 (mp0) cc_final: 0.8003 (mp0) REVERT: C 980 ASP cc_start: 0.8534 (t70) cc_final: 0.8330 (t70) REVERT: D 196 MET cc_start: 0.5388 (OUTLIER) cc_final: 0.4458 (ttp) REVERT: D 550 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8181 (mt-10) REVERT: D 561 ILE cc_start: 0.8947 (tt) cc_final: 0.8647 (mp) REVERT: D 620 GLU cc_start: 0.8210 (mp0) cc_final: 0.7963 (mp0) REVERT: D 980 ASP cc_start: 0.8521 (t70) cc_final: 0.8286 (t70) outliers start: 64 outliers final: 26 residues processed: 455 average time/residue: 0.6277 time to fit residues: 336.0792 Evaluate side-chains 431 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 400 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 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 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 402 GLU 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 561 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 201 optimal weight: 6.9990 chunk 186 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 145 optimal weight: 0.7980 chunk 348 optimal weight: 0.9980 chunk 233 optimal weight: 3.9990 chunk 339 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 D 610 GLN D 839 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.182784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.114402 restraints weight = 34714.176| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.49 r_work: 0.3125 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28724 Z= 0.138 Angle : 0.477 7.520 38972 Z= 0.249 Chirality : 0.041 0.143 4472 Planarity : 0.004 0.069 4904 Dihedral : 4.303 52.746 3820 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.42 % Allowed : 13.05 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.14), residues: 3492 helix: 0.39 (0.13), residues: 1608 sheet: 0.92 (0.26), residues: 436 loop : 0.14 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1048 TYR 0.016 0.001 TYR D1095 PHE 0.019 0.001 PHE C 317 TRP 0.007 0.001 TRP C 218 HIS 0.004 0.001 HIS C 269 Details of bonding type rmsd covalent geometry : bond 0.00324 (28724) covalent geometry : angle 0.47741 (38972) hydrogen bonds : bond 0.03798 ( 1148) hydrogen bonds : angle 4.50832 ( 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 494 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 419 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 196 MET cc_start: 0.5500 (OUTLIER) cc_final: 0.4517 (ttp) REVERT: A 271 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7834 (mm) REVERT: A 394 ARG cc_start: 0.8819 (ttp80) cc_final: 0.8574 (ttp80) REVERT: A 550 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8279 (mt-10) REVERT: A 620 GLU cc_start: 0.8285 (mp0) cc_final: 0.8067 (mp0) REVERT: A 854 VAL cc_start: 0.9075 (m) cc_final: 0.8777 (t) REVERT: B 196 MET cc_start: 0.5146 (OUTLIER) cc_final: 0.4254 (ttp) REVERT: B 550 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8245 (mt-10) REVERT: B 561 ILE cc_start: 0.8928 (tt) cc_final: 0.8597 (mp) REVERT: B 620 GLU cc_start: 0.8102 (mp0) cc_final: 0.7775 (mp0) REVERT: B 1011 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8591 (mp) REVERT: B 1093 LYS cc_start: 0.8968 (mtmt) cc_final: 0.8735 (mtpp) REVERT: C 196 MET cc_start: 0.5382 (OUTLIER) cc_final: 0.4422 (ttp) REVERT: C 394 ARG cc_start: 0.8822 (ttp80) cc_final: 0.8603 (ttp80) REVERT: C 550 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8273 (mt-10) REVERT: C 620 GLU cc_start: 0.8277 (mp0) cc_final: 0.8041 (mp0) REVERT: C 844 GLU cc_start: 0.8807 (pt0) cc_final: 0.8526 (pt0) REVERT: C 980 ASP cc_start: 0.8493 (t70) cc_final: 0.8246 (t70) REVERT: D 196 MET cc_start: 0.5153 (OUTLIER) cc_final: 0.4259 (ttp) REVERT: D 550 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8186 (mt-10) REVERT: D 561 ILE cc_start: 0.8962 (tt) cc_final: 0.8737 (mp) REVERT: D 620 GLU cc_start: 0.8227 (mp0) cc_final: 0.8027 (mp0) REVERT: D 844 GLU cc_start: 0.8795 (pt0) cc_final: 0.8494 (pt0) REVERT: D 980 ASP cc_start: 0.8477 (t70) cc_final: 0.8205 (t70) REVERT: D 983 ASP cc_start: 0.6538 (p0) cc_final: 0.6272 (p0) outliers start: 75 outliers final: 29 residues processed: 470 average time/residue: 0.6322 time to fit residues: 349.1281 Evaluate side-chains 444 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 409 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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 1012 MET 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 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 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 1013 SER Chi-restraints excluded: chain C residue 1120 VAL Chi-restraints excluded: chain D residue 193 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 138 optimal weight: 4.9990 chunk 326 optimal weight: 0.0050 chunk 227 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 137 optimal weight: 0.0570 chunk 135 optimal weight: 3.9990 chunk 315 optimal weight: 0.6980 chunk 242 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.3516 ------------------------------------------------------------------------------- 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 = 0.4092 r_free = 0.4092 target = 0.181609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.113541 restraints weight = 34811.884| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.48 r_work: 0.3092 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 28724 Z= 0.160 Angle : 0.498 9.078 38972 Z= 0.258 Chirality : 0.042 0.138 4472 Planarity : 0.004 0.068 4904 Dihedral : 4.324 51.203 3820 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.52 % Allowed : 14.02 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.14), residues: 3492 helix: 0.45 (0.13), residues: 1584 sheet: 0.87 (0.26), residues: 436 loop : 0.39 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C1048 TYR 0.019 0.001 TYR C1095 PHE 0.024 0.001 PHE B 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 0.00378 (28724) covalent geometry : angle 0.49776 (38972) hydrogen bonds : bond 0.03838 ( 1148) hydrogen bonds : angle 4.45731 ( 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 504 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 426 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: A 196 MET cc_start: 0.5413 (OUTLIER) cc_final: 0.4457 (ttp) REVERT: A 271 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7852 (mm) REVERT: A 394 ARG cc_start: 0.8857 (ttp80) cc_final: 0.8636 (ttp80) REVERT: A 550 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8275 (mt-10) REVERT: A 584 GLU cc_start: 0.8573 (mm-30) cc_final: 0.7708 (pp20) REVERT: B 176 MET cc_start: 0.7297 (ppp) cc_final: 0.7030 (ppp) REVERT: B 196 MET cc_start: 0.5169 (OUTLIER) cc_final: 0.4271 (ttp) REVERT: B 230 MET cc_start: 0.7533 (mtp) cc_final: 0.7282 (mtt) REVERT: B 550 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8168 (mt-10) REVERT: B 561 ILE cc_start: 0.8949 (tt) cc_final: 0.8699 (mp) REVERT: B 620 GLU cc_start: 0.8189 (mp0) cc_final: 0.7940 (mp0) REVERT: B 874 ASN cc_start: 0.8598 (t0) cc_final: 0.8287 (t0) REVERT: B 1093 LYS cc_start: 0.8969 (mtmt) cc_final: 0.8746 (mtpp) REVERT: C 196 MET cc_start: 0.5309 (OUTLIER) cc_final: 0.4322 (ttp) REVERT: C 394 ARG cc_start: 0.8854 (ttp80) cc_final: 0.8652 (ttp80) REVERT: C 550 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8264 (mt-10) REVERT: C 844 GLU cc_start: 0.8776 (pt0) cc_final: 0.8444 (pt0) REVERT: C 1011 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8625 (mp) REVERT: D 196 MET cc_start: 0.5176 (OUTLIER) cc_final: 0.4293 (ttp) REVERT: D 550 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8227 (mt-10) REVERT: D 561 ILE cc_start: 0.8980 (tt) cc_final: 0.8754 (mp) REVERT: D 844 GLU cc_start: 0.8768 (pt0) cc_final: 0.8405 (pt0) REVERT: D 913 GLU cc_start: 0.8627 (mp0) cc_final: 0.8289 (mp0) REVERT: D 980 ASP cc_start: 0.8482 (t70) cc_final: 0.8183 (t70) REVERT: D 983 ASP cc_start: 0.6597 (p0) cc_final: 0.6392 (p0) outliers start: 78 outliers final: 33 residues processed: 480 average time/residue: 0.6146 time to fit residues: 346.6520 Evaluate side-chains 433 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 394 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 318 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 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 B residue 1133 THR Chi-restraints excluded: chain C residue 196 MET 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 561 ILE Chi-restraints excluded: chain C residue 1011 LEU 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 318 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 Chi-restraints excluded: chain D residue 1133 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 34 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 294 optimal weight: 0.2980 chunk 78 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 57 optimal weight: 0.1980 chunk 136 optimal weight: 2.9990 chunk 347 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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 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** C 920 ASN D 610 GLN ** D 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.182116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.114623 restraints weight = 34877.382| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.47 r_work: 0.3107 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 28724 Z= 0.126 Angle : 0.491 8.534 38972 Z= 0.255 Chirality : 0.041 0.139 4472 Planarity : 0.004 0.067 4904 Dihedral : 4.249 49.788 3820 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.23 % Allowed : 15.37 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.14), residues: 3492 helix: 0.53 (0.13), residues: 1584 sheet: 0.86 (0.26), residues: 436 loop : 0.42 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D1048 TYR 0.014 0.001 TYR B 308 PHE 0.019 0.001 PHE B 317 TRP 0.009 0.001 TRP B 114 HIS 0.003 0.000 HIS D 269 Details of bonding type rmsd covalent geometry : bond 0.00299 (28724) covalent geometry : angle 0.49061 (38972) hydrogen bonds : bond 0.03513 ( 1148) hydrogen bonds : angle 4.39365 ( 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 483 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 414 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: A 196 MET cc_start: 0.5407 (OUTLIER) cc_final: 0.4499 (ttp) REVERT: A 271 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7847 (mm) REVERT: A 394 ARG cc_start: 0.8857 (ttp80) cc_final: 0.8630 (ttp80) REVERT: A 550 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8321 (mt-10) REVERT: A 584 GLU cc_start: 0.8554 (mm-30) cc_final: 0.7669 (pp20) REVERT: A 913 GLU cc_start: 0.8566 (mp0) cc_final: 0.8232 (mp0) REVERT: B 196 MET cc_start: 0.5043 (OUTLIER) cc_final: 0.4163 (ttp) REVERT: B 550 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8215 (mt-10) REVERT: B 854 VAL cc_start: 0.8990 (m) cc_final: 0.8743 (t) REVERT: B 1093 LYS cc_start: 0.8980 (mtmt) cc_final: 0.8752 (mtpp) REVERT: B 1140 MET cc_start: 0.8948 (mtm) cc_final: 0.8732 (mtp) REVERT: C 196 MET cc_start: 0.5199 (OUTLIER) cc_final: 0.4325 (ttp) REVERT: C 271 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7906 (mm) REVERT: C 394 ARG cc_start: 0.8851 (ttp80) cc_final: 0.8643 (ttp80) REVERT: C 550 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8286 (mt-10) REVERT: C 620 GLU cc_start: 0.8545 (mp0) cc_final: 0.8335 (mp0) REVERT: C 913 GLU cc_start: 0.8595 (mp0) cc_final: 0.8260 (mp0) REVERT: C 1011 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8633 (mp) REVERT: D 196 MET cc_start: 0.5140 (OUTLIER) cc_final: 0.4272 (ttp) REVERT: D 550 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8212 (mt-10) REVERT: D 620 GLU cc_start: 0.8529 (mp0) cc_final: 0.8299 (mp0) REVERT: D 844 GLU cc_start: 0.8742 (pt0) cc_final: 0.8457 (pt0) REVERT: D 913 GLU cc_start: 0.8611 (mp0) cc_final: 0.8275 (mp0) REVERT: D 980 ASP cc_start: 0.8454 (t70) cc_final: 0.8181 (t70) REVERT: D 1011 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8648 (mp) outliers start: 69 outliers final: 31 residues processed: 463 average time/residue: 0.6129 time to fit residues: 334.1771 Evaluate side-chains 440 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 401 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 295 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 561 ILE Chi-restraints excluded: chain C residue 1011 LEU 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 318 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 1011 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 205 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 345 optimal weight: 3.9990 chunk 226 optimal weight: 4.9990 chunk 204 optimal weight: 5.9990 chunk 317 optimal weight: 1.9990 chunk 120 optimal weight: 0.0170 chunk 216 optimal weight: 0.6980 chunk 242 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 overall best weight: 1.9424 ------------------------------------------------------------------------------- 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 165 GLN 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 165 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 = 0.4069 r_free = 0.4069 target = 0.179475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.111584 restraints weight = 34783.281| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.44 r_work: 0.3064 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2935 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2935 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 28724 Z= 0.214 Angle : 0.555 8.986 38972 Z= 0.286 Chirality : 0.044 0.137 4472 Planarity : 0.005 0.063 4904 Dihedral : 4.430 47.543 3818 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.16 % Allowed : 16.31 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.14), residues: 3492 helix: 0.40 (0.13), residues: 1568 sheet: 0.78 (0.26), residues: 424 loop : 0.33 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 407 TYR 0.012 0.001 TYR B1095 PHE 0.023 0.002 PHE B 317 TRP 0.011 0.001 TRP A 218 HIS 0.004 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00516 (28724) covalent geometry : angle 0.55461 (38972) hydrogen bonds : bond 0.04120 ( 1148) hydrogen bonds : angle 4.52195 ( 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 476 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 409 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: A 196 MET cc_start: 0.5417 (OUTLIER) cc_final: 0.4469 (ttp) REVERT: A 271 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7899 (mm) REVERT: A 394 ARG cc_start: 0.8866 (ttp80) cc_final: 0.8659 (ttp80) REVERT: A 550 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8322 (mt-10) REVERT: A 584 GLU cc_start: 0.8550 (mm-30) cc_final: 0.7733 (pp20) REVERT: A 844 GLU cc_start: 0.8822 (pt0) cc_final: 0.8511 (pt0) REVERT: A 913 GLU cc_start: 0.8605 (mp0) cc_final: 0.8263 (mp0) REVERT: A 1011 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8670 (mp) REVERT: B 196 MET cc_start: 0.5012 (OUTLIER) cc_final: 0.4149 (ttp) REVERT: B 368 GLU cc_start: 0.8530 (pm20) cc_final: 0.8328 (pp20) REVERT: B 550 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8200 (mt-10) REVERT: B 584 GLU cc_start: 0.8524 (mm-30) cc_final: 0.7662 (pp20) REVERT: B 620 GLU cc_start: 0.8561 (mp0) cc_final: 0.8251 (mp0) REVERT: B 844 GLU cc_start: 0.8829 (pt0) cc_final: 0.8520 (pt0) REVERT: B 874 ASN cc_start: 0.8729 (t0) cc_final: 0.8524 (t0) REVERT: B 913 GLU cc_start: 0.8637 (mp0) cc_final: 0.8240 (mp0) REVERT: B 1011 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8669 (mp) REVERT: B 1093 LYS cc_start: 0.8997 (mtmt) cc_final: 0.8792 (mtpp) REVERT: C 176 MET cc_start: 0.7513 (ppp) cc_final: 0.7249 (ppp) REVERT: C 196 MET cc_start: 0.5218 (OUTLIER) cc_final: 0.4315 (ttp) REVERT: C 271 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7919 (mm) REVERT: C 394 ARG cc_start: 0.8867 (ttp80) cc_final: 0.8665 (ttp80) REVERT: C 550 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8252 (OUTLIER) REVERT: C 584 GLU cc_start: 0.8513 (mm-30) cc_final: 0.7686 (pp20) REVERT: C 844 GLU cc_start: 0.8817 (pt0) cc_final: 0.8506 (pt0) REVERT: C 913 GLU cc_start: 0.8602 (mp0) cc_final: 0.8257 (mp0) REVERT: D 196 MET cc_start: 0.5141 (OUTLIER) cc_final: 0.4228 (ttp) REVERT: D 368 GLU cc_start: 0.8545 (pm20) cc_final: 0.8339 (pp20) REVERT: D 550 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8249 (OUTLIER) REVERT: D 584 GLU cc_start: 0.8492 (mm-30) cc_final: 0.7672 (pp20) REVERT: D 913 GLU cc_start: 0.8591 (mp0) cc_final: 0.8301 (mp0) REVERT: D 983 ASP cc_start: 0.6521 (p0) cc_final: 0.6285 (p0) REVERT: D 1011 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8679 (mp) outliers start: 67 outliers final: 36 residues processed: 461 average time/residue: 0.6402 time to fit residues: 345.7446 Evaluate side-chains 440 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 397 time to evaluate : 1.104 ------------------------------------------------------------------------------- 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 1011 LEU 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 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 B residue 1133 THR 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 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 Chi-restraints excluded: chain D residue 1133 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 325 optimal weight: 1.9990 chunk 326 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 197 optimal weight: 8.9990 chunk 185 optimal weight: 8.9990 chunk 207 optimal weight: 1.9990 chunk 223 optimal weight: 0.8980 chunk 153 optimal weight: 0.9980 chunk 182 optimal weight: 1.9990 chunk 310 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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** D 610 GLN ** D 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.181111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.113931 restraints weight = 34773.100| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.44 r_work: 0.3107 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 28724 Z= 0.131 Angle : 0.522 8.870 38972 Z= 0.269 Chirality : 0.041 0.136 4472 Planarity : 0.004 0.065 4904 Dihedral : 4.299 46.026 3816 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.97 % Allowed : 17.38 % Favored : 80.65 % 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: 0.57 (0.14), residues: 3492 helix: 0.49 (0.13), residues: 1568 sheet: 0.79 (0.26), residues: 424 loop : 0.34 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 407 TYR 0.016 0.001 TYR D1095 PHE 0.025 0.001 PHE A 317 TRP 0.007 0.001 TRP A 218 HIS 0.004 0.000 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00313 (28724) covalent geometry : angle 0.52211 (38972) hydrogen bonds : bond 0.03483 ( 1148) hydrogen bonds : angle 4.36273 ( 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 488 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 427 time to evaluate : 1.153 Fit side-chains REVERT: A 196 MET cc_start: 0.5367 (OUTLIER) cc_final: 0.4451 (ttp) REVERT: A 271 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7889 (mm) REVERT: A 368 GLU cc_start: 0.8482 (pm20) cc_final: 0.8241 (pp20) REVERT: A 394 ARG cc_start: 0.8875 (ttp80) cc_final: 0.8672 (ttp80) REVERT: A 550 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8279 (mt-10) REVERT: A 584 GLU cc_start: 0.8569 (mm-30) cc_final: 0.7797 (pp20) REVERT: A 620 GLU cc_start: 0.8527 (mp0) cc_final: 0.8252 (mp0) REVERT: A 913 GLU cc_start: 0.8580 (mp0) cc_final: 0.8233 (mp0) REVERT: B 196 MET cc_start: 0.4963 (OUTLIER) cc_final: 0.4098 (ttp) REVERT: B 550 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8188 (mt-10) REVERT: B 584 GLU cc_start: 0.8482 (mm-30) cc_final: 0.7646 (pp20) REVERT: B 608 ASN cc_start: 0.8818 (m110) cc_final: 0.8532 (m110) REVERT: B 620 GLU cc_start: 0.8508 (mp0) cc_final: 0.7907 (mp0) REVERT: B 844 GLU cc_start: 0.8802 (pt0) cc_final: 0.8439 (pt0) REVERT: B 854 VAL cc_start: 0.9011 (m) cc_final: 0.8769 (t) REVERT: B 913 GLU cc_start: 0.8656 (mp0) cc_final: 0.8251 (mp0) REVERT: B 1093 LYS cc_start: 0.8977 (mtmt) cc_final: 0.8775 (mtpp) REVERT: C 176 MET cc_start: 0.7521 (ppp) cc_final: 0.7301 (ppp) REVERT: C 196 MET cc_start: 0.5215 (OUTLIER) cc_final: 0.4347 (ttp) REVERT: C 271 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7933 (mm) REVERT: C 550 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8318 (mt-10) REVERT: C 584 GLU cc_start: 0.8504 (mm-30) cc_final: 0.7690 (pp20) REVERT: C 913 GLU cc_start: 0.8580 (mp0) cc_final: 0.8235 (mp0) REVERT: C 1140 MET cc_start: 0.9009 (mtp) cc_final: 0.8790 (mtm) REVERT: D 196 MET cc_start: 0.5067 (OUTLIER) cc_final: 0.4646 (pmm) REVERT: D 235 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7758 (mt) REVERT: D 368 GLU cc_start: 0.8513 (pm20) cc_final: 0.8301 (pp20) REVERT: D 550 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8266 (mt-10) REVERT: D 584 GLU cc_start: 0.8469 (mm-30) cc_final: 0.7680 (pp20) REVERT: D 844 GLU cc_start: 0.8797 (pt0) cc_final: 0.8508 (pt0) REVERT: D 913 GLU cc_start: 0.8565 (mp0) cc_final: 0.8222 (mp0) REVERT: D 1055 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7792 (tm-30) REVERT: D 1140 MET cc_start: 0.8999 (mtp) cc_final: 0.8782 (mtm) outliers start: 61 outliers final: 32 residues processed: 472 average time/residue: 0.5889 time to fit residues: 326.4274 Evaluate side-chains 447 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 408 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 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 A residue 1140 MET 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 B residue 1133 THR 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 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 235 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 1013 SER Chi-restraints excluded: chain D residue 1120 VAL Chi-restraints excluded: chain D residue 1133 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 71 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 190 optimal weight: 20.0000 chunk 244 optimal weight: 0.5980 chunk 236 optimal weight: 0.0670 chunk 97 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 179 optimal weight: 7.9990 chunk 311 optimal weight: 0.9980 chunk 104 optimal weight: 7.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- 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 = 0.4097 r_free = 0.4097 target = 0.182178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.115172 restraints weight = 34603.768| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.44 r_work: 0.3127 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2984 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2984 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2961 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= 0.112 Angle : 0.521 14.076 38972 Z= 0.265 Chirality : 0.041 0.161 4472 Planarity : 0.004 0.065 4904 Dihedral : 4.204 44.683 3816 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.78 % Allowed : 17.99 % Favored : 80.23 % 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: 0.56 (0.14), residues: 3492 helix: 0.49 (0.13), residues: 1596 sheet: 0.82 (0.26), residues: 440 loop : 0.31 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 407 TYR 0.016 0.001 TYR B1095 PHE 0.027 0.001 PHE A 175 TRP 0.015 0.001 TRP A 114 HIS 0.003 0.000 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00262 (28724) covalent geometry : angle 0.52140 (38972) hydrogen bonds : bond 0.03268 ( 1148) hydrogen bonds : angle 4.27980 ( 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 480 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 425 time to evaluate : 0.918 Fit side-chains REVERT: A 176 MET cc_start: 0.7908 (pmm) cc_final: 0.7240 (pmm) REVERT: A 196 MET cc_start: 0.5376 (OUTLIER) cc_final: 0.4449 (ttp) REVERT: A 271 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7908 (mm) REVERT: A 368 GLU cc_start: 0.8500 (pm20) cc_final: 0.8256 (pp20) REVERT: A 394 ARG cc_start: 0.8865 (ttp80) cc_final: 0.8660 (ttp80) REVERT: A 550 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8259 (mt-10) REVERT: A 584 GLU cc_start: 0.8557 (mm-30) cc_final: 0.7795 (pp20) REVERT: A 620 GLU cc_start: 0.8484 (mp0) cc_final: 0.8005 (mp0) REVERT: A 844 GLU cc_start: 0.8817 (pt0) cc_final: 0.8527 (pt0) REVERT: A 913 GLU cc_start: 0.8588 (mp0) cc_final: 0.8245 (mp0) REVERT: A 1011 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8650 (mp) REVERT: B 196 MET cc_start: 0.4853 (OUTLIER) cc_final: 0.4055 (ttp) REVERT: B 230 MET cc_start: 0.7584 (mtp) cc_final: 0.7345 (mtt) REVERT: B 550 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8203 (mt-10) REVERT: B 608 ASN cc_start: 0.8803 (m110) cc_final: 0.8579 (m110) REVERT: B 620 GLU cc_start: 0.8490 (mp0) cc_final: 0.8044 (mp0) REVERT: B 854 VAL cc_start: 0.8976 (m) cc_final: 0.8740 (t) REVERT: B 1011 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8651 (mp) REVERT: B 1140 MET cc_start: 0.8984 (mtp) cc_final: 0.8783 (mtm) REVERT: C 176 MET cc_start: 0.7482 (ppp) cc_final: 0.7270 (ppp) REVERT: C 196 MET cc_start: 0.5224 (OUTLIER) cc_final: 0.4340 (ttp) REVERT: C 271 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7924 (mm) REVERT: C 368 GLU cc_start: 0.8499 (pm20) cc_final: 0.8253 (pp20) REVERT: C 550 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8285 (mt-10) REVERT: C 584 GLU cc_start: 0.8478 (mm-30) cc_final: 0.7709 (pp20) REVERT: C 844 GLU cc_start: 0.8820 (pt0) cc_final: 0.8533 (pt0) REVERT: C 913 GLU cc_start: 0.8571 (mp0) cc_final: 0.8227 (mp0) REVERT: C 1140 MET cc_start: 0.9003 (mtp) cc_final: 0.8798 (OUTLIER) REVERT: D 196 MET cc_start: 0.5131 (OUTLIER) cc_final: 0.4221 (ttp) REVERT: D 235 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7787 (mt) REVERT: D 550 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8253 (mt-10) REVERT: D 913 GLU cc_start: 0.8572 (mp0) cc_final: 0.8226 (mp0) REVERT: D 1055 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7820 (tm-30) REVERT: D 1140 MET cc_start: 0.8994 (mtp) cc_final: 0.8782 (mtm) outliers start: 55 outliers final: 26 residues processed: 463 average time/residue: 0.6208 time to fit residues: 336.5804 Evaluate side-chains 447 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 413 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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 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 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 B residue 1133 THR 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 1120 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 235 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 Chi-restraints excluded: chain D residue 1133 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 344 optimal weight: 0.9990 chunk 168 optimal weight: 3.9990 chunk 240 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 179 optimal weight: 1.9990 chunk 348 optimal weight: 0.0670 chunk 21 optimal weight: 0.5980 chunk 225 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 304 optimal weight: 0.9980 overall best weight: 0.6520 ------------------------------------------------------------------------------- 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 = 0.4100 r_free = 0.4100 target = 0.182484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.115497 restraints weight = 34508.051| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.45 r_work: 0.3130 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 28724 Z= 0.115 Angle : 0.535 13.388 38972 Z= 0.271 Chirality : 0.041 0.171 4472 Planarity : 0.004 0.065 4904 Dihedral : 4.166 43.740 3816 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.23 % Allowed : 18.67 % Favored : 80.10 % 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: 0.43 (0.14), residues: 3492 helix: 0.43 (0.13), residues: 1632 sheet: 0.83 (0.26), residues: 440 loop : 0.14 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 407 TYR 0.015 0.001 TYR C1095 PHE 0.021 0.001 PHE B 317 TRP 0.016 0.001 TRP C 114 HIS 0.004 0.000 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00273 (28724) covalent geometry : angle 0.53459 (38972) hydrogen bonds : bond 0.03242 ( 1148) hydrogen bonds : angle 4.30131 ( 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 464 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 426 time to evaluate : 1.009 Fit side-chains REVERT: A 176 MET cc_start: 0.7957 (pmm) cc_final: 0.7298 (pmm) REVERT: A 196 MET cc_start: 0.5310 (OUTLIER) cc_final: 0.4400 (ttp) REVERT: A 271 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7903 (mm) REVERT: A 368 GLU cc_start: 0.8500 (pm20) cc_final: 0.8260 (pp20) REVERT: A 394 ARG cc_start: 0.8869 (ttp80) cc_final: 0.8663 (ttp80) REVERT: A 550 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8258 (mt-10) REVERT: A 584 GLU cc_start: 0.8569 (mm-30) cc_final: 0.7816 (pp20) REVERT: A 620 GLU cc_start: 0.8491 (mp0) cc_final: 0.8096 (mp0) REVERT: A 844 GLU cc_start: 0.8814 (pt0) cc_final: 0.8533 (pt0) REVERT: A 913 GLU cc_start: 0.8576 (mp0) cc_final: 0.8232 (mp0) REVERT: B 196 MET cc_start: 0.4839 (OUTLIER) cc_final: 0.4064 (ttp) REVERT: B 230 MET cc_start: 0.7559 (mtp) cc_final: 0.7321 (mtt) REVERT: B 368 GLU cc_start: 0.8490 (pm20) cc_final: 0.8289 (pp20) REVERT: B 550 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8199 (mt-10) REVERT: B 608 ASN cc_start: 0.8809 (m110) cc_final: 0.8579 (m110) REVERT: B 620 GLU cc_start: 0.8506 (mp0) cc_final: 0.7884 (mp0) REVERT: B 844 GLU cc_start: 0.8823 (pt0) cc_final: 0.8552 (pt0) REVERT: B 854 VAL cc_start: 0.8968 (m) cc_final: 0.8746 (t) REVERT: C 196 MET cc_start: 0.5129 (OUTLIER) cc_final: 0.4246 (ttp) REVERT: C 271 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7853 (mm) REVERT: C 368 GLU cc_start: 0.8496 (pm20) cc_final: 0.8253 (pp20) REVERT: C 550 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8275 (mt-10) REVERT: C 584 GLU cc_start: 0.8498 (mm-30) cc_final: 0.7726 (pp20) REVERT: C 844 GLU cc_start: 0.8801 (pt0) cc_final: 0.8467 (pt0) REVERT: C 913 GLU cc_start: 0.8569 (mp0) cc_final: 0.8223 (mp0) REVERT: C 1140 MET cc_start: 0.9008 (mtp) cc_final: 0.8799 (OUTLIER) REVERT: D 196 MET cc_start: 0.5092 (OUTLIER) cc_final: 0.4206 (ttp) REVERT: D 550 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8256 (mt-10) REVERT: D 584 GLU cc_start: 0.8478 (mm-30) cc_final: 0.7688 (pp20) REVERT: D 620 GLU cc_start: 0.8507 (mp0) cc_final: 0.8248 (mp0) REVERT: D 844 GLU cc_start: 0.8837 (pt0) cc_final: 0.8505 (pt0) REVERT: D 913 GLU cc_start: 0.8575 (mp0) cc_final: 0.8231 (mp0) REVERT: D 1140 MET cc_start: 0.9003 (mtp) cc_final: 0.8795 (mtm) outliers start: 38 outliers final: 24 residues processed: 448 average time/residue: 0.6331 time to fit residues: 331.6182 Evaluate side-chains 446 residues out of total 3096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 417 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 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 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 B residue 1133 THR 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 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 557 SER Chi-restraints excluded: chain D residue 1120 VAL Chi-restraints excluded: chain D residue 1133 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 143 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 341 optimal weight: 0.9980 chunk 193 optimal weight: 0.1980 chunk 244 optimal weight: 0.6980 chunk 212 optimal weight: 1.9990 chunk 140 optimal weight: 0.0370 chunk 91 optimal weight: 0.0000 chunk 175 optimal weight: 0.7980 chunk 113 optimal weight: 9.9990 chunk 222 optimal weight: 3.9990 overall best weight: 0.3462 ------------------------------------------------------------------------------- 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 479 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.183897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.117333 restraints weight = 34694.865| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.46 r_work: 0.3153 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 28724 Z= 0.100 Angle : 0.523 12.948 38972 Z= 0.265 Chirality : 0.040 0.139 4472 Planarity : 0.004 0.065 4904 Dihedral : 4.051 42.380 3816 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.39 % Allowed : 18.48 % Favored : 80.14 % 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: 0.46 (0.13), residues: 1656 sheet: 0.86 (0.26), residues: 440 loop : 0.14 (0.16), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 407 TYR 0.017 0.001 TYR B1095 PHE 0.017 0.001 PHE B 317 TRP 0.008 0.001 TRP D 289 HIS 0.004 0.000 HIS C 269 Details of bonding type rmsd covalent geometry : bond 0.00232 (28724) covalent geometry : angle 0.52329 (38972) hydrogen bonds : bond 0.02970 ( 1148) hydrogen bonds : angle 4.18712 ( 3108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15460.53 seconds wall clock time: 262 minutes 15.45 seconds (15735.45 seconds total)