Starting phenix.real_space_refine on Tue Jul 7 05:43:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e8h_31019/07_2026/7e8h_31019.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e8h_31019/07_2026/7e8h_31019.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7e8h_31019/07_2026/7e8h_31019.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e8h_31019/07_2026/7e8h_31019.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e8h_31019/07_2026/7e8h_31019.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e8h_31019/07_2026/7e8h_31019.map" } resolution = 4.5 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 216 5.16 5 C 28726 2.51 5 N 7612 2.21 5 O 8340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 44894 Number of models: 1 Model: "" Number of chains: 12 Chain: "J" Number of atoms: 6071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 756, 6071 Classifications: {'peptide': 756} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 721} Chain breaks: 1 Chain: "I" Number of atoms: 6093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 6093 Classifications: {'peptide': 760} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 724} Chain: "F" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1459 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 4, 'TRANS': 171} Chain breaks: 1 Chain: "B" Number of atoms: 3675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3675 Classifications: {'peptide': 459} Link IDs: {'PTRANS': 20, 'TRANS': 438} Chain breaks: 3 Chain: "E" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1466 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 4, 'TRANS': 172} Chain breaks: 1 Chain: "A" Number of atoms: 3683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3683 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 20, 'TRANS': 439} Chain breaks: 3 Chain: "L" Number of atoms: 6071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 756, 6071 Classifications: {'peptide': 756} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 721} Chain breaks: 1 Chain: "K" Number of atoms: 6093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 6093 Classifications: {'peptide': 760} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 724} Chain: "H" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1459 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 4, 'TRANS': 171} Chain breaks: 1 Chain: "D" Number of atoms: 3675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3675 Classifications: {'peptide': 459} Link IDs: {'PTRANS': 20, 'TRANS': 438} Chain breaks: 3 Chain: "G" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1466 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 4, 'TRANS': 172} Chain breaks: 1 Chain: "C" Number of atoms: 3683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3683 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 20, 'TRANS': 439} Chain breaks: 3 Time building chain proxies: 7.57, per 1000 atoms: 0.17 Number of scatterers: 44894 At special positions: 0 Unit cell: (159.426, 215.576, 206.552, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 216 16.00 O 8340 8.00 N 7612 7.00 C 28726 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS J 349 " - pdb=" SG CYS J 356 " distance=2.03 Simple disulfide: pdb=" SG CYS J 465 " - pdb=" SG CYS J 468 " distance=2.03 Simple disulfide: pdb=" SG CYS J 474 " - pdb=" SG CYS J 492 " distance=2.03 Simple disulfide: pdb=" SG CYS J 673 " - pdb=" SG CYS J 784 " distance=2.03 Simple disulfide: pdb=" SG CYS I 349 " - pdb=" SG CYS I 356 " distance=2.03 Simple disulfide: pdb=" SG CYS I 465 " - pdb=" SG CYS I 468 " distance=2.04 Simple disulfide: pdb=" SG CYS I 474 " - pdb=" SG CYS I 492 " distance=2.03 Simple disulfide: pdb=" SG CYS I 673 " - pdb=" SG CYS I 784 " distance=2.03 Simple disulfide: pdb=" SG CYS L 349 " - pdb=" SG CYS L 356 " distance=2.03 Simple disulfide: pdb=" SG CYS L 465 " - pdb=" SG CYS L 468 " distance=2.03 Simple disulfide: pdb=" SG CYS L 474 " - pdb=" SG CYS L 492 " distance=2.03 Simple disulfide: pdb=" SG CYS L 673 " - pdb=" SG CYS L 784 " distance=2.03 Simple disulfide: pdb=" SG CYS K 349 " - pdb=" SG CYS K 356 " distance=2.03 Simple disulfide: pdb=" SG CYS K 465 " - pdb=" SG CYS K 468 " distance=2.03 Simple disulfide: pdb=" SG CYS K 474 " - pdb=" SG CYS K 492 " distance=2.03 Simple disulfide: pdb=" SG CYS K 673 " - pdb=" SG CYS K 784 " distance=2.03 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: 3.51 Conformation dependent library (CDL) restraints added in 1.6 seconds 11032 Ramachandran restraints generated. 5516 Oldfield, 0 Emsley, 5516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10552 Finding SS restraints... Secondary structure from input PDB file: 186 helices and 54 sheets defined 43.6% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'J' and resid 31 through 56 Processing helix chain 'J' and resid 70 through 76 Processing helix chain 'J' and resid 77 through 80 Processing helix chain 'J' and resid 118 through 124 removed outlier: 3.636A pdb=" N LYS J 121 " --> pdb=" O GLU J 118 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER J 124 " --> pdb=" O LYS J 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 228 through 234 Processing helix chain 'J' and resid 517 through 526 Processing helix chain 'J' and resid 582 through 592 Processing helix chain 'J' and resid 607 through 614 removed outlier: 3.601A pdb=" N LEU J 611 " --> pdb=" O GLY J 607 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL J 614 " --> pdb=" O LEU J 610 " (cutoff:3.500A) Processing helix chain 'J' and resid 621 through 635 Processing helix chain 'J' and resid 650 through 659 Processing helix chain 'J' and resid 682 through 686 Processing helix chain 'J' and resid 687 through 696 removed outlier: 4.083A pdb=" N ARG J 693 " --> pdb=" O ALA J 689 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR J 694 " --> pdb=" O PHE J 690 " (cutoff:3.500A) Processing helix chain 'J' and resid 704 through 708 removed outlier: 3.997A pdb=" N MET J 707 " --> pdb=" O ALA J 704 " (cutoff:3.500A) Processing helix chain 'J' and resid 711 through 715 removed outlier: 3.515A pdb=" N VAL J 714 " --> pdb=" O ALA J 711 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER J 715 " --> pdb=" O HIS J 712 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 711 through 715' Processing helix chain 'J' and resid 734 through 749 removed outlier: 4.131A pdb=" N THR J 738 " --> pdb=" O HIS J 734 " (cutoff:3.500A) Processing helix chain 'J' and resid 766 through 784 removed outlier: 3.863A pdb=" N GLU J 783 " --> pdb=" O ASN J 779 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 54 removed outlier: 3.632A pdb=" N CYS I 45 " --> pdb=" O ILE I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 76 Processing helix chain 'I' and resid 118 through 124 removed outlier: 3.609A pdb=" N LYS I 121 " --> pdb=" O GLU I 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 228 through 234 Processing helix chain 'I' and resid 517 through 527 Processing helix chain 'I' and resid 582 through 590 Processing helix chain 'I' and resid 607 through 613 Processing helix chain 'I' and resid 620 through 635 Processing helix chain 'I' and resid 650 through 659 Processing helix chain 'I' and resid 682 through 686 Processing helix chain 'I' and resid 687 through 696 removed outlier: 3.790A pdb=" N ARG I 693 " --> pdb=" O ALA I 689 " (cutoff:3.500A) Processing helix chain 'I' and resid 712 through 716 removed outlier: 3.558A pdb=" N SER I 715 " --> pdb=" O HIS I 712 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA I 716 " --> pdb=" O ARG I 713 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 712 through 716' Processing helix chain 'I' and resid 734 through 749 removed outlier: 4.353A pdb=" N THR I 738 " --> pdb=" O HIS I 734 " (cutoff:3.500A) Processing helix chain 'I' and resid 766 through 786 Processing helix chain 'F' and resid 49 through 64 Processing helix chain 'F' and resid 70 through 82 Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'F' and resid 100 through 103 Processing helix chain 'F' and resid 107 through 120 removed outlier: 3.536A pdb=" N PHE F 111 " --> pdb=" O LYS F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 135 Processing helix chain 'F' and resid 143 through 156 removed outlier: 3.545A pdb=" N MET F 147 " --> pdb=" O ASN F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 182 removed outlier: 3.701A pdb=" N ARG F 172 " --> pdb=" O GLU F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 202 Processing helix chain 'F' and resid 202 through 208 removed outlier: 3.734A pdb=" N MET F 206 " --> pdb=" O ASP F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 214 removed outlier: 3.923A pdb=" N GLN F 213 " --> pdb=" O LEU F 209 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN F 214 " --> pdb=" O GLN F 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 209 through 214' Processing helix chain 'B' and resid 5 through 7 No H-bonds generated for 'chain 'B' and resid 5 through 7' Processing helix chain 'B' and resid 8 through 20 removed outlier: 3.535A pdb=" N ALA B 16 " --> pdb=" O ALA B 12 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE B 17 " --> pdb=" O ARG B 13 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY B 18 " --> pdb=" O ALA B 14 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TRP B 19 " --> pdb=" O ALA B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 90 through 102 removed outlier: 3.506A pdb=" N HIS B 94 " --> pdb=" O ASP B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 122 Processing helix chain 'B' and resid 125 through 129 removed outlier: 3.716A pdb=" N ILE B 128 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE B 129 " --> pdb=" O PRO B 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 125 through 129' Processing helix chain 'B' and resid 130 through 152 removed outlier: 3.631A pdb=" N GLU B 135 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLU B 136 " --> pdb=" O CYS B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 177 removed outlier: 3.819A pdb=" N ARG B 173 " --> pdb=" O GLN B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 207 Processing helix chain 'B' and resid 207 through 212 Processing helix chain 'B' and resid 228 through 250 removed outlier: 3.513A pdb=" N LEU B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP B 233 " --> pdb=" O PHE B 229 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N THR B 234 " --> pdb=" O PHE B 230 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 260 Processing helix chain 'B' and resid 260 through 283 Proline residue: B 272 - end of helix Processing helix chain 'B' and resid 288 through 296 Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 307 through 320 removed outlier: 4.206A pdb=" N ARG B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 347 Processing helix chain 'B' and resid 356 through 369 removed outlier: 3.565A pdb=" N TRP B 362 " --> pdb=" O PRO B 358 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR B 363 " --> pdb=" O ALA B 359 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR B 369 " --> pdb=" O ILE B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 400 removed outlier: 3.531A pdb=" N ILE B 385 " --> pdb=" O ILE B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 450 Processing helix chain 'B' and resid 473 through 490 removed outlier: 3.793A pdb=" N GLN B 477 " --> pdb=" O SER B 473 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 64 removed outlier: 3.785A pdb=" N GLU E 63 " --> pdb=" O GLY E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 80 Processing helix chain 'E' and resid 87 through 99 Processing helix chain 'E' and resid 100 through 103 removed outlier: 3.615A pdb=" N THR E 103 " --> pdb=" O THR E 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 100 through 103' Processing helix chain 'E' and resid 108 through 121 Processing helix chain 'E' and resid 122 through 135 removed outlier: 4.605A pdb=" N LEU E 127 " --> pdb=" O VAL E 123 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ARG E 128 " --> pdb=" O HIS E 124 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TRP E 129 " --> pdb=" O GLU E 125 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR E 130 " --> pdb=" O LYS E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 156 Processing helix chain 'E' and resid 157 through 159 No H-bonds generated for 'chain 'E' and resid 157 through 159' Processing helix chain 'E' and resid 169 through 182 removed outlier: 4.031A pdb=" N LYS E 181 " --> pdb=" O VAL E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 200 removed outlier: 4.457A pdb=" N GLN E 200 " --> pdb=" O LEU E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 214 removed outlier: 3.918A pdb=" N MET E 206 " --> pdb=" O ASP E 202 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN E 210 " --> pdb=" O MET E 206 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU E 211 " --> pdb=" O ARG E 207 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N PHE E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASN E 214 " --> pdb=" O GLN E 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 7 No H-bonds generated for 'chain 'A' and resid 5 through 7' Processing helix chain 'A' and resid 8 through 18 removed outlier: 3.593A pdb=" N GLY A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 88 through 102 removed outlier: 3.607A pdb=" N HIS A 94 " --> pdb=" O ASP A 90 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 95 " --> pdb=" O ILE A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 122 Processing helix chain 'A' and resid 133 through 152 Processing helix chain 'A' and resid 168 through 177 removed outlier: 3.531A pdb=" N ARG A 173 " --> pdb=" O GLN A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 205 removed outlier: 3.792A pdb=" N LEU A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR A 191 " --> pdb=" O PHE A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 251 Processing helix chain 'A' and resid 253 through 259 removed outlier: 3.570A pdb=" N ARG A 259 " --> pdb=" O TYR A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 281 Proline residue: A 272 - end of helix removed outlier: 3.924A pdb=" N ASP A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 296 removed outlier: 3.521A pdb=" N LEU A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 305 removed outlier: 3.573A pdb=" N ARG A 305 " --> pdb=" O LYS A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 320 removed outlier: 3.984A pdb=" N ARG A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 346 Processing helix chain 'A' and resid 356 through 369 removed outlier: 3.755A pdb=" N TRP A 362 " --> pdb=" O PRO A 358 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR A 367 " --> pdb=" O TYR A 363 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR A 369 " --> pdb=" O ILE A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 400 Processing helix chain 'A' and resid 401 through 450 Processing helix chain 'A' and resid 473 through 489 Processing helix chain 'L' and resid 32 through 56 Processing helix chain 'L' and resid 70 through 76 Processing helix chain 'L' and resid 77 through 80 Processing helix chain 'L' and resid 118 through 124 removed outlier: 3.636A pdb=" N LYS L 121 " --> pdb=" O GLU L 118 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER L 124 " --> pdb=" O LYS L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 228 through 234 Processing helix chain 'L' and resid 517 through 526 Processing helix chain 'L' and resid 582 through 592 Processing helix chain 'L' and resid 607 through 614 removed outlier: 3.601A pdb=" N LEU L 611 " --> pdb=" O GLY L 607 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL L 614 " --> pdb=" O LEU L 610 " (cutoff:3.500A) Processing helix chain 'L' and resid 621 through 635 Processing helix chain 'L' and resid 650 through 659 Processing helix chain 'L' and resid 682 through 686 Processing helix chain 'L' and resid 687 through 696 removed outlier: 4.084A pdb=" N ARG L 693 " --> pdb=" O ALA L 689 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TYR L 694 " --> pdb=" O PHE L 690 " (cutoff:3.500A) Processing helix chain 'L' and resid 704 through 708 removed outlier: 3.997A pdb=" N MET L 707 " --> pdb=" O ALA L 704 " (cutoff:3.500A) Processing helix chain 'L' and resid 711 through 715 removed outlier: 3.514A pdb=" N VAL L 714 " --> pdb=" O ALA L 711 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER L 715 " --> pdb=" O HIS L 712 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 711 through 715' Processing helix chain 'L' and resid 734 through 749 removed outlier: 4.130A pdb=" N THR L 738 " --> pdb=" O HIS L 734 " (cutoff:3.500A) Processing helix chain 'L' and resid 766 through 784 removed outlier: 3.863A pdb=" N GLU L 783 " --> pdb=" O ASN L 779 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 54 removed outlier: 3.632A pdb=" N CYS K 45 " --> pdb=" O ILE K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 76 Processing helix chain 'K' and resid 118 through 124 removed outlier: 3.609A pdb=" N LYS K 121 " --> pdb=" O GLU K 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 228 through 234 Processing helix chain 'K' and resid 517 through 527 Processing helix chain 'K' and resid 582 through 590 Processing helix chain 'K' and resid 607 through 613 Processing helix chain 'K' and resid 620 through 635 Processing helix chain 'K' and resid 650 through 659 Processing helix chain 'K' and resid 682 through 686 Processing helix chain 'K' and resid 687 through 696 removed outlier: 3.791A pdb=" N ARG K 693 " --> pdb=" O ALA K 689 " (cutoff:3.500A) Processing helix chain 'K' and resid 712 through 716 removed outlier: 3.558A pdb=" N SER K 715 " --> pdb=" O HIS K 712 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA K 716 " --> pdb=" O ARG K 713 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 712 through 716' Processing helix chain 'K' and resid 734 through 749 removed outlier: 4.355A pdb=" N THR K 738 " --> pdb=" O HIS K 734 " (cutoff:3.500A) Processing helix chain 'K' and resid 766 through 786 Processing helix chain 'H' and resid 49 through 64 Processing helix chain 'H' and resid 70 through 82 Processing helix chain 'H' and resid 88 through 99 Processing helix chain 'H' and resid 100 through 103 Processing helix chain 'H' and resid 107 through 120 removed outlier: 3.537A pdb=" N PHE H 111 " --> pdb=" O LYS H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 135 Processing helix chain 'H' and resid 143 through 156 removed outlier: 3.545A pdb=" N MET H 147 " --> pdb=" O ASN H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 182 removed outlier: 3.702A pdb=" N ARG H 172 " --> pdb=" O GLU H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 202 Processing helix chain 'H' and resid 202 through 208 removed outlier: 3.733A pdb=" N MET H 206 " --> pdb=" O ASP H 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 214 removed outlier: 3.923A pdb=" N GLN H 213 " --> pdb=" O LEU H 209 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN H 214 " --> pdb=" O GLN H 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 209 through 214' Processing helix chain 'D' and resid 5 through 7 No H-bonds generated for 'chain 'D' and resid 5 through 7' Processing helix chain 'D' and resid 8 through 20 removed outlier: 3.539A pdb=" N ALA D 16 " --> pdb=" O ALA D 12 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE D 17 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY D 18 " --> pdb=" O ALA D 14 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TRP D 19 " --> pdb=" O ALA D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 61 Processing helix chain 'D' and resid 70 through 74 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.505A pdb=" N HIS D 94 " --> pdb=" O ASP D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 122 Processing helix chain 'D' and resid 125 through 129 removed outlier: 3.715A pdb=" N ILE D 128 " --> pdb=" O ILE D 125 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE D 129 " --> pdb=" O PRO D 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 125 through 129' Processing helix chain 'D' and resid 130 through 152 removed outlier: 3.630A pdb=" N GLU D 135 " --> pdb=" O ASP D 131 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N GLU D 136 " --> pdb=" O CYS D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 177 removed outlier: 3.819A pdb=" N ARG D 173 " --> pdb=" O GLN D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 207 Processing helix chain 'D' and resid 207 through 212 Processing helix chain 'D' and resid 228 through 250 removed outlier: 3.514A pdb=" N LEU D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP D 233 " --> pdb=" O PHE D 229 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N THR D 234 " --> pdb=" O PHE D 230 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU D 243 " --> pdb=" O ILE D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 260 Processing helix chain 'D' and resid 260 through 283 Proline residue: D 272 - end of helix Processing helix chain 'D' and resid 288 through 296 Processing helix chain 'D' and resid 298 through 303 Processing helix chain 'D' and resid 307 through 320 removed outlier: 4.206A pdb=" N ARG D 311 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE D 312 " --> pdb=" O GLN D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 347 Processing helix chain 'D' and resid 356 through 369 removed outlier: 3.565A pdb=" N TRP D 362 " --> pdb=" O PRO D 358 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR D 363 " --> pdb=" O ALA D 359 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR D 369 " --> pdb=" O ILE D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 400 removed outlier: 3.532A pdb=" N ILE D 385 " --> pdb=" O ILE D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 450 Processing helix chain 'D' and resid 473 through 490 removed outlier: 3.793A pdb=" N GLN D 477 " --> pdb=" O SER D 473 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 64 removed outlier: 3.785A pdb=" N GLU G 63 " --> pdb=" O GLY G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 80 Processing helix chain 'G' and resid 87 through 99 Processing helix chain 'G' and resid 100 through 103 removed outlier: 3.617A pdb=" N THR G 103 " --> pdb=" O THR G 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 100 through 103' Processing helix chain 'G' and resid 108 through 121 Processing helix chain 'G' and resid 122 through 135 removed outlier: 4.604A pdb=" N LEU G 127 " --> pdb=" O VAL G 123 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ARG G 128 " --> pdb=" O HIS G 124 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N TRP G 129 " --> pdb=" O GLU G 125 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR G 130 " --> pdb=" O LYS G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 156 Processing helix chain 'G' and resid 157 through 159 No H-bonds generated for 'chain 'G' and resid 157 through 159' Processing helix chain 'G' and resid 169 through 182 removed outlier: 4.014A pdb=" N LYS G 181 " --> pdb=" O VAL G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 192 through 200 removed outlier: 4.457A pdb=" N GLN G 200 " --> pdb=" O LEU G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 214 removed outlier: 3.920A pdb=" N MET G 206 " --> pdb=" O ASP G 202 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN G 210 " --> pdb=" O MET G 206 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU G 211 " --> pdb=" O ARG G 207 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N PHE G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASN G 214 " --> pdb=" O GLN G 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 7 No H-bonds generated for 'chain 'C' and resid 5 through 7' Processing helix chain 'C' and resid 8 through 18 removed outlier: 3.593A pdb=" N GLY C 18 " --> pdb=" O ALA C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 88 through 102 removed outlier: 3.607A pdb=" N HIS C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE C 95 " --> pdb=" O ILE C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 122 Processing helix chain 'C' and resid 133 through 152 Processing helix chain 'C' and resid 168 through 177 removed outlier: 3.532A pdb=" N ARG C 173 " --> pdb=" O GLN C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 205 removed outlier: 3.792A pdb=" N LEU C 185 " --> pdb=" O SER C 181 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR C 191 " --> pdb=" O PHE C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 251 Processing helix chain 'C' and resid 253 through 259 removed outlier: 3.571A pdb=" N ARG C 259 " --> pdb=" O TYR C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 281 Proline residue: C 272 - end of helix removed outlier: 3.924A pdb=" N ASP C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 296 removed outlier: 3.522A pdb=" N LEU C 292 " --> pdb=" O ALA C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 305 removed outlier: 3.573A pdb=" N ARG C 305 " --> pdb=" O LYS C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 320 removed outlier: 3.984A pdb=" N ARG C 311 " --> pdb=" O SER C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 346 Processing helix chain 'C' and resid 356 through 369 removed outlier: 3.756A pdb=" N TRP C 362 " --> pdb=" O PRO C 358 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR C 363 " --> pdb=" O ALA C 359 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR C 367 " --> pdb=" O TYR C 363 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N THR C 369 " --> pdb=" O ILE C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 400 Processing helix chain 'C' and resid 401 through 450 Processing helix chain 'C' and resid 473 through 489 Processing sheet with id=AA1, first strand: chain 'J' and resid 103 through 107 removed outlier: 6.836A pdb=" N VAL J 103 " --> pdb=" O LEU J 116 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU J 116 " --> pdb=" O VAL J 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 129 through 132 removed outlier: 3.943A pdb=" N ARG J 129 " --> pdb=" O SER J 142 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL J 145 " --> pdb=" O THR J 154 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR J 154 " --> pdb=" O VAL J 145 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 192 through 195 Processing sheet with id=AA4, first strand: chain 'J' and resid 305 through 307 removed outlier: 3.681A pdb=" N ALA J 254 " --> pdb=" O ALA J 241 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ALA J 241 " --> pdb=" O ALA J 254 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY J 225 " --> pdb=" O ALA J 241 " (cutoff:3.500A) removed outlier: 11.758A pdb=" N TRP J 243 " --> pdb=" O TYR J 223 " (cutoff:3.500A) removed outlier: 16.362A pdb=" N TYR J 223 " --> pdb=" O TRP J 243 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY J 225 " --> pdb=" O ALA J 254 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA J 254 " --> pdb=" O GLY J 225 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 263 through 266 Processing sheet with id=AA6, first strand: chain 'J' and resid 319 through 325 removed outlier: 5.589A pdb=" N ILE J 321 " --> pdb=" O LEU J 337 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU J 337 " --> pdb=" O ILE J 321 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET J 323 " --> pdb=" O THR J 335 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N VAL J 343 " --> pdb=" O ASN J 338 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N SER J 344 " --> pdb=" O GLU J 361 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLU J 361 " --> pdb=" O SER J 344 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU J 346 " --> pdb=" O LYS J 359 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 384 through 390 Processing sheet with id=AA8, first strand: chain 'J' and resid 425 through 432 removed outlier: 5.834A pdb=" N ILE J 428 " --> pdb=" O LEU J 441 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU J 441 " --> pdb=" O ILE J 428 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS J 437 " --> pdb=" O ASP J 432 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 478 through 481 removed outlier: 6.199A pdb=" N VAL J 502 " --> pdb=" O ASP J 513 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ASP J 513 " --> pdb=" O VAL J 502 " (cutoff:3.500A) removed outlier: 9.879A pdb=" N ASN J 504 " --> pdb=" O MET J 511 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N MET J 511 " --> pdb=" O ASN J 504 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 531 through 534 removed outlier: 3.613A pdb=" N LEU J 549 " --> pdb=" O VAL J 595 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL J 595 " --> pdb=" O LEU J 549 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N CYS J 598 " --> pdb=" O VAL J 565 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS J 673 " --> pdb=" O VAL J 644 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL J 646 " --> pdb=" O CYS J 673 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY J 648 " --> pdb=" O SER J 675 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N GLN J 755 " --> pdb=" O PHE J 722 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE J 724 " --> pdb=" O GLN J 755 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N TYR J 757 " --> pdb=" O ILE J 724 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N HIS J 726 " --> pdb=" O TYR J 757 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 537 through 539 Processing sheet with id=AB3, first strand: chain 'I' and resid 104 through 107 Processing sheet with id=AB4, first strand: chain 'I' and resid 129 through 132 Processing sheet with id=AB5, first strand: chain 'I' and resid 192 through 195 removed outlier: 3.791A pdb=" N VAL I 214 " --> pdb=" O ILE I 200 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N TYR I 202 " --> pdb=" O ARG I 212 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ARG I 212 " --> pdb=" O TYR I 202 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 222 through 224 Processing sheet with id=AB7, first strand: chain 'I' and resid 222 through 224 removed outlier: 4.709A pdb=" N LEU I 294 " --> pdb=" O MET I 308 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 263 through 266 Processing sheet with id=AB9, first strand: chain 'I' and resid 319 through 326 removed outlier: 5.653A pdb=" N ILE I 321 " --> pdb=" O LEU I 337 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU I 337 " --> pdb=" O ILE I 321 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N MET I 323 " --> pdb=" O THR I 335 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR I 335 " --> pdb=" O MET I 323 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N VAL I 343 " --> pdb=" O ASN I 338 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N SER I 344 " --> pdb=" O GLU I 361 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLU I 361 " --> pdb=" O SER I 344 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU I 346 " --> pdb=" O LYS I 359 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 384 through 390 Processing sheet with id=AC2, first strand: chain 'I' and resid 427 through 432 removed outlier: 6.571A pdb=" N TYR I 439 " --> pdb=" O LEU I 429 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N TYR I 431 " --> pdb=" O LYS I 437 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LYS I 437 " --> pdb=" O TYR I 431 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLU I 444 " --> pdb=" O ARG I 449 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ARG I 449 " --> pdb=" O GLU I 444 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 478 through 481 removed outlier: 6.544A pdb=" N VAL I 502 " --> pdb=" O ASP I 513 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASP I 513 " --> pdb=" O VAL I 502 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 531 through 533 removed outlier: 3.992A pdb=" N VAL I 595 " --> pdb=" O LEU I 549 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N CYS I 598 " --> pdb=" O VAL I 565 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N TYR I 560 " --> pdb=" O ASP I 640 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N THR I 642 " --> pdb=" O TYR I 560 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N LEU I 562 " --> pdb=" O THR I 642 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL I 644 " --> pdb=" O LEU I 562 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N LEU I 564 " --> pdb=" O VAL I 644 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL I 646 " --> pdb=" O LEU I 564 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL I 566 " --> pdb=" O VAL I 646 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLY I 648 " --> pdb=" O VAL I 566 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL I 646 " --> pdb=" O CYS I 673 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY I 648 " --> pdb=" O SER I 675 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 537 through 539 Processing sheet with id=AC6, first strand: chain 'B' and resid 51 through 55 removed outlier: 9.218A pdb=" N TYR B 83 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N VAL B 44 " --> pdb=" O TYR B 83 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N PHE B 85 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ASN B 46 " --> pdb=" O PHE B 85 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 68 through 70 Processing sheet with id=AC8, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AC9, first strand: chain 'A' and resid 50 through 51 Processing sheet with id=AD1, first strand: chain 'L' and resid 103 through 107 removed outlier: 6.836A pdb=" N VAL L 103 " --> pdb=" O LEU L 116 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU L 116 " --> pdb=" O VAL L 103 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 129 through 132 removed outlier: 3.943A pdb=" N ARG L 129 " --> pdb=" O SER L 142 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL L 145 " --> pdb=" O THR L 154 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR L 154 " --> pdb=" O VAL L 145 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 192 through 195 Processing sheet with id=AD4, first strand: chain 'L' and resid 305 through 307 removed outlier: 3.680A pdb=" N ALA L 254 " --> pdb=" O ALA L 241 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ALA L 241 " --> pdb=" O ALA L 254 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY L 225 " --> pdb=" O ALA L 241 " (cutoff:3.500A) removed outlier: 11.757A pdb=" N TRP L 243 " --> pdb=" O TYR L 223 " (cutoff:3.500A) removed outlier: 16.361A pdb=" N TYR L 223 " --> pdb=" O TRP L 243 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLY L 225 " --> pdb=" O ALA L 254 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA L 254 " --> pdb=" O GLY L 225 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 263 through 266 Processing sheet with id=AD6, first strand: chain 'L' and resid 319 through 325 removed outlier: 5.589A pdb=" N ILE L 321 " --> pdb=" O LEU L 337 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU L 337 " --> pdb=" O ILE L 321 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET L 323 " --> pdb=" O THR L 335 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N VAL L 343 " --> pdb=" O ASN L 338 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER L 344 " --> pdb=" O GLU L 361 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLU L 361 " --> pdb=" O SER L 344 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU L 346 " --> pdb=" O LYS L 359 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 384 through 390 Processing sheet with id=AD8, first strand: chain 'L' and resid 425 through 432 removed outlier: 5.834A pdb=" N ILE L 428 " --> pdb=" O LEU L 441 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU L 441 " --> pdb=" O ILE L 428 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS L 437 " --> pdb=" O ASP L 432 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 478 through 481 removed outlier: 6.199A pdb=" N VAL L 502 " --> pdb=" O ASP L 513 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ASP L 513 " --> pdb=" O VAL L 502 " (cutoff:3.500A) removed outlier: 9.878A pdb=" N ASN L 504 " --> pdb=" O MET L 511 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N MET L 511 " --> pdb=" O ASN L 504 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 531 through 534 removed outlier: 3.613A pdb=" N LEU L 549 " --> pdb=" O VAL L 595 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL L 595 " --> pdb=" O LEU L 549 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N CYS L 598 " --> pdb=" O VAL L 565 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS L 673 " --> pdb=" O VAL L 644 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL L 646 " --> pdb=" O CYS L 673 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY L 648 " --> pdb=" O SER L 675 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N GLN L 755 " --> pdb=" O PHE L 722 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE L 724 " --> pdb=" O GLN L 755 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N TYR L 757 " --> pdb=" O ILE L 724 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N HIS L 726 " --> pdb=" O TYR L 757 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 537 through 539 Processing sheet with id=AE3, first strand: chain 'K' and resid 104 through 107 Processing sheet with id=AE4, first strand: chain 'K' and resid 129 through 132 Processing sheet with id=AE5, first strand: chain 'K' and resid 192 through 195 removed outlier: 3.791A pdb=" N VAL K 214 " --> pdb=" O ILE K 200 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N TYR K 202 " --> pdb=" O ARG K 212 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ARG K 212 " --> pdb=" O TYR K 202 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 222 through 224 Processing sheet with id=AE7, first strand: chain 'K' and resid 222 through 224 removed outlier: 4.710A pdb=" N LEU K 294 " --> pdb=" O MET K 308 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 263 through 266 Processing sheet with id=AE9, first strand: chain 'K' and resid 319 through 326 removed outlier: 5.655A pdb=" N ILE K 321 " --> pdb=" O LEU K 337 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU K 337 " --> pdb=" O ILE K 321 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N MET K 323 " --> pdb=" O THR K 335 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR K 335 " --> pdb=" O MET K 323 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N VAL K 343 " --> pdb=" O ASN K 338 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N SER K 344 " --> pdb=" O GLU K 361 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLU K 361 " --> pdb=" O SER K 344 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU K 346 " --> pdb=" O LYS K 359 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 384 through 390 Processing sheet with id=AF2, first strand: chain 'K' and resid 427 through 432 removed outlier: 6.571A pdb=" N TYR K 439 " --> pdb=" O LEU K 429 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N TYR K 431 " --> pdb=" O LYS K 437 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LYS K 437 " --> pdb=" O TYR K 431 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLU K 444 " --> pdb=" O ARG K 449 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ARG K 449 " --> pdb=" O GLU K 444 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 478 through 481 removed outlier: 6.544A pdb=" N VAL K 502 " --> pdb=" O ASP K 513 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASP K 513 " --> pdb=" O VAL K 502 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 531 through 533 removed outlier: 3.993A pdb=" N VAL K 595 " --> pdb=" O LEU K 549 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N CYS K 598 " --> pdb=" O VAL K 565 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N TYR K 560 " --> pdb=" O ASP K 640 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N THR K 642 " --> pdb=" O TYR K 560 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N LEU K 562 " --> pdb=" O THR K 642 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL K 644 " --> pdb=" O LEU K 562 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LEU K 564 " --> pdb=" O VAL K 644 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL K 646 " --> pdb=" O LEU K 564 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL K 566 " --> pdb=" O VAL K 646 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLY K 648 " --> pdb=" O VAL K 566 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL K 646 " --> pdb=" O CYS K 673 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY K 648 " --> pdb=" O SER K 675 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 537 through 539 Processing sheet with id=AF6, first strand: chain 'D' and resid 51 through 55 removed outlier: 9.215A pdb=" N TYR D 83 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL D 44 " --> pdb=" O TYR D 83 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N PHE D 85 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASN D 46 " --> pdb=" O PHE D 85 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 68 through 70 Processing sheet with id=AF8, first strand: chain 'C' and resid 42 through 43 Processing sheet with id=AF9, first strand: chain 'C' and resid 50 through 51 2015 hydrogen bonds defined for protein. 5709 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: 10.67 Time building geometry restraints manager: 4.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14443 1.34 - 1.46: 10030 1.46 - 1.58: 21175 1.58 - 1.70: 0 1.70 - 1.82: 344 Bond restraints: 45992 Sorted by residual: bond pdb=" C LEU D 400 " pdb=" N PRO D 401 " ideal model delta sigma weight residual 1.336 1.355 -0.019 9.80e-03 1.04e+04 3.77e+00 bond pdb=" C LEU B 400 " pdb=" N PRO B 401 " ideal model delta sigma weight residual 1.336 1.354 -0.018 9.80e-03 1.04e+04 3.42e+00 bond pdb=" C ILE J 162 " pdb=" N PRO J 163 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.87e+00 bond pdb=" C ILE L 162 " pdb=" N PRO L 163 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.76e+00 bond pdb=" CG GLU L 307 " pdb=" CD GLU L 307 " ideal model delta sigma weight residual 1.516 1.483 0.033 2.50e-02 1.60e+03 1.72e+00 ... (remaining 45987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 60893 1.72 - 3.44: 1134 3.44 - 5.15: 194 5.15 - 6.87: 65 6.87 - 8.59: 26 Bond angle restraints: 62312 Sorted by residual: angle pdb=" N VAL D 227 " pdb=" CA VAL D 227 " pdb=" C VAL D 227 " ideal model delta sigma weight residual 112.80 107.38 5.42 1.15e+00 7.56e-01 2.22e+01 angle pdb=" N VAL B 227 " pdb=" CA VAL B 227 " pdb=" C VAL B 227 " ideal model delta sigma weight residual 112.80 107.38 5.42 1.15e+00 7.56e-01 2.22e+01 angle pdb=" N GLU C 117 " pdb=" CA GLU C 117 " pdb=" CB GLU C 117 " ideal model delta sigma weight residual 110.28 116.45 -6.17 1.55e+00 4.16e-01 1.58e+01 angle pdb=" N GLU A 117 " pdb=" CA GLU A 117 " pdb=" CB GLU A 117 " ideal model delta sigma weight residual 110.28 116.43 -6.15 1.55e+00 4.16e-01 1.57e+01 angle pdb=" N THR K 249 " pdb=" CA THR K 249 " pdb=" C THR K 249 " ideal model delta sigma weight residual 114.56 109.88 4.68 1.27e+00 6.20e-01 1.36e+01 ... (remaining 62307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 24627 17.86 - 35.72: 2314 35.72 - 53.58: 398 53.58 - 71.44: 53 71.44 - 89.30: 46 Dihedral angle restraints: 27438 sinusoidal: 11064 harmonic: 16374 Sorted by residual: dihedral pdb=" CB CYS J 673 " pdb=" SG CYS J 673 " pdb=" SG CYS J 784 " pdb=" CB CYS J 784 " ideal model delta sinusoidal sigma weight residual 93.00 3.70 89.30 1 1.00e+01 1.00e-02 9.48e+01 dihedral pdb=" CB CYS L 673 " pdb=" SG CYS L 673 " pdb=" SG CYS L 784 " pdb=" CB CYS L 784 " ideal model delta sinusoidal sigma weight residual 93.00 3.73 89.27 1 1.00e+01 1.00e-02 9.48e+01 dihedral pdb=" CB CYS I 474 " pdb=" SG CYS I 474 " pdb=" SG CYS I 492 " pdb=" CB CYS I 492 " ideal model delta sinusoidal sigma weight residual 93.00 10.91 82.09 1 1.00e+01 1.00e-02 8.28e+01 ... (remaining 27435 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 5233 0.048 - 0.096: 1260 0.096 - 0.143: 324 0.143 - 0.191: 7 0.191 - 0.239: 6 Chirality restraints: 6830 Sorted by residual: chirality pdb=" CB ILE I 548 " pdb=" CA ILE I 548 " pdb=" CG1 ILE I 548 " pdb=" CG2 ILE I 548 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB ILE K 548 " pdb=" CA ILE K 548 " pdb=" CG1 ILE K 548 " pdb=" CG2 ILE K 548 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB ILE I 438 " pdb=" CA ILE I 438 " pdb=" CG1 ILE I 438 " pdb=" CG2 ILE I 438 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 6827 not shown) Planarity restraints: 7980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 329 " 0.014 2.00e-02 2.50e+03 1.72e-02 5.16e+00 pdb=" CG PHE A 329 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE A 329 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE A 329 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 329 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 329 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 329 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 329 " 0.014 2.00e-02 2.50e+03 1.70e-02 5.08e+00 pdb=" CG PHE C 329 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE C 329 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE C 329 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE C 329 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 329 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C 329 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 400 " 0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO D 401 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO D 401 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 401 " 0.028 5.00e-02 4.00e+02 ... (remaining 7977 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 925 2.65 - 3.21: 45865 3.21 - 3.78: 76174 3.78 - 4.34: 101611 4.34 - 4.90: 157717 Nonbonded interactions: 382292 Sorted by model distance: nonbonded pdb=" OH TYR K 654 " pdb=" O THR K 708 " model vdw 2.089 3.040 nonbonded pdb=" OH TYR I 654 " pdb=" O THR I 708 " model vdw 2.090 3.040 nonbonded pdb=" O HIS E 92 " pdb=" ND2 ASN E 96 " model vdw 2.097 3.120 nonbonded pdb=" O MET B 238 " pdb=" OG1 THR B 241 " model vdw 2.115 3.040 nonbonded pdb=" O MET D 238 " pdb=" OG1 THR D 241 " model vdw 2.115 3.040 ... (remaining 382287 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: 0.05 Found NCS groups: ncs_group { reference = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'A' selection = chain 'C' } Set up NCS constraints Number of NCS constrained groups: 6 pdb_interpretation.ncs_group { reference = chain 'J' selection = chain 'L' } pdb_interpretation.ncs_group { reference = chain 'I' selection = chain 'K' } pdb_interpretation.ncs_group { reference = chain 'F' selection = chain 'H' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' } pdb_interpretation.ncs_group { reference = chain 'E' selection = chain 'G' } pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.690 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 37.260 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6184 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 0.033 46008 Z= 0.120 Angle : 0.618 8.590 62344 Z= 0.324 Chirality : 0.044 0.239 6830 Planarity : 0.004 0.049 7980 Dihedral : 14.211 86.941 16838 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.89 % Favored : 93.04 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % 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: -0.78 (0.11), residues: 5516 helix: 0.57 (0.11), residues: 2150 sheet: -0.39 (0.19), residues: 756 loop : -1.50 (0.13), residues: 2610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 141 TYR 0.023 0.001 TYR K 153 PHE 0.040 0.001 PHE A 329 TRP 0.017 0.001 TRP G 129 HIS 0.004 0.001 HIS H 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (45992) covalent geometry : angle 0.61764 / 0.32 (62312) SS BOND : bond 0.00199 / 0.11 ( 16) SS BOND : angle 0.70051 / 0.40 ( 32) hydrogen bonds : bond 0.14816 / 9.95 ( 2011) hydrogen bonds : angle 6.54001 / 4.55 ( 5709) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11032 Ramachandran restraints generated. 5516 Oldfield, 0 Emsley, 5516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11032 Ramachandran restraints generated. 5516 Oldfield, 0 Emsley, 5516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 634 LEU cc_start: 0.7675 (tp) cc_final: 0.7425 (mt) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.0757 time to fit residues: 4.9516 Evaluate side-chains 30 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.241 Evaluate side-chains 41 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.172 Fit side-chains revert: symmetry clash REVERT: I 460 ASN cc_start: 0.5838 (p0) cc_final: 0.5504 (p0) REVERT: I 511 MET cc_start: 0.5550 (mpp) cc_final: 0.3732 (mtp) REVERT: I 763 TYR cc_start: 0.7362 (m-10) cc_final: 0.7102 (m-10) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0580 time to fit residues: 3.6372 Evaluate side-chains 26 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.233 Evaluate side-chains 22 residues out of total 161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.065 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0340 time to fit residues: 0.9555 Evaluate side-chains 12 residues out of total 161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.040 Evaluate side-chains 36 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.085 Fit side-chains REVERT: B 329 PHE cc_start: 0.7233 (t80) cc_final: 0.7028 (t80) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0330 time to fit residues: 1.8246 Evaluate side-chains 27 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.136 Evaluate side-chains 23 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.057 Fit side-chains REVERT: E 76 GLN cc_start: 0.7265 (tp40) cc_final: 0.6836 (pp30) REVERT: E 129 TRP cc_start: 0.6142 (m-90) cc_final: 0.5789 (m-10) REVERT: E 182 MET cc_start: 0.5182 (tpp) cc_final: 0.3883 (mmm) REVERT: E 206 MET cc_start: 0.5106 (mmp) cc_final: 0.4903 (mmm) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0474 time to fit residues: 1.2844 Evaluate side-chains 15 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.058 Evaluate side-chains 30 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.137 Fit side-chains REVERT: A 20 MET cc_start: 0.6009 (mpp) cc_final: 0.5691 (mtt) REVERT: A 368 MET cc_start: 0.7507 (mpp) cc_final: 0.6500 (mpp) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0398 time to fit residues: 1.8148 Evaluate side-chains 24 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 394 optimal weight: 40.0000 chunk 430 optimal weight: 10.0000 chunk 41 optimal weight: 20.0000 chunk 265 optimal weight: 7.9990 chunk 523 optimal weight: 8.9990 chunk 497 optimal weight: 0.0040 chunk 414 optimal weight: 20.0000 chunk 310 optimal weight: 0.0770 chunk 488 optimal weight: 50.0000 chunk 366 optimal weight: 10.0000 chunk 223 optimal weight: 10.0000 overall best weight: 5.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 191 GLN ** I 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 392 GLN ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.046392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.037437 restraints weight = 75723.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.037792 restraints weight = 64597.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.038232 restraints weight = 51062.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.038295 restraints weight = 44883.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.038455 restraints weight = 39810.108| |-----------------------------------------------------------------------------| r_work (final): 0.3393 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.043465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.033378 restraints weight = 69085.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.034345 restraints weight = 44917.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.034982 restraints weight = 33278.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.035378 restraints weight = 27430.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.035634 restraints weight = 24267.956| |-----------------------------------------------------------------------------| r_work (final): 0.3231 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.071135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.065139 restraints weight = 13289.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.065687 restraints weight = 10756.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.066080 restraints weight = 9204.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.066442 restraints weight = 8172.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.066659 restraints weight = 7343.952| |-----------------------------------------------------------------------------| r_work (final): 0.3975 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.075302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.054769 restraints weight = 31664.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.055991 restraints weight = 18115.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.056629 restraints weight = 12675.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.057078 restraints weight = 10391.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.057428 restraints weight = 9261.375| |-----------------------------------------------------------------------------| r_work (final): 0.3343 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.070021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.064012 restraints weight = 14045.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.064287 restraints weight = 12510.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.064562 restraints weight = 11227.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.064769 restraints weight = 10329.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.064816 restraints weight = 9704.583| |-----------------------------------------------------------------------------| r_work (final): 0.3952 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.073602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.052731 restraints weight = 29038.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.053854 restraints weight = 17270.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.054562 restraints weight = 12283.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.055083 restraints weight = 9853.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.055291 restraints weight = 8625.644| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6424 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 46008 Z= 0.164 Angle : 0.616 12.261 62344 Z= 0.327 Chirality : 0.044 0.255 6830 Planarity : 0.004 0.045 7980 Dihedral : 4.565 25.321 6130 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.36 % Favored : 92.60 % Rotamer: Outliers : 0.33 % Allowed : 6.42 % Favored : 93.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % 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: -0.84 (0.11), residues: 5516 helix: 0.56 (0.11), residues: 2194 sheet: -0.50 (0.19), residues: 772 loop : -1.58 (0.13), residues: 2550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 207 TYR 0.033 0.002 TYR G 93 PHE 0.025 0.002 PHE B 194 TRP 0.010 0.001 TRP J 229 HIS 0.004 0.001 HIS F 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (45992) covalent geometry : angle 0.61619 / 0.33 (62312) SS BOND : bond 0.00220 / 0.10 ( 16) SS BOND : angle 0.76561 / 0.49 ( 32) hydrogen bonds : bond 0.04484 / 3.01 ( 2011) hydrogen bonds : angle 5.63574 / 3.91 ( 5709) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11032 Ramachandran restraints generated. 5516 Oldfield, 0 Emsley, 5516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11032 Ramachandran restraints generated. 5516 Oldfield, 0 Emsley, 5516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 38 average time/residue: 0.0631 time to fit residues: 3.6039 Evaluate side-chains 28 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.176 Evaluate side-chains 33 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: I 499 MET cc_start: 0.8795 (mmp) cc_final: 0.8075 (mmm) REVERT: I 763 TYR cc_start: 0.7685 (m-10) cc_final: 0.7366 (m-10) outliers start: 1 outliers final: 0 residues processed: 32 average time/residue: 0.0687 time to fit residues: 3.2389 Evaluate side-chains 25 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.201 Evaluate side-chains 21 residues out of total 161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.038 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 21 average time/residue: 0.0446 time to fit residues: 1.0919 Evaluate side-chains 13 residues out of total 161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.059 Evaluate side-chains 32 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.139 Fit side-chains REVERT: B 92 PHE cc_start: 0.9200 (t80) cc_final: 0.8670 (t80) REVERT: B 155 ASP cc_start: 0.7602 (m-30) cc_final: 0.6888 (t0) REVERT: B 194 PHE cc_start: 0.8920 (m-80) cc_final: 0.8658 (m-10) REVERT: B 329 PHE cc_start: 0.8656 (t80) cc_final: 0.8157 (t80) outliers start: 1 outliers final: 0 residues processed: 32 average time/residue: 0.0408 time to fit residues: 1.9614 Evaluate side-chains 24 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.099 Evaluate side-chains 22 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.071 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 21 average time/residue: 0.0613 time to fit residues: 1.5312 Evaluate side-chains 11 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.062 Evaluate side-chains 31 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.153 Fit side-chains REVERT: A 27 MET cc_start: 0.1509 (tpt) cc_final: 0.0951 (ttt) REVERT: A 117 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8177 (pp20) REVERT: A 368 MET cc_start: 0.8082 (mpp) cc_final: 0.6861 (mpp) outliers start: 3 outliers final: 0 residues processed: 29 average time/residue: 0.0351 time to fit residues: 1.5899 Evaluate side-chains 24 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 341 optimal weight: 0.6980 chunk 114 optimal weight: 0.0060 chunk 348 optimal weight: 3.9990 chunk 276 optimal weight: 40.0000 chunk 376 optimal weight: 8.9990 chunk 6 optimal weight: 0.0970 chunk 307 optimal weight: 0.0470 chunk 495 optimal weight: 40.0000 chunk 409 optimal weight: 0.4980 chunk 256 optimal weight: 9.9990 chunk 447 optimal weight: 30.0000 overall best weight: 0.2692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 65 GLN ** J 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 191 GLN ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 GLN A 490 ASN ** G 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.047754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.036648 restraints weight = 81851.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.038054 restraints weight = 47375.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.038936 restraints weight = 33635.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.039484 restraints weight = 27070.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.039751 restraints weight = 23699.275| |-----------------------------------------------------------------------------| r_work (final): 0.3375 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.044315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.034157 restraints weight = 69787.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.035201 restraints weight = 44190.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.035871 restraints weight = 32553.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.036291 restraints weight = 26726.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.036560 restraints weight = 23487.534| |-----------------------------------------------------------------------------| r_work (final): 0.3265 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.069791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.062859 restraints weight = 16381.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.063780 restraints weight = 12098.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.064378 restraints weight = 9601.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.064829 restraints weight = 8068.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.065165 restraints weight = 7073.551| |-----------------------------------------------------------------------------| r_work (final): 0.3995 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.077912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.057147 restraints weight = 32819.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.058465 restraints weight = 18520.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.059186 restraints weight = 12984.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.059506 restraints weight = 10571.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.059883 restraints weight = 9607.321| |-----------------------------------------------------------------------------| r_work (final): 0.3390 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.069124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.065058 restraints weight = 17346.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.065983 restraints weight = 11610.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.066637 restraints weight = 8321.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.067131 restraints weight = 6220.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.067419 restraints weight = 4792.184| |-----------------------------------------------------------------------------| r_work (final): 0.4001 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.074685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.054160 restraints weight = 28618.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.055370 restraints weight = 16970.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.056173 restraints weight = 11928.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.056722 restraints weight = 9446.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.057099 restraints weight = 8109.664| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6225 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 46008 Z= 0.123 Angle : 0.600 9.403 62344 Z= 0.308 Chirality : 0.044 0.203 6830 Planarity : 0.004 0.066 7980 Dihedral : 4.494 25.713 6130 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.49 % Favored : 93.47 % Rotamer: Outliers : 0.12 % Allowed : 2.62 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % 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: -0.81 (0.11), residues: 5516 helix: 0.59 (0.11), residues: 2198 sheet: -0.42 (0.19), residues: 750 loop : -1.58 (0.12), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 207 TYR 0.013 0.001 TYR I 182 PHE 0.027 0.001 PHE F 212 TRP 0.011 0.001 TRP C 19 HIS 0.004 0.001 HIS C 491 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (45992) covalent geometry : angle 0.59945 / 0.31 (62312) SS BOND : bond 0.00315 / 0.18 ( 16) SS BOND : angle 1.04897 / 0.76 ( 32) hydrogen bonds : bond 0.03908 / 2.65 ( 2011) hydrogen bonds : angle 5.29363 / 3.67 ( 5709) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11032 Ramachandran restraints generated. 5516 Oldfield, 0 Emsley, 5516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11032 Ramachandran restraints generated. 5516 Oldfield, 0 Emsley, 5516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 641 ARG cc_start: 0.6230 (ttp80) cc_final: 0.5863 (ptt-90) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0814 time to fit residues: 4.4486 Evaluate side-chains 31 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.153 Evaluate side-chains 36 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: K 87 LYS cc_start: 0.8880 (tptp) cc_final: 0.8583 (tppt) REVERT: K 264 MET cc_start: 0.5258 (mmt) cc_final: 0.5052 (mmt) REVERT: K 499 MET cc_start: 0.8701 (mmp) cc_final: 0.7997 (mmm) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0679 time to fit residues: 3.6141 Evaluate side-chains 26 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.247 Evaluate side-chains 20 residues out of total 161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.058 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0629 time to fit residues: 1.4592 Evaluate side-chains 12 residues out of total 161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.059 Evaluate side-chains 39 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.142 Fit side-chains REVERT: D 92 PHE cc_start: 0.9153 (t80) cc_final: 0.8598 (t80) REVERT: D 155 ASP cc_start: 0.7704 (m-30) cc_final: 0.7026 (t0) REVERT: D 329 PHE cc_start: 0.8558 (t80) cc_final: 0.7970 (t80) outliers start: 1 outliers final: 0 residues processed: 39 average time/residue: 0.0388 time to fit residues: 2.1470 Evaluate side-chains 27 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.138 Evaluate side-chains 23 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.062 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0487 time to fit residues: 1.3365 Evaluate side-chains 14 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.036 Evaluate side-chains 37 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.099 Fit side-chains REVERT: A 27 MET cc_start: 0.0539 (tpt) cc_final: -0.0281 (mtm) REVERT: A 117 GLU cc_start: 0.8766 (pm20) cc_final: 0.8191 (pp20) REVERT: A 240 PHE cc_start: 0.8966 (m-10) cc_final: 0.8756 (m-80) REVERT: A 342 MET cc_start: 0.9096 (mmt) cc_final: 0.8812 (mmm) REVERT: A 445 MET cc_start: 0.4082 (tmm) cc_final: 0.3490 (mmm) REVERT: A 490 ASN cc_start: 0.5996 (OUTLIER) cc_final: 0.5715 (m-40) outliers start: 2 outliers final: 0 residues processed: 36 average time/residue: 0.0473 time to fit residues: 2.3518 Evaluate side-chains 28 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 169 optimal weight: 0.8980 chunk 504 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 116 optimal weight: 0.0030 chunk 348 optimal weight: 8.9990 chunk 205 optimal weight: 0.9980 chunk 264 optimal weight: 0.0040 chunk 366 optimal weight: 0.0870 chunk 324 optimal weight: 8.9990 chunk 270 optimal weight: 7.9990 chunk 491 optimal weight: 2.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 483 HIS L 65 GLN ** L 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 191 GLN D 33 GLN ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 GLN D 491 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.047806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.037846 restraints weight = 73643.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.038632 restraints weight = 45361.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.038839 restraints weight = 36211.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.038985 restraints weight = 34407.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.039114 restraints weight = 32413.960| |-----------------------------------------------------------------------------| r_work (final): 0.3407 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.045107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.034915 restraints weight = 68095.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.035962 restraints weight = 43372.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.036607 restraints weight = 32207.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.037040 restraints weight = 26532.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.037328 restraints weight = 23331.344| |-----------------------------------------------------------------------------| r_work (final): 0.3297 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.071085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.064956 restraints weight = 13164.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.065535 restraints weight = 10589.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.065976 restraints weight = 9110.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.066426 restraints weight = 8162.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.066637 restraints weight = 7356.512| |-----------------------------------------------------------------------------| r_work (final): 0.3940 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.077411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.056930 restraints weight = 30812.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.058249 restraints weight = 17805.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.059075 restraints weight = 12467.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.059580 restraints weight = 9967.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.059687 restraints weight = 8756.279| |-----------------------------------------------------------------------------| r_work (final): 0.3399 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.067880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.064067 restraints weight = 231256.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.064762 restraints weight = 187860.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.064779 restraints weight = 158902.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.064910 restraints weight = 146707.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.064952 restraints weight = 134601.334| |-----------------------------------------------------------------------------| r_work (final): 0.4049 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.074815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.055031 restraints weight = 27061.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.056138 restraints weight = 16673.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.056904 restraints weight = 11968.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.057326 restraints weight = 9637.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.057684 restraints weight = 8424.452| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6299 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 46008 Z= 0.117 Angle : 0.579 9.376 62344 Z= 0.299 Chirality : 0.044 0.289 6830 Planarity : 0.004 0.062 7980 Dihedral : 4.407 27.495 6130 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.85 % Favored : 93.11 % Rotamer: Outliers : 0.08 % Allowed : 4.05 % Favored : 95.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % 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: -0.77 (0.11), residues: 5516 helix: 0.60 (0.11), residues: 2192 sheet: -0.31 (0.19), residues: 764 loop : -1.57 (0.13), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 207 TYR 0.045 0.001 TYR G 93 PHE 0.018 0.001 PHE C 338 TRP 0.024 0.001 TRP C 8 HIS 0.009 0.001 HIS C 491 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 (45992) covalent geometry : angle 0.57842 / 0.30 (62312) SS BOND : bond 0.00285 / 0.15 ( 16) SS BOND : angle 0.86221 / 0.62 ( 32) hydrogen bonds : bond 0.03678 / 2.46 ( 2011) hydrogen bonds : angle 5.08777 / 3.52 ( 5709) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11032 Ramachandran restraints generated. 5516 Oldfield, 0 Emsley, 5516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11032 Ramachandran restraints generated. 5516 Oldfield, 0 Emsley, 5516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0695 time to fit residues: 3.8440 Evaluate side-chains 32 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.242 Evaluate side-chains 36 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: I 223 TYR cc_start: 0.7769 (m-80) cc_final: 0.7419 (m-10) REVERT: I 499 MET cc_start: 0.8825 (mmp) cc_final: 0.8191 (mmm) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0659 time to fit residues: 3.5809 Evaluate side-chains 26 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.242 Evaluate side-chains 21 residues out of total 161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.059 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0810 time to fit residues: 1.9158 Evaluate side-chains 12 residues out of total 161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.059 Evaluate side-chains 38 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.141 Fit side-chains REVERT: D 27 MET cc_start: -0.3714 (ppp) cc_final: -0.5085 (tpt) REVERT: D 33 GLN cc_start: 0.2142 (OUTLIER) cc_final: 0.1697 (pp30) REVERT: D 92 PHE cc_start: 0.9153 (t80) cc_final: 0.8603 (t80) REVERT: D 155 ASP cc_start: 0.7750 (m-30) cc_final: 0.7073 (t0) REVERT: D 329 PHE cc_start: 0.8610 (t80) cc_final: 0.8069 (t80) outliers start: 1 outliers final: 0 residues processed: 38 average time/residue: 0.0478 time to fit residues: 2.5830 Evaluate side-chains 29 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.146 Evaluate side-chains 24 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.062 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0349 time to fit residues: 1.0728 Evaluate side-chains 11 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.061 Evaluate side-chains 38 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.143 Fit side-chains revert: symmetry clash REVERT: C 27 MET cc_start: 0.0608 (tpt) cc_final: -0.0033 (ptp) REVERT: C 245 LEU cc_start: 0.9363 (mm) cc_final: 0.9089 (pp) REVERT: C 368 MET cc_start: 0.8777 (mmt) cc_final: 0.8411 (mmt) outliers start: 1 outliers final: 0 residues processed: 37 average time/residue: 0.0527 time to fit residues: 2.7077 Evaluate side-chains 27 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 462 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 9 optimal weight: 20.0000 chunk 354 optimal weight: 0.3980 chunk 440 optimal weight: 20.0000 chunk 290 optimal weight: 0.5980 chunk 344 optimal weight: 10.0000 chunk 253 optimal weight: 1.9990 chunk 121 optimal weight: 10.0000 chunk 500 optimal weight: 0.5980 chunk 386 optimal weight: 0.2980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 190 GLN I 191 GLN ** E 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 HIS ** L 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 181 GLN ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.047984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.037896 restraints weight = 72179.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.038633 restraints weight = 45355.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.038977 restraints weight = 36032.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.039059 restraints weight = 35500.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.039041 restraints weight = 31619.138| |-----------------------------------------------------------------------------| r_work (final): 0.3398 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.045190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.035046 restraints weight = 67851.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.036105 restraints weight = 43205.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.036744 restraints weight = 32057.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.037200 restraints weight = 26464.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.037472 restraints weight = 23258.068| |-----------------------------------------------------------------------------| r_work (final): 0.3304 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.071437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.065008 restraints weight = 13136.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 16)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.065395 restraints weight = 10863.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.065913 restraints weight = 9585.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.066155 restraints weight = 8514.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.066475 restraints weight = 7904.386| |-----------------------------------------------------------------------------| r_work (final): 0.4000 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.077535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.057086 restraints weight = 30418.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.058296 restraints weight = 17439.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.059176 restraints weight = 12281.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.059614 restraints weight = 9753.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.059927 restraints weight = 8578.008| |-----------------------------------------------------------------------------| r_work (final): 0.3407 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.068176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.065146 restraints weight = 233083.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.065295 restraints weight = 195532.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.065299 restraints weight = 172698.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.065377 restraints weight = 161931.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.065404 restraints weight = 158274.403| |-----------------------------------------------------------------------------| r_work (final): 0.4045 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.075795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.055909 restraints weight = 27828.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.057030 restraints weight = 17081.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.057826 restraints weight = 12215.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.058327 restraints weight = 9810.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.058597 restraints weight = 8530.591| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6282 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 46008 Z= 0.116 Angle : 0.577 8.269 62344 Z= 0.298 Chirality : 0.044 0.202 6830 Planarity : 0.004 0.077 7980 Dihedral : 4.345 25.399 6130 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.45 % Favored : 93.51 % Rotamer: Outliers : 0.04 % Allowed : 2.21 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % 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: -0.72 (0.11), residues: 5516 helix: 0.62 (0.11), residues: 2216 sheet: -0.20 (0.19), residues: 764 loop : -1.57 (0.13), residues: 2536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 527 TYR 0.018 0.001 TYR E 163 PHE 0.013 0.001 PHE K 764 TRP 0.013 0.001 TRP A 19 HIS 0.005 0.001 HIS D 491 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (45992) covalent geometry : angle 0.57715 / 0.30 (62312) SS BOND : bond 0.00447 / 0.26 ( 16) SS BOND : angle 1.01211 / 0.62 ( 32) hydrogen bonds : bond 0.03550 / 2.39 ( 2011) hydrogen bonds : angle 5.00474 / 3.46 ( 5709) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11032 Ramachandran restraints generated. 5516 Oldfield, 0 Emsley, 5516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11032 Ramachandran restraints generated. 5516 Oldfield, 0 Emsley, 5516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 266 LEU cc_start: 0.8654 (mt) cc_final: 0.8067 (pp) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0619 time to fit residues: 3.4303 Evaluate side-chains 30 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.305 Evaluate side-chains 39 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: I 223 TYR cc_start: 0.7817 (m-80) cc_final: 0.7450 (m-10) REVERT: I 264 MET cc_start: 0.5311 (mmt) cc_final: 0.4830 (mmt) REVERT: I 499 MET cc_start: 0.8745 (mmp) cc_final: 0.8121 (mmm) REVERT: I 511 MET cc_start: 0.5580 (mtm) cc_final: 0.5353 (mtt) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0642 time to fit residues: 3.7277 Evaluate side-chains 25 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.242 Evaluate side-chains 21 residues out of total 161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.059 Fit side-chains REVERT: H 182 MET cc_start: -0.4329 (mmm) cc_final: -0.4609 (mmt) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0638 time to fit residues: 1.5513 Evaluate side-chains 11 residues out of total 161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.042 Evaluate side-chains 40 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.096 Fit side-chains REVERT: D 27 MET cc_start: -0.4042 (ppp) cc_final: -0.5523 (tpt) REVERT: D 92 PHE cc_start: 0.9171 (t80) cc_final: 0.8629 (t80) REVERT: D 155 ASP cc_start: 0.7844 (m-30) cc_final: 0.7186 (t0) REVERT: D 329 PHE cc_start: 0.8617 (t80) cc_final: 0.8092 (t80) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0477 time to fit residues: 2.6286 Evaluate side-chains 28 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.142 Evaluate side-chains 22 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.048 Fit side-chains REVERT: E 157 MET cc_start: 0.3010 (tpt) cc_final: 0.2558 (tpt) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0330 time to fit residues: 0.9239 Evaluate side-chains 13 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.057 Evaluate side-chains 36 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.0678 (tpt) cc_final: 0.0367 (ptm) REVERT: A 245 LEU cc_start: 0.9367 (mm) cc_final: 0.9120 (pp) REVERT: A 368 MET cc_start: 0.8817 (mmt) cc_final: 0.8467 (mmt) outliers start: 1 outliers final: 0 residues processed: 35 average time/residue: 0.0534 time to fit residues: 2.5244 Evaluate side-chains 28 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 348 optimal weight: 0.9980 chunk 359 optimal weight: 0.9980 chunk 373 optimal weight: 30.0000 chunk 275 optimal weight: 0.0010 chunk 541 optimal weight: 6.9990 chunk 265 optimal weight: 8.9990 chunk 403 optimal weight: 7.9990 chunk 201 optimal weight: 6.9990 chunk 444 optimal weight: 0.0670 chunk 402 optimal weight: 20.0000 chunk 394 optimal weight: 0.2980 overall best weight: 0.4724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 99 GLN ** J 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 181 GLN J 191 GLN I 191 GLN ** I 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 HIS ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.048216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.038549 restraints weight = 71869.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.038536 restraints weight = 47463.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.038798 restraints weight = 39814.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.038933 restraints weight = 36940.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.038981 restraints weight = 35321.811| |-----------------------------------------------------------------------------| r_work (final): 0.3389 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.044948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.034636 restraints weight = 66997.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.035742 restraints weight = 42154.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.036439 restraints weight = 31014.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.036851 restraints weight = 25373.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.037147 restraints weight = 22320.386| |-----------------------------------------------------------------------------| r_work (final): 0.3299 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.073355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.066371 restraints weight = 12947.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.066931 restraints weight = 10822.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.067391 restraints weight = 9468.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.067770 restraints weight = 8552.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.067921 restraints weight = 7855.913| |-----------------------------------------------------------------------------| r_work (final): 0.4017 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.077382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.057261 restraints weight = 30457.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.058520 restraints weight = 17645.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.059220 restraints weight = 12324.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.059796 restraints weight = 9969.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.060028 restraints weight = 8693.179| |-----------------------------------------------------------------------------| r_work (final): 0.3408 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.068576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.065624 restraints weight = 241993.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.065817 restraints weight = 193706.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.065770 restraints weight = 189982.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.065840 restraints weight = 174602.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.065846 restraints weight = 176513.069| |-----------------------------------------------------------------------------| r_work (final): 0.4075 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.076577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.056258 restraints weight = 27966.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.057428 restraints weight = 17028.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.058223 restraints weight = 12176.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.058679 restraints weight = 9764.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.059026 restraints weight = 8526.909| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6272 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 46008 Z= 0.110 Angle : 0.569 8.324 62344 Z= 0.292 Chirality : 0.044 0.243 6830 Planarity : 0.004 0.065 7980 Dihedral : 4.277 24.512 6130 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.85 % Favored : 93.11 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % 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: -0.67 (0.11), residues: 5516 helix: 0.69 (0.11), residues: 2194 sheet: -0.19 (0.19), residues: 754 loop : -1.55 (0.12), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 527 TYR 0.014 0.001 TYR F 163 PHE 0.016 0.001 PHE B 361 TRP 0.016 0.001 TRP H 129 HIS 0.003 0.001 HIS A 491 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (45992) covalent geometry : angle 0.56896 / 0.29 (62312) SS BOND : bond 0.00211 / 0.12 ( 16) SS BOND : angle 0.82838 / 0.54 ( 32) hydrogen bonds : bond 0.03428 / 2.30 ( 2011) hydrogen bonds : angle 4.91079 / 3.40 ( 5709) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11032 Ramachandran restraints generated. 5516 Oldfield, 0 Emsley, 5516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11032 Ramachandran restraints generated. 5516 Oldfield, 0 Emsley, 5516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 309 MET cc_start: 0.8502 (tpp) cc_final: 0.8294 (tpp) REVERT: J 529 MET cc_start: 0.7542 (ppp) cc_final: 0.7324 (ppp) REVERT: J 669 GLN cc_start: 0.8569 (mt0) cc_final: 0.8252 (mp10) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0679 time to fit residues: 3.6395 Evaluate side-chains 31 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.193 Evaluate side-chains 37 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: K 223 TYR cc_start: 0.7816 (m-80) cc_final: 0.7458 (m-10) REVERT: K 499 MET cc_start: 0.8765 (mmp) cc_final: 0.8137 (mmm) REVERT: K 511 MET cc_start: 0.5644 (mtm) cc_final: 0.5440 (mtt) REVERT: K 587 MET cc_start: 0.8840 (pmm) cc_final: 0.8637 (pmm) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0642 time to fit residues: 3.6144 Evaluate side-chains 27 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.245 Evaluate side-chains 21 residues out of total 161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.062 Fit side-chains REVERT: F 182 MET cc_start: -0.4379 (mmm) cc_final: -0.4616 (mmt) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0624 time to fit residues: 1.5188 Evaluate side-chains 12 residues out of total 161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.049 Evaluate side-chains 39 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.086 Fit side-chains REVERT: B 27 MET cc_start: -0.4171 (ppp) cc_final: -0.5575 (tpt) REVERT: B 92 PHE cc_start: 0.9096 (t80) cc_final: 0.8545 (t80) REVERT: B 155 ASP cc_start: 0.7822 (m-30) cc_final: 0.7152 (t0) REVERT: B 329 PHE cc_start: 0.8574 (t80) cc_final: 0.8019 (t80) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0455 time to fit residues: 2.5254 Evaluate side-chains 30 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.144 Evaluate side-chains 22 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.062 Fit side-chains REVERT: G 157 MET cc_start: 0.2830 (tpt) cc_final: 0.2491 (tpt) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0349 time to fit residues: 0.9944 Evaluate side-chains 13 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.060 Evaluate side-chains 35 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.1031 (tpt) cc_final: 0.0634 (ptm) REVERT: A 52 PHE cc_start: 0.7555 (m-10) cc_final: 0.7265 (m-80) REVERT: A 117 GLU cc_start: 0.8758 (pm20) cc_final: 0.8127 (pp20) REVERT: A 245 LEU cc_start: 0.9331 (mm) cc_final: 0.9113 (pp) REVERT: A 303 PHE cc_start: 0.8837 (m-80) cc_final: 0.8432 (m-80) REVERT: A 368 MET cc_start: 0.8769 (mmt) cc_final: 0.8393 (mmt) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0600 time to fit residues: 2.8104 Evaluate side-chains 32 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 403 optimal weight: 7.9990 chunk 425 optimal weight: 4.9990 chunk 42 optimal weight: 0.0060 chunk 259 optimal weight: 0.0570 chunk 526 optimal weight: 4.9990 chunk 178 optimal weight: 7.9990 chunk 524 optimal weight: 6.9990 chunk 222 optimal weight: 1.9990 chunk 199 optimal weight: 6.9990 chunk 265 optimal weight: 5.9990 chunk 546 optimal weight: 2.9990 overall best weight: 2.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 99 GLN ** J 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 181 GLN J 191 GLN ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 33 GLN ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 446 GLN K 191 GLN K 547 GLN ** G 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 HIS G 96 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.047779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.038205 restraints weight = 72727.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.038403 restraints weight = 46186.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.038659 restraints weight = 39743.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.038770 restraints weight = 38108.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.038827 restraints weight = 33464.949| |-----------------------------------------------------------------------------| r_work (final): 0.3387 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.045028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.034774 restraints weight = 68323.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.035816 restraints weight = 43103.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.036517 restraints weight = 32008.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.036960 restraints weight = 26154.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.037091 restraints weight = 22854.548| |-----------------------------------------------------------------------------| r_work (final): 0.3292 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.071764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.064871 restraints weight = 13224.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.065421 restraints weight = 10853.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.065834 restraints weight = 9400.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.066220 restraints weight = 8445.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.066471 restraints weight = 7680.905| |-----------------------------------------------------------------------------| r_work (final): 0.4009 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.076792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.056544 restraints weight = 30813.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.057851 restraints weight = 17873.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.058536 restraints weight = 12444.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.059129 restraints weight = 10083.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.059363 restraints weight = 8812.696| |-----------------------------------------------------------------------------| r_work (final): 0.3394 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.072430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.065275 restraints weight = 13861.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.065587 restraints weight = 11830.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.065728 restraints weight = 10579.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.066216 restraints weight = 9906.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.066335 restraints weight = 9310.849| |-----------------------------------------------------------------------------| r_work (final): 0.3972 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.076491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.055308 restraints weight = 28532.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.056516 restraints weight = 17449.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.057188 restraints weight = 12496.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.057737 restraints weight = 10155.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.057976 restraints weight = 8895.750| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6341 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 46008 Z= 0.116 Angle : 0.580 10.723 62344 Z= 0.299 Chirality : 0.044 0.230 6830 Planarity : 0.004 0.058 7980 Dihedral : 4.273 25.488 6130 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.67 % Favored : 93.29 % Rotamer: Outliers : 0.04 % Allowed : 1.55 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % 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: -0.63 (0.11), residues: 5516 helix: 0.73 (0.11), residues: 2196 sheet: -0.18 (0.19), residues: 758 loop : -1.53 (0.13), residues: 2562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 207 TYR 0.029 0.001 TYR F 93 PHE 0.015 0.001 PHE A 338 TRP 0.052 0.001 TRP D 19 HIS 0.009 0.001 HIS C 491 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (45992) covalent geometry : angle 0.58032 / 0.30 (62312) SS BOND : bond 0.00189 / 0.10 ( 16) SS BOND : angle 0.71527 / 0.45 ( 32) hydrogen bonds : bond 0.03443 / 2.31 ( 2011) hydrogen bonds : angle 4.93145 / 3.41 ( 5709) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11032 Ramachandran restraints generated. 5516 Oldfield, 0 Emsley, 5516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11032 Ramachandran restraints generated. 5516 Oldfield, 0 Emsley, 5516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 266 LEU cc_start: 0.8653 (mt) cc_final: 0.8094 (pp) REVERT: J 309 MET cc_start: 0.8525 (tpp) cc_final: 0.8316 (tpp) REVERT: J 669 GLN cc_start: 0.8596 (mt0) cc_final: 0.8271 (mp10) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0661 time to fit residues: 3.5960 Evaluate side-chains 32 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.241 Evaluate side-chains 36 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: I 499 MET cc_start: 0.8674 (mmp) cc_final: 0.8068 (mmm) REVERT: I 511 MET cc_start: 0.5670 (mtm) cc_final: 0.5458 (mtt) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0697 time to fit residues: 3.6844 Evaluate side-chains 27 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.237 Evaluate side-chains 21 residues out of total 161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.060 Fit side-chains REVERT: H 182 MET cc_start: -0.4395 (mmm) cc_final: -0.4597 (mmt) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0641 time to fit residues: 1.5600 Evaluate side-chains 13 residues out of total 161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.036 Evaluate side-chains 39 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.107 Fit side-chains REVERT: B 27 MET cc_start: -0.4210 (ppp) cc_final: -0.5696 (tpt) REVERT: B 92 PHE cc_start: 0.9097 (t80) cc_final: 0.8552 (t80) REVERT: B 155 ASP cc_start: 0.7786 (m-30) cc_final: 0.7103 (t0) REVERT: B 329 PHE cc_start: 0.8569 (t80) cc_final: 0.8058 (t80) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0355 time to fit residues: 2.0430 Evaluate side-chains 29 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.139 Evaluate side-chains 23 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.059 Fit side-chains REVERT: G 214 ASN cc_start: 0.5992 (p0) cc_final: 0.5744 (p0) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0280 time to fit residues: 0.8475 Evaluate side-chains 14 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.070 Evaluate side-chains 33 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 PHE cc_start: 0.7573 (m-10) cc_final: 0.7274 (m-80) REVERT: A 245 LEU cc_start: 0.9391 (mm) cc_final: 0.9131 (pp) REVERT: A 303 PHE cc_start: 0.8802 (m-80) cc_final: 0.8331 (m-80) REVERT: A 368 MET cc_start: 0.8803 (mmt) cc_final: 0.8404 (mmm) outliers start: 1 outliers final: 0 residues processed: 33 average time/residue: 0.0594 time to fit residues: 2.5885 Evaluate side-chains 29 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 428 optimal weight: 0.1980 chunk 455 optimal weight: 0.2980 chunk 316 optimal weight: 0.9980 chunk 491 optimal weight: 4.9990 chunk 90 optimal weight: 8.9990 chunk 527 optimal weight: 3.9990 chunk 221 optimal weight: 50.0000 chunk 460 optimal weight: 0.7980 chunk 297 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 chunk 231 optimal weight: 0.0170 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 99 GLN ** J 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 191 GLN I 191 GLN ** I 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 547 GLN ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 GLN B 480 HIS ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.048151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.037303 restraints weight = 72149.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.038386 restraints weight = 47578.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.039046 restraints weight = 36624.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.039427 restraints weight = 31209.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.039610 restraints weight = 28297.223| |-----------------------------------------------------------------------------| r_work (final): 0.3418 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.044995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.034619 restraints weight = 65589.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.035693 restraints weight = 41651.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.036372 restraints weight = 31076.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.036819 restraints weight = 25430.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.037083 restraints weight = 22364.021| |-----------------------------------------------------------------------------| r_work (final): 0.3304 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.073572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.065379 restraints weight = 14632.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.066425 restraints weight = 10897.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.067150 restraints weight = 8805.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.067733 restraints weight = 7570.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.068046 restraints weight = 6702.870| |-----------------------------------------------------------------------------| r_work (final): 0.4028 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.077301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.057036 restraints weight = 30047.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.058252 restraints weight = 17841.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.058949 restraints weight = 12631.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.059534 restraints weight = 10258.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.059774 restraints weight = 9006.652| |-----------------------------------------------------------------------------| r_work (final): 0.3413 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.073252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.065604 restraints weight = 13921.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.065905 restraints weight = 12258.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.066150 restraints weight = 11257.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.066150 restraints weight = 10519.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.066149 restraints weight = 10519.067| |-----------------------------------------------------------------------------| r_work (final): 0.3910 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.076658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.056644 restraints weight = 28169.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.057744 restraints weight = 17434.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.058524 restraints weight = 12625.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.058925 restraints weight = 10165.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.059288 restraints weight = 8961.969| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6423 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 46008 Z= 0.113 Angle : 0.596 12.950 62344 Z= 0.304 Chirality : 0.044 0.234 6830 Planarity : 0.004 0.058 7980 Dihedral : 4.249 24.706 6130 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.78 % Favored : 93.18 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % 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: -0.63 (0.11), residues: 5516 helix: 0.69 (0.11), residues: 2206 sheet: -0.11 (0.19), residues: 754 loop : -1.51 (0.13), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 207 TYR 0.023 0.001 TYR F 93 PHE 0.038 0.001 PHE J 79 TRP 0.041 0.001 TRP D 19 HIS 0.005 0.001 HIS G 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (45992) covalent geometry : angle 0.59634 / 0.30 (62312) SS BOND : bond 0.00175 / 0.10 ( 16) SS BOND : angle 0.71225 / 0.47 ( 32) hydrogen bonds : bond 0.03425 / 2.31 ( 2011) hydrogen bonds : angle 4.88231 / 3.39 ( 5709) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11032 Ramachandran restraints generated. 5516 Oldfield, 0 Emsley, 5516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11032 Ramachandran restraints generated. 5516 Oldfield, 0 Emsley, 5516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 669 GLN cc_start: 0.8482 (mt0) cc_final: 0.8190 (mp10) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0796 time to fit residues: 4.0982 Evaluate side-chains 32 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.248 Evaluate side-chains 37 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 87 LYS cc_start: 0.8859 (tptp) cc_final: 0.8628 (pttt) REVERT: K 499 MET cc_start: 0.8811 (mmp) cc_final: 0.8156 (mmm) REVERT: K 546 MET cc_start: 0.6304 (tmm) cc_final: 0.6094 (tmm) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0700 time to fit residues: 3.8890 Evaluate side-chains 29 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.266 Evaluate side-chains 20 residues out of total 161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.056 Fit side-chains REVERT: H 72 ASP cc_start: 0.7940 (m-30) cc_final: 0.7684 (m-30) REVERT: H 182 MET cc_start: -0.4216 (mmm) cc_final: -0.4494 (mmm) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0439 time to fit residues: 1.0738 Evaluate side-chains 12 residues out of total 161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.066 Evaluate side-chains 40 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.144 Fit side-chains REVERT: D 92 PHE cc_start: 0.9125 (t80) cc_final: 0.8579 (t80) REVERT: D 149 GLN cc_start: 0.7997 (tm-30) cc_final: 0.7621 (tp40) REVERT: D 155 ASP cc_start: 0.7972 (m-30) cc_final: 0.7248 (t0) REVERT: D 329 PHE cc_start: 0.8611 (t80) cc_final: 0.8079 (t80) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0413 time to fit residues: 2.4374 Evaluate side-chains 29 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.153 Evaluate side-chains 22 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.066 Fit side-chains REVERT: E 157 MET cc_start: 0.2391 (tpt) cc_final: 0.2104 (tpt) REVERT: E 177 VAL cc_start: 0.4873 (t) cc_final: 0.4534 (t) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0354 time to fit residues: 1.0093 Evaluate side-chains 12 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.058 Evaluate side-chains 32 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 PHE cc_start: 0.7604 (m-10) cc_final: 0.7313 (m-80) REVERT: A 245 LEU cc_start: 0.9387 (mm) cc_final: 0.9113 (pp) REVERT: A 303 PHE cc_start: 0.8840 (m-80) cc_final: 0.8310 (m-80) REVERT: A 368 MET cc_start: 0.8775 (mmt) cc_final: 0.8355 (mmm) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0638 time to fit residues: 2.7242 Evaluate side-chains 29 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 78 optimal weight: 0.0470 chunk 413 optimal weight: 10.0000 chunk 31 optimal weight: 0.0980 chunk 473 optimal weight: 5.9990 chunk 87 optimal weight: 0.0170 chunk 19 optimal weight: 0.4980 chunk 142 optimal weight: 0.0020 chunk 194 optimal weight: 5.9990 chunk 318 optimal weight: 0.0020 chunk 282 optimal weight: 3.9990 chunk 542 optimal weight: 9.9990 overall best weight: 0.0332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 151 HIS J 191 GLN ** E 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 GLN ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 191 GLN ** K 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 547 GLN K 606 GLN ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.048640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.037880 restraints weight = 71917.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.038949 restraints weight = 48083.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.039625 restraints weight = 36902.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.039952 restraints weight = 31232.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.040021 restraints weight = 28571.347| |-----------------------------------------------------------------------------| r_work (final): 0.3432 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.045051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.034836 restraints weight = 65449.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.035966 restraints weight = 41351.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.036696 restraints weight = 30380.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.037152 restraints weight = 24592.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.037438 restraints weight = 21487.859| |-----------------------------------------------------------------------------| r_work (final): 0.3313 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.074033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.066827 restraints weight = 13408.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.067308 restraints weight = 11172.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.067751 restraints weight = 9909.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.067751 restraints weight = 8867.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.067751 restraints weight = 8867.057| |-----------------------------------------------------------------------------| r_work (final): 0.4019 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.077834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.058056 restraints weight = 29552.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.059357 restraints weight = 17559.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.060129 restraints weight = 12409.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.060662 restraints weight = 9975.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.060886 restraints weight = 8730.251| |-----------------------------------------------------------------------------| r_work (final): 0.3439 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.073487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.066135 restraints weight = 14277.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.066468 restraints weight = 12519.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.066468 restraints weight = 11249.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.066468 restraints weight = 11249.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.066468 restraints weight = 11249.401| |-----------------------------------------------------------------------------| r_work (final): 0.3960 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.077206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.057086 restraints weight = 28550.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.058240 restraints weight = 17708.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.058896 restraints weight = 12762.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.059461 restraints weight = 10363.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.059592 restraints weight = 9046.227| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6307 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 46008 Z= 0.113 Angle : 0.596 9.088 62344 Z= 0.305 Chirality : 0.044 0.180 6830 Planarity : 0.004 0.058 7980 Dihedral : 4.202 24.169 6130 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.38 % Favored : 93.58 % Rotamer: Outliers : 0.04 % Allowed : 0.65 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.11), residues: 5516 helix: 0.69 (0.11), residues: 2208 sheet: 0.00 (0.19), residues: 762 loop : -1.55 (0.13), residues: 2546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 527 TYR 0.021 0.001 TYR H 93 PHE 0.036 0.001 PHE B 194 TRP 0.049 0.001 TRP D 19 HIS 0.010 0.001 HIS C 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (45992) covalent geometry : angle 0.59588 / 0.30 (62312) SS BOND : bond 0.00167 / 0.10 ( 16) SS BOND : angle 0.69680 / 0.46 ( 32) hydrogen bonds : bond 0.03402 / 2.30 ( 2011) hydrogen bonds : angle 4.83912 / 3.36 ( 5709) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11032 Ramachandran restraints generated. 5516 Oldfield, 0 Emsley, 5516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11032 Ramachandran restraints generated. 5516 Oldfield, 0 Emsley, 5516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 309 MET cc_start: 0.8432 (tpp) cc_final: 0.8197 (tpp) REVERT: L 669 GLN cc_start: 0.8439 (mt0) cc_final: 0.8172 (mp10) REVERT: L 712 HIS cc_start: 0.6625 (p-80) cc_final: 0.6286 (p-80) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0765 time to fit residues: 4.0065 Evaluate side-chains 33 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.242 Evaluate side-chains 40 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: K 223 TYR cc_start: 0.7823 (m-80) cc_final: 0.7510 (m-10) REVERT: K 309 MET cc_start: 0.8844 (mmp) cc_final: 0.7713 (ptt) REVERT: K 391 PRO cc_start: 0.7541 (Cg_exo) cc_final: 0.7320 (Cg_endo) REVERT: K 499 MET cc_start: 0.8724 (mmp) cc_final: 0.8116 (mmm) REVERT: K 546 MET cc_start: 0.6253 (tmm) cc_final: 0.6038 (tmm) outliers start: 1 outliers final: 0 residues processed: 40 average time/residue: 0.0651 time to fit residues: 3.9265 Evaluate side-chains 25 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.149 Evaluate side-chains 22 residues out of total 161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.037 Fit side-chains REVERT: H 182 MET cc_start: -0.4251 (mmm) cc_final: -0.4525 (mmm) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0435 time to fit residues: 1.1154 Evaluate side-chains 13 residues out of total 161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.061 Evaluate side-chains 39 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.103 Fit side-chains REVERT: D 92 PHE cc_start: 0.9073 (t80) cc_final: 0.8516 (t80) REVERT: D 155 ASP cc_start: 0.7959 (m-30) cc_final: 0.7315 (t0) REVERT: D 194 PHE cc_start: 0.8941 (m-80) cc_final: 0.8716 (m-10) REVERT: D 329 PHE cc_start: 0.8624 (t80) cc_final: 0.8189 (t80) REVERT: D 333 MET cc_start: 0.8581 (mtp) cc_final: 0.7699 (mtp) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0482 time to fit residues: 2.5592 Evaluate side-chains 28 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.145 Evaluate side-chains 21 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.061 Fit side-chains revert: symmetry clash REVERT: G 157 MET cc_start: 0.2345 (tpt) cc_final: 0.2122 (tpt) REVERT: G 214 ASN cc_start: 0.6011 (p0) cc_final: 0.5791 (p0) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0476 time to fit residues: 1.2192 Evaluate side-chains 15 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.058 Evaluate side-chains 35 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.139 Fit side-chains revert: symmetry clash REVERT: A 52 PHE cc_start: 0.7692 (m-10) cc_final: 0.7274 (m-80) REVERT: A 245 LEU cc_start: 0.9402 (mm) cc_final: 0.9128 (pp) REVERT: A 303 PHE cc_start: 0.8832 (m-80) cc_final: 0.8284 (m-80) REVERT: A 368 MET cc_start: 0.8753 (mmt) cc_final: 0.8378 (mmt) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0561 time to fit residues: 2.6610 Evaluate side-chains 31 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 49 optimal weight: 8.9990 chunk 64 optimal weight: 0.0170 chunk 477 optimal weight: 8.9990 chunk 475 optimal weight: 7.9990 chunk 58 optimal weight: 20.0000 chunk 405 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 388 optimal weight: 30.0000 chunk 436 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 426 optimal weight: 2.9990 overall best weight: 3.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 181 GLN L 191 GLN K 191 GLN ** K 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 779 ASN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.047522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.037569 restraints weight = 72254.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.038157 restraints weight = 52665.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.038729 restraints weight = 38813.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.038624 restraints weight = 37551.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.038742 restraints weight = 34777.504| |-----------------------------------------------------------------------------| r_work (final): 0.3406 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.044540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.034221 restraints weight = 66977.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.035280 restraints weight = 42773.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.035985 restraints weight = 31614.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.036437 restraints weight = 25880.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.036720 restraints weight = 22675.858| |-----------------------------------------------------------------------------| r_work (final): 0.3293 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.072101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.065427 restraints weight = 13598.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.065859 restraints weight = 11620.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.066258 restraints weight = 10335.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 16)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.066390 restraints weight = 9377.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.066680 restraints weight = 8922.628| |-----------------------------------------------------------------------------| r_work (final): 0.3985 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.076486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.056710 restraints weight = 29527.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.057943 restraints weight = 17550.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.058763 restraints weight = 12519.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.059183 restraints weight = 10015.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.059495 restraints weight = 8809.444| |-----------------------------------------------------------------------------| r_work (final): 0.3408 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.073312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.066279 restraints weight = 14023.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.066553 restraints weight = 12199.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.066782 restraints weight = 11224.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.066836 restraints weight = 10545.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.066836 restraints weight = 10185.552| |-----------------------------------------------------------------------------| r_work (final): 0.3927 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.076130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.055808 restraints weight = 28805.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.056904 restraints weight = 17768.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.057575 restraints weight = 12846.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.058082 restraints weight = 10472.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.058349 restraints weight = 9158.080| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6338 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 46008 Z= 0.125 Angle : 0.607 8.875 62344 Z= 0.312 Chirality : 0.044 0.189 6830 Planarity : 0.004 0.050 7980 Dihedral : 4.269 22.822 6130 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.82 % Favored : 93.15 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % 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: -0.55 (0.12), residues: 5516 helix: 0.72 (0.11), residues: 2202 sheet: 0.07 (0.19), residues: 778 loop : -1.50 (0.13), residues: 2536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 207 TYR 0.020 0.001 TYR H 93 PHE 0.031 0.001 PHE D 194 TRP 0.042 0.001 TRP D 19 HIS 0.006 0.001 HIS G 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (45992) covalent geometry : angle 0.60668 / 0.31 (62312) SS BOND : bond 0.00233 / 0.12 ( 16) SS BOND : angle 0.90803 / 0.58 ( 32) hydrogen bonds : bond 0.03370 / 2.28 ( 2011) hydrogen bonds : angle 4.89143 / 3.40 ( 5709) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11032 Ramachandran restraints generated. 5516 Oldfield, 0 Emsley, 5516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11032 Ramachandran restraints generated. 5516 Oldfield, 0 Emsley, 5516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 266 LEU cc_start: 0.8674 (mt) cc_final: 0.8066 (pp) REVERT: J 309 MET cc_start: 0.8435 (tpp) cc_final: 0.8096 (tpt) REVERT: J 669 GLN cc_start: 0.8559 (mt0) cc_final: 0.8238 (mp10) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0642 time to fit residues: 3.5235 Evaluate side-chains 31 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.239 Evaluate side-chains 36 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: I 223 TYR cc_start: 0.7816 (m-80) cc_final: 0.7491 (m-10) REVERT: I 499 MET cc_start: 0.8721 (mmp) cc_final: 0.8081 (mmm) REVERT: I 546 MET cc_start: 0.6326 (tmm) cc_final: 0.6124 (tmm) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0612 time to fit residues: 3.4382 Evaluate side-chains 25 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.245 Evaluate side-chains 21 residues out of total 161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.061 Fit side-chains REVERT: H 72 ASP cc_start: 0.7721 (m-30) cc_final: 0.7487 (m-30) REVERT: H 182 MET cc_start: -0.4376 (mmm) cc_final: -0.4606 (mmm) REVERT: H 206 MET cc_start: 0.3024 (mmp) cc_final: 0.2799 (mmp) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0613 time to fit residues: 1.4925 Evaluate side-chains 12 residues out of total 161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.060 Evaluate side-chains 36 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.143 Fit side-chains REVERT: D 92 PHE cc_start: 0.9071 (t80) cc_final: 0.8528 (t80) REVERT: D 155 ASP cc_start: 0.7976 (m-30) cc_final: 0.7314 (t0) REVERT: D 194 PHE cc_start: 0.8932 (m-80) cc_final: 0.8650 (m-10) REVERT: D 329 PHE cc_start: 0.8624 (t80) cc_final: 0.8148 (t80) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0412 time to fit residues: 2.2285 Evaluate side-chains 29 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.147 Evaluate side-chains 22 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.067 Fit side-chains REVERT: E 214 ASN cc_start: 0.5969 (p0) cc_final: 0.5768 (p0) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0434 time to fit residues: 1.1476 Evaluate side-chains 14 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.039 Evaluate side-chains 30 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.129 Fit side-chains REVERT: A 52 PHE cc_start: 0.7723 (m-10) cc_final: 0.7159 (m-80) REVERT: A 245 LEU cc_start: 0.9395 (mm) cc_final: 0.9145 (pp) REVERT: A 303 PHE cc_start: 0.8879 (m-80) cc_final: 0.8385 (m-80) REVERT: A 368 MET cc_start: 0.8842 (mmt) cc_final: 0.8479 (mmt) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0298 time to fit residues: 1.3468 Evaluate side-chains 25 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 338 optimal weight: 1.9990 chunk 265 optimal weight: 6.9990 chunk 176 optimal weight: 9.9990 chunk 31 optimal weight: 0.0370 chunk 230 optimal weight: 40.0000 chunk 498 optimal weight: 8.9990 chunk 442 optimal weight: 6.9990 chunk 332 optimal weight: 20.0000 chunk 226 optimal weight: 6.9990 chunk 104 optimal weight: 0.0030 chunk 67 optimal weight: 2.9990 overall best weight: 2.4074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 181 GLN J 191 GLN J 528 GLN I 191 GLN ** I 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 779 ASN ** E 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 GLN ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.047916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.037755 restraints weight = 71956.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.038206 restraints weight = 48686.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.038327 restraints weight = 37998.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.038566 restraints weight = 38434.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.038909 restraints weight = 35914.332| |-----------------------------------------------------------------------------| r_work (final): 0.3400 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.044626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.034251 restraints weight = 67074.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.035307 restraints weight = 43253.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.035974 restraints weight = 32124.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.036437 restraints weight = 26393.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.036739 restraints weight = 23072.010| |-----------------------------------------------------------------------------| r_work (final): 0.3293 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.070730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.061925 restraints weight = 17493.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.062913 restraints weight = 13122.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.063634 restraints weight = 10558.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 16)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.064078 restraints weight = 8944.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.064490 restraints weight = 7974.335| |-----------------------------------------------------------------------------| r_work (final): 0.3894 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.076734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.057037 restraints weight = 29754.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.058286 restraints weight = 17889.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.059036 restraints weight = 12675.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.059599 restraints weight = 10182.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.059899 restraints weight = 8799.873| |-----------------------------------------------------------------------------| r_work (final): 0.3409 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.073429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.066158 restraints weight = 14047.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.066515 restraints weight = 12052.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.066693 restraints weight = 11014.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.066940 restraints weight = 10370.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.067028 restraints weight = 10028.534| |-----------------------------------------------------------------------------| r_work (final): 0.3930 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.075553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.055274 restraints weight = 28015.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.056387 restraints weight = 17295.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.057134 restraints weight = 12581.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.057601 restraints weight = 10128.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.057886 restraints weight = 8877.304| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6571 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 46008 Z= 0.118 Angle : 0.602 10.737 62344 Z= 0.309 Chirality : 0.044 0.197 6830 Planarity : 0.004 0.049 7980 Dihedral : 4.250 23.092 6130 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.60 % Favored : 93.36 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % 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 (0.12), residues: 5516 helix: 0.73 (0.11), residues: 2198 sheet: 0.03 (0.19), residues: 758 loop : -1.50 (0.13), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.000 ARG F 207 TYR 0.018 0.001 TYR I 153 PHE 0.032 0.001 PHE D 194 TRP 0.046 0.001 TRP D 19 HIS 0.006 0.001 HIS E 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (45992) covalent geometry : angle 0.60214 / 0.31 (62312) SS BOND : bond 0.00208 / 0.11 ( 16) SS BOND : angle 0.79804 / 0.51 ( 32) hydrogen bonds : bond 0.03368 / 2.27 ( 2011) hydrogen bonds : angle 4.85989 / 3.38 ( 5709) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4756.64 seconds wall clock time: 85 minutes 18.45 seconds (5118.45 seconds total)