Starting phenix.real_space_refine on Wed Aug 27 01:11:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e8h_31019/08_2025/7e8h_31019.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e8h_31019/08_2025/7e8h_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_31019/08_2025/7e8h_31019.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e8h_31019/08_2025/7e8h_31019.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e8h_31019/08_2025/7e8h_31019.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e8h_31019/08_2025/7e8h_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 8.42, per 1000 atoms: 0.19 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: 3.35 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.26 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: 8.71 Time building geometry restraints manager: 4.25 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: 0.09 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: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 35.960 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.120 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: 0.010 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6331 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 aren 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 covalent geometry : bond 0.00249 (45992) covalent geometry : angle 0.61764 (62312) SS BOND : bond 0.00199 ( 16) SS BOND : angle 0.70051 ( 32) hydrogen bonds : bond 0.14816 ( 2011) hydrogen bonds : angle 6.54001 ( 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 : 0.147 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: 0.0736 time to fit residues: 4.6681 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 : 0.159 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 : 0.241 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: 0.7101 (m-10) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0583 time to fit residues: 3.5876 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 : 0.274 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 : 0.058 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0353 time to fit residues: 0.9767 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 : 0.099 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: 0.0369 time to fit residues: 1.9529 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 : 0.141 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 : 0.049 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: 0.0572 time to fit residues: 1.5430 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 : 0.047 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 : 0.143 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: 0.0376 time to fit residues: 1.6834 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 : 0.094 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 191 GLN ** I 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 392 GLN I 755 GLN Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.046389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.036844 restraints weight = 74998.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.037461 restraints weight = 48947.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.037545 restraints weight = 41898.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.037628 restraints weight = 39417.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.037672 restraints weight = 38070.086| |-----------------------------------------------------------------------------| r_work (final): 0.3353 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.043464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.033393 restraints weight = 69125.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.034380 restraints weight = 44613.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.034998 restraints weight = 33074.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.035399 restraints weight = 27338.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.035648 restraints weight = 24169.916| |-----------------------------------------------------------------------------| 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 = 40)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.065166 restraints weight = 13289.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.065722 restraints weight = 10657.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.066132 restraints weight = 9146.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.066484 restraints weight = 8070.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.066704 restraints weight = 7264.182| |-----------------------------------------------------------------------------| r_work (final): 0.3975 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.075370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.054827 restraints weight = 31615.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.056063 restraints weight = 18021.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.056838 restraints weight = 12652.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.057191 restraints weight = 10250.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.057441 restraints weight = 9209.357| |-----------------------------------------------------------------------------| r_work (final): 0.3341 |-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 = 54)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.063986 restraints weight = 14044.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.064353 restraints weight = 12073.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.064516 restraints weight = 10845.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.064796 restraints weight = 10176.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.064879 restraints weight = 9580.528| |-----------------------------------------------------------------------------| r_work (final): 0.3957 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.073665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.052926 restraints weight = 29023.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.054044 restraints weight = 17417.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.054798 restraints weight = 12405.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.055203 restraints weight = 9968.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.055515 restraints weight = 8761.624| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6529 moved from start: 0.1071 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 aren 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 covalent geometry : bond 0.00345 (45992) covalent geometry : angle 0.61619 (62312) SS BOND : bond 0.00220 ( 16) SS BOND : angle 0.76561 ( 32) hydrogen bonds : bond 0.04484 ( 2011) hydrogen bonds : angle 5.63577 ( 5709) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9092 Ramachandran restraints generated. 4546 Oldfield, 0 Emsley, 4546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9092 Ramachandran restraints generated. 4546 Oldfield, 0 Emsley, 4546 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 : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 38 average time/residue: 0.0658 time to fit residues: 3.7294 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 : 0.270 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 : 0.171 Fit side-chains revert: symmetry clash REVERT: I 499 MET cc_start: 0.8794 (mmp) cc_final: 0.8074 (mmm) REVERT: I 763 TYR cc_start: 0.7684 (m-10) cc_final: 0.7365 (m-10) outliers start: 1 outliers final: 0 residues processed: 32 average time/residue: 0.0510 time to fit residues: 2.5163 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 : 0.146 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: 0.0410 time to fit residues: 1.0249 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 : 0.142 Fit side-chains REVERT: B 92 PHE cc_start: 0.9183 (t80) cc_final: 0.8654 (t80) REVERT: B 155 ASP cc_start: 0.7595 (m-30) cc_final: 0.6891 (t0) REVERT: B 194 PHE cc_start: 0.8918 (m-80) cc_final: 0.8657 (m-10) REVERT: B 329 PHE cc_start: 0.8648 (t80) cc_final: 0.8149 (t80) outliers start: 1 outliers final: 0 residues processed: 32 average time/residue: 0.0337 time to fit residues: 1.6200 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 : 0.094 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 : 0.059 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 21 average time/residue: 0.0566 time to fit residues: 1.3872 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 : 0.036 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 : 0.141 Fit side-chains REVERT: A 27 MET cc_start: 0.1507 (tpt) cc_final: 0.0951 (ttt) REVERT: A 117 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8185 (pp20) REVERT: A 368 MET cc_start: 0.8070 (mpp) cc_final: 0.6853 (mpp) outliers start: 3 outliers final: 0 residues processed: 29 average time/residue: 0.0358 time to fit residues: 1.5640 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 : 0.144 ------------------------------------------------------------------------------- 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: 20.0000 chunk 114 optimal weight: 40.0000 chunk 348 optimal weight: 2.9990 chunk 276 optimal weight: 0.7980 chunk 376 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 307 optimal weight: 20.0000 chunk 495 optimal weight: 50.0000 chunk 409 optimal weight: 5.9990 chunk 256 optimal weight: 2.9990 chunk 447 optimal weight: 30.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 191 GLN I 755 GLN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.046507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.035564 restraints weight = 83712.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.036930 restraints weight = 48236.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.037774 restraints weight = 34100.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.038258 restraints weight = 27765.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.038509 restraints weight = 24592.350| |-----------------------------------------------------------------------------| r_work (final): 0.3329 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.043629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.033556 restraints weight = 71354.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.034533 restraints weight = 46096.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.035184 restraints weight = 34295.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.035581 restraints weight = 28183.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.035852 restraints weight = 24869.978| |-----------------------------------------------------------------------------| r_work (final): 0.3234 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.070699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.064721 restraints weight = 13277.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.065288 restraints weight = 10450.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.065740 restraints weight = 8884.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.066149 restraints weight = 7886.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.066224 restraints weight = 7217.436| |-----------------------------------------------------------------------------| r_work (final): 0.3962 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.076025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.055206 restraints weight = 34166.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.056306 restraints weight = 19702.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.057073 restraints weight = 14103.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.057419 restraints weight = 11616.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.057499 restraints weight = 10471.723| |-----------------------------------------------------------------------------| r_work (final): 0.3333 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.069957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.064061 restraints weight = 14185.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.064221 restraints weight = 12904.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.064419 restraints weight = 11767.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.064580 restraints weight = 10980.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.064619 restraints weight = 10441.264| |-----------------------------------------------------------------------------| r_work (final): 0.3953 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.073802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.052980 restraints weight = 29881.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.054072 restraints weight = 18149.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.054834 restraints weight = 12804.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.055224 restraints weight = 10255.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.055588 restraints weight = 9016.669| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6529 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.572 46008 Z= 0.251 Angle : 0.630 20.759 62344 Z= 0.333 Chirality : 0.044 0.254 6830 Planarity : 0.004 0.066 7980 Dihedral : 4.565 25.321 6130 Min Nonbonded Distance : 0.839 Molprobity Statistics. All-atom Clashscore : 29.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.36 % Favored : 92.60 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % 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 aren 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 E 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 covalent geometry : bond 0.00346 (45992) covalent geometry : angle 0.61623 (62312) SS BOND : bond 0.20305 ( 16) SS BOND : angle 5.86369 ( 32) hydrogen bonds : bond 0.04484 ( 2011) hydrogen bonds : angle 5.63584 ( 5709) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 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 : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 529 MET cc_start: 0.7496 (ppp) cc_final: 0.7274 (ppp) REVERT: J 641 ARG cc_start: 0.6185 (ttp80) cc_final: 0.5854 (ptt-90) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0782 time to fit residues: 3.9222 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 : 0.230 Evaluate side-chains 30 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: I 499 MET cc_start: 0.8761 (mmp) cc_final: 0.8042 (mmm) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0614 time to fit residues: 2.8147 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 : 0.158 Evaluate side-chains 19 residues out of total 161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.088 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0327 time to fit residues: 0.8091 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 32 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.105 Fit side-chains REVERT: B 92 PHE cc_start: 0.9184 (t80) cc_final: 0.8649 (t80) REVERT: B 155 ASP cc_start: 0.7597 (m-30) cc_final: 0.6922 (t0) REVERT: B 194 PHE cc_start: 0.8903 (m-80) cc_final: 0.8648 (m-10) REVERT: B 329 PHE cc_start: 0.8583 (t80) cc_final: 0.8093 (t80) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0305 time to fit residues: 1.5022 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 : 0.141 Evaluate side-chains 19 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.043 Fit side-chains revert: symmetry clash REVERT: G 214 ASN cc_start: 0.5720 (p0) cc_final: 0.5458 (p0) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0287 time to fit residues: 0.7135 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 : 0.036 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 : 0.084 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.6498 (mmp) cc_final: 0.6271 (mmm) REVERT: A 27 MET cc_start: 0.0059 (tpt) cc_final: -0.0877 (ttt) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0452 time to fit residues: 1.8502 Evaluate side-chains 22 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 794, in minimization_ncs weight = real_space_weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 394, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 126, in refine minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 424, in __init__ minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 456, in compute_functional_and_gradients t,g = self.target_and_grads_object.target_and_gradients( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 242, in target_and_gradients t_restraints, g_restraints = restraints_target_and_grads( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 110, in restraints_target_and_grads ef = restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.5863 > 50: distance: 0 - 1: 8.671 distance: 0 - 12: 16.941 distance: 2 - 3: 5.290 distance: 3 - 4: 6.392 distance: 4 - 6: 5.785 distance: 5 - 7: 7.471 distance: 5 - 8: 5.742 distance: 6 - 7: 4.587 distance: 7 - 9: 7.675 distance: 8 - 10: 7.087 distance: 9 - 11: 15.062 distance: 10 - 11: 16.944 distance: 12 - 13: 21.134 distance: 13 - 14: 6.535 distance: 14 - 15: 19.362 distance: 14 - 16: 9.264 distance: 16 - 17: 3.658 distance: 16 - 22: 4.870 distance: 17 - 18: 4.643 distance: 17 - 20: 8.508 distance: 18 - 19: 23.670 distance: 18 - 23: 6.260 distance: 20 - 21: 5.196 distance: 21 - 22: 4.026 distance: 23 - 24: 10.263 distance: 24 - 25: 7.494 distance: 24 - 27: 5.898 distance: 25 - 26: 9.099 distance: 25 - 32: 4.955 distance: 27 - 28: 8.395 distance: 28 - 29: 27.056 distance: 29 - 30: 21.230 distance: 30 - 31: 19.468 distance: 32 - 33: 20.722 distance: 33 - 34: 13.356 distance: 34 - 35: 29.903 distance: 34 - 36: 12.857 distance: 36 - 37: 33.437 distance: 37 - 38: 37.130 distance: 37 - 40: 30.457 distance: 38 - 39: 44.257 distance: 38 - 45: 41.856 distance: 40 - 41: 22.214 distance: 42 - 43: 12.077 distance: 42 - 44: 6.518 distance: 45 - 46: 20.264 distance: 46 - 47: 33.150 distance: 46 - 49: 7.672 distance: 47 - 48: 42.477 distance: 47 - 54: 21.883 distance: 49 - 50: 28.445 distance: 50 - 51: 37.161 distance: 51 - 52: 41.566 distance: 51 - 53: 41.636 distance: 54 - 55: 13.824 distance: 55 - 56: 24.330 distance: 55 - 58: 19.848 distance: 56 - 57: 15.953 distance: 56 - 62: 31.345 distance: 58 - 59: 10.752 distance: 59 - 60: 31.453 distance: 59 - 61: 12.887 distance: 62 - 63: 28.763 distance: 63 - 64: 26.909 distance: 63 - 66: 27.468 distance: 64 - 65: 27.363 distance: 64 - 70: 10.415 distance: 66 - 67: 16.352 distance: 66 - 68: 21.186 distance: 67 - 69: 30.653 distance: 70 - 71: 23.962 distance: 71 - 72: 6.179 distance: 71 - 74: 30.724 distance: 72 - 73: 33.355 distance: 72 - 81: 16.427 distance: 74 - 75: 14.575 distance: 75 - 76: 13.337 distance: 75 - 77: 10.252 distance: 76 - 78: 14.727 distance: 77 - 79: 3.692 distance: 78 - 80: 7.425 distance: 79 - 80: 8.960 distance: 81 - 82: 7.714