Starting phenix.real_space_refine on Mon Jul 6 17:34:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hih_34816/07_2026/8hih_34816.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hih_34816/07_2026/8hih_34816.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hih_34816/07_2026/8hih_34816.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hih_34816/07_2026/8hih_34816.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hih_34816/07_2026/8hih_34816.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hih_34816/07_2026/8hih_34816.map" } resolution = 3.66 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3273 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 154 5.49 5 Mg 1 5.21 5 S 104 5.16 5 C 21549 2.51 5 N 6252 2.21 5 O 7002 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35064 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1716 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 210} Chain: "B" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1765 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 221} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 8554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1111, 8554 Classifications: {'peptide': 1111} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1048} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 4, 'ARG:plan': 3, 'GLU:plan': 4, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 9890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1268, 9890 Classifications: {'peptide': 1268} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 59, 'TRANS': 1207} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "E" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 649 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "F" Number of atoms: 2534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2534 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 313} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 28 Chain: "G" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 433 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 55} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "K" Number of atoms: 1584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1584 Classifications: {'DNA': 77} Link IDs: {'rna3p': 76} Chain: "L" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1586 Classifications: {'DNA': 77} Link IDs: {'rna3p': 76} Chain: "O" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1609 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 10, 'TRANS': 206} Chain breaks: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3, 'GLN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "P" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1565 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 5, 'PTRANS': 10, 'TRANS': 197} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 2, 'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "N" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1612 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 206} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 1, 'GLN:plan1': 2, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "Q" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1564 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'CIS': 6, 'PTRANS': 10, 'TRANS': 196} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19088 SG CYS D 891 68.772 42.805 63.015 1.00245.53 S ATOM 19715 SG CYS D 978 71.636 42.294 65.237 1.00232.35 S ATOM 12532 SG CYS D 60 72.713 109.768 63.138 1.00252.53 S ATOM 12550 SG CYS D 62 74.256 112.928 61.948 1.00253.11 S ATOM 12659 SG CYS D 75 71.795 111.289 59.616 1.00255.59 S ATOM 12685 SG CYS D 78 74.946 109.527 60.129 1.00236.85 S Time building chain proxies: 6.27, per 1000 atoms: 0.18 Number of scatterers: 35064 At special positions: 0 Unit cell: (171.36, 159.46, 184.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 104 16.00 P 154 15.00 Mg 1 11.99 O 7002 8.00 N 6252 7.00 C 21549 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.51 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 891 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 978 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 60 " Number of angles added : 6 8258 Ramachandran restraints generated. 4129 Oldfield, 0 Emsley, 4129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7648 Finding SS restraints... Secondary structure from input PDB file: 155 helices and 54 sheets defined 42.3% alpha, 12.7% beta 58 base pairs and 99 stacking pairs defined. Time for finding SS restraints: 4.62 Creating SS restraints... Processing helix chain 'A' and resid 30 through 45 removed outlier: 3.905A pdb=" N LEU A 34 " --> pdb=" O PHE A 30 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 203 through 224 removed outlier: 3.623A pdb=" N GLU A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 46 removed outlier: 3.767A pdb=" N THR B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 removed outlier: 4.033A pdb=" N ILE B 76 " --> pdb=" O ASP B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 224 removed outlier: 4.173A pdb=" N ALA B 207 " --> pdb=" O SER B 203 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU B 208 " --> pdb=" O PRO B 204 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 66 Processing helix chain 'C' and resid 67 through 75 Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 118 through 125 Processing helix chain 'C' and resid 233 through 239 removed outlier: 3.979A pdb=" N LEU C 237 " --> pdb=" O PRO C 233 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS C 239 " --> pdb=" O THR C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 242 No H-bonds generated for 'chain 'C' and resid 240 through 242' Processing helix chain 'C' and resid 244 through 252 removed outlier: 3.846A pdb=" N ILE C 248 " --> pdb=" O THR C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 264 removed outlier: 3.715A pdb=" N SER C 260 " --> pdb=" O GLU C 256 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N THR C 261 " --> pdb=" O ILE C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 282 Processing helix chain 'C' and resid 290 through 301 removed outlier: 4.540A pdb=" N GLU C 297 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N PHE C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 335 through 350 removed outlier: 3.530A pdb=" N VAL C 339 " --> pdb=" O GLU C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 406 Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 444 through 450 Processing helix chain 'C' and resid 470 through 474 Processing helix chain 'C' and resid 476 through 480 Processing helix chain 'C' and resid 533 through 538 removed outlier: 3.713A pdb=" N ASP C 537 " --> pdb=" O ALA C 533 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARG C 538 " --> pdb=" O ASP C 534 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 533 through 538' Processing helix chain 'C' and resid 589 through 594 removed outlier: 3.567A pdb=" N ILE C 594 " --> pdb=" O THR C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 613 removed outlier: 3.534A pdb=" N MET C 607 " --> pdb=" O ASN C 603 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG C 613 " --> pdb=" O ALA C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 637 removed outlier: 4.170A pdb=" N ARG C 633 " --> pdb=" O GLY C 629 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 778 through 782 removed outlier: 3.567A pdb=" N ALA C 782 " --> pdb=" O GLU C 779 " (cutoff:3.500A) Processing helix chain 'C' and resid 815 through 825 Processing helix chain 'C' and resid 900 through 904 removed outlier: 4.005A pdb=" N ASP C 903 " --> pdb=" O PRO C 900 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET C 904 " --> pdb=" O VAL C 901 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 900 through 904' Processing helix chain 'C' and resid 922 through 926 removed outlier: 4.116A pdb=" N MET C 926 " --> pdb=" O PRO C 923 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 943 Processing helix chain 'C' and resid 953 through 959 removed outlier: 4.567A pdb=" N ARG C 958 " --> pdb=" O ASP C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 991 removed outlier: 3.691A pdb=" N SER C 990 " --> pdb=" O GLN C 986 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N CYS C 991 " --> pdb=" O GLY C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1069 through 1079 removed outlier: 4.066A pdb=" N ALA C1075 " --> pdb=" O MET C1071 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1091 Processing helix chain 'C' and resid 1095 through 1106 Processing helix chain 'C' and resid 1118 through 1130 Processing helix chain 'D' and resid 16 through 24 removed outlier: 3.753A pdb=" N GLN D 22 " --> pdb=" O GLU D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 112 through 118 Processing helix chain 'D' and resid 122 through 130 removed outlier: 3.750A pdb=" N LYS D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ILE D 128 " --> pdb=" O ASP D 124 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 185 removed outlier: 3.628A pdb=" N GLU D 147 " --> pdb=" O MET D 143 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER D 149 " --> pdb=" O HIS D 145 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N THR D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS D 176 " --> pdb=" O ALA D 172 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU D 183 " --> pdb=" O ALA D 179 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 228 removed outlier: 4.021A pdb=" N VAL D 197 " --> pdb=" O ALA D 193 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG D 198 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU D 202 " --> pdb=" O ARG D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 removed outlier: 4.313A pdb=" N ARG D 247 " --> pdb=" O GLU D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 267 removed outlier: 3.788A pdb=" N ILE D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 284 Processing helix chain 'D' and resid 286 through 305 removed outlier: 3.508A pdb=" N ARG D 291 " --> pdb=" O GLN D 287 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LYS D 294 " --> pdb=" O LEU D 290 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 339 through 361 Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 401 through 407 removed outlier: 3.863A pdb=" N LEU D 406 " --> pdb=" O SER D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 417 Processing helix chain 'D' and resid 445 through 452 Processing helix chain 'D' and resid 452 through 462 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 481 through 491 removed outlier: 3.920A pdb=" N ASP D 485 " --> pdb=" O PRO D 481 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 578 through 590 Processing helix chain 'D' and resid 614 through 624 Processing helix chain 'D' and resid 643 through 652 Processing helix chain 'D' and resid 667 through 675 Processing helix chain 'D' and resid 689 through 704 Processing helix chain 'D' and resid 705 through 725 removed outlier: 3.565A pdb=" N ASP D 714 " --> pdb=" O ALA D 710 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR D 725 " --> pdb=" O PHE D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 762 removed outlier: 3.614A pdb=" N VAL D 756 " --> pdb=" O ARG D 752 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS D 758 " --> pdb=" O ASP D 754 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 793 removed outlier: 3.718A pdb=" N LEU D 774 " --> pdb=" O ARG D 770 " (cutoff:3.500A) Processing helix chain 'D' and resid 797 through 805 Processing helix chain 'D' and resid 810 through 816 Processing helix chain 'D' and resid 845 through 882 removed outlier: 3.832A pdb=" N HIS D 854 " --> pdb=" O PHE D 850 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY D 859 " --> pdb=" O GLY D 855 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR D 863 " --> pdb=" O GLY D 859 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ALA D 864 " --> pdb=" O LEU D 860 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU D 865 " --> pdb=" O ALA D 861 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR D 867 " --> pdb=" O THR D 863 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP D 879 " --> pdb=" O ARG D 875 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 955 Processing helix chain 'D' and resid 964 through 968 Processing helix chain 'D' and resid 976 through 980 Processing helix chain 'D' and resid 994 through 1005 removed outlier: 3.648A pdb=" N VAL D 998 " --> pdb=" O ALA D 994 " (cutoff:3.500A) Processing helix chain 'D' and resid 1006 through 1010 Processing helix chain 'D' and resid 1027 through 1037 Processing helix chain 'D' and resid 1117 through 1125 removed outlier: 3.861A pdb=" N VAL D1121 " --> pdb=" O ASP D1117 " (cutoff:3.500A) Processing helix chain 'D' and resid 1125 through 1145 removed outlier: 3.927A pdb=" N GLU D1129 " --> pdb=" O GLN D1125 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL D1130 " --> pdb=" O GLY D1126 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN D1145 " --> pdb=" O VAL D1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1163 removed outlier: 4.109A pdb=" N ILE D1154 " --> pdb=" O HIS D1150 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1195 removed outlier: 4.080A pdb=" N ALA D1195 " --> pdb=" O ARG D1191 " (cutoff:3.500A) Processing helix chain 'D' and resid 1209 through 1216 Processing helix chain 'D' and resid 1219 through 1225 Processing helix chain 'D' and resid 1228 through 1239 removed outlier: 3.859A pdb=" N ASP D1235 " --> pdb=" O ARG D1231 " (cutoff:3.500A) Processing helix chain 'D' and resid 1247 through 1255 Processing helix chain 'D' and resid 1264 through 1269 Processing helix chain 'D' and resid 1275 through 1281 Processing helix chain 'E' and resid 33 through 37 Processing helix chain 'E' and resid 39 through 47 removed outlier: 3.619A pdb=" N ASP E 45 " --> pdb=" O ASP E 41 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG E 46 " --> pdb=" O GLU E 42 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL E 47 " --> pdb=" O LEU E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 71 removed outlier: 4.116A pdb=" N ARG E 60 " --> pdb=" O TYR E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 removed outlier: 3.526A pdb=" N ALA E 101 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 221 removed outlier: 3.773A pdb=" N ALA F 215 " --> pdb=" O ALA F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 236 Processing helix chain 'F' and resid 242 through 266 Processing helix chain 'F' and resid 274 through 299 removed outlier: 4.649A pdb=" N ASP F 280 " --> pdb=" O ALA F 276 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N MET F 281 " --> pdb=" O GLN F 277 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASP F 289 " --> pdb=" O CYS F 285 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA F 291 " --> pdb=" O ASP F 287 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LYS F 292 " --> pdb=" O GLY F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 307 removed outlier: 3.579A pdb=" N VAL F 303 " --> pdb=" O ASN F 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 335 removed outlier: 4.071A pdb=" N GLU F 333 " --> pdb=" O ILE F 329 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS F 334 " --> pdb=" O ARG F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 340 Processing helix chain 'F' and resid 342 through 363 removed outlier: 3.771A pdb=" N THR F 348 " --> pdb=" O SER F 344 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TRP F 349 " --> pdb=" O THR F 345 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TRP F 350 " --> pdb=" O TYR F 346 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE F 355 " --> pdb=" O ILE F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 391 removed outlier: 3.922A pdb=" N GLN F 388 " --> pdb=" O ARG F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 403 removed outlier: 4.348A pdb=" N LYS F 401 " --> pdb=" O GLU F 397 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU F 402 " --> pdb=" O GLU F 398 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET F 403 " --> pdb=" O LEU F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 418 Processing helix chain 'F' and resid 434 through 439 Processing helix chain 'F' and resid 448 through 467 Processing helix chain 'F' and resid 468 through 479 Processing helix chain 'F' and resid 488 through 497 removed outlier: 3.587A pdb=" N GLY F 493 " --> pdb=" O LEU F 489 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLN F 494 " --> pdb=" O ASP F 490 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Processing helix chain 'F' and resid 499 through 515 removed outlier: 3.613A pdb=" N SER F 508 " --> pdb=" O ARG F 504 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS F 513 " --> pdb=" O LYS F 509 " (cutoff:3.500A) Processing helix chain 'F' and resid 516 through 524 removed outlier: 3.683A pdb=" N SER F 520 " --> pdb=" O HIS F 516 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL F 522 " --> pdb=" O SER F 518 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 254 Processing helix chain 'G' and resid 257 through 266 Processing helix chain 'G' and resid 271 through 278 Processing helix chain 'G' and resid 279 through 285 removed outlier: 3.506A pdb=" N LEU G 283 " --> pdb=" O THR G 279 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU G 284 " --> pdb=" O GLU G 280 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP G 285 " --> pdb=" O SER G 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 279 through 285' Processing helix chain 'G' and resid 290 through 304 removed outlier: 3.539A pdb=" N ILE G 294 " --> pdb=" O GLY G 290 " (cutoff:3.500A) Processing helix chain 'O' and resid 17 through 23 removed outlier: 4.024A pdb=" N SER O 21 " --> pdb=" O PRO O 18 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU O 23 " --> pdb=" O LEU O 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 34 through 38 Processing helix chain 'O' and resid 53 through 64 Processing helix chain 'O' and resid 86 through 90 Processing helix chain 'O' and resid 100 through 113 Processing helix chain 'O' and resid 151 through 164 removed outlier: 3.572A pdb=" N GLU O 156 " --> pdb=" O TYR O 152 " (cutoff:3.500A) Processing helix chain 'O' and resid 170 through 179 removed outlier: 3.797A pdb=" N HIS O 176 " --> pdb=" O ALA O 172 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU O 177 " --> pdb=" O GLN O 173 " (cutoff:3.500A) Processing helix chain 'O' and resid 188 through 202 removed outlier: 3.638A pdb=" N GLY O 202 " --> pdb=" O ARG O 198 " (cutoff:3.500A) Processing helix chain 'O' and resid 203 through 206 Processing helix chain 'P' and resid 12 through 17 removed outlier: 3.727A pdb=" N VAL P 16 " --> pdb=" O TYR P 12 " (cutoff:3.500A) Processing helix chain 'P' and resid 18 through 22 removed outlier: 3.537A pdb=" N SER P 21 " --> pdb=" O PRO P 18 " (cutoff:3.500A) Processing helix chain 'P' and resid 34 through 38 Processing helix chain 'P' and resid 53 through 64 Processing helix chain 'P' and resid 79 through 83 removed outlier: 4.305A pdb=" N VAL P 83 " --> pdb=" O GLY P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 86 through 90 removed outlier: 3.746A pdb=" N TRP P 89 " --> pdb=" O SER P 86 " (cutoff:3.500A) Processing helix chain 'P' and resid 100 through 113 Processing helix chain 'P' and resid 151 through 164 Processing helix chain 'P' and resid 170 through 176 removed outlier: 4.081A pdb=" N HIS P 176 " --> pdb=" O ALA P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 188 through 201 removed outlier: 3.518A pdb=" N VAL P 192 " --> pdb=" O ARG P 188 " (cutoff:3.500A) Processing helix chain 'N' and resid 12 through 17 removed outlier: 4.255A pdb=" N VAL N 16 " --> pdb=" O TYR N 12 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU N 17 " --> pdb=" O PRO N 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 12 through 17' Processing helix chain 'N' and resid 17 through 22 removed outlier: 4.291A pdb=" N SER N 21 " --> pdb=" O LEU N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 33 through 40 removed outlier: 3.857A pdb=" N ALA N 40 " --> pdb=" O LEU N 37 " (cutoff:3.500A) Processing helix chain 'N' and resid 54 through 65 Processing helix chain 'N' and resid 100 through 112 Processing helix chain 'N' and resid 151 through 163 removed outlier: 3.791A pdb=" N GLU N 156 " --> pdb=" O TYR N 152 " (cutoff:3.500A) Processing helix chain 'N' and resid 171 through 179 Processing helix chain 'N' and resid 188 through 199 Processing helix chain 'N' and resid 202 through 207 removed outlier: 4.376A pdb=" N ALA N 207 " --> pdb=" O PRO N 203 " (cutoff:3.500A) Processing helix chain 'Q' and resid 17 through 23 removed outlier: 3.780A pdb=" N LEU Q 20 " --> pdb=" O LEU Q 17 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER Q 21 " --> pdb=" O PRO Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 34 through 38 Processing helix chain 'Q' and resid 53 through 65 removed outlier: 3.869A pdb=" N GLY Q 57 " --> pdb=" O ASP Q 53 " (cutoff:3.500A) Processing helix chain 'Q' and resid 86 through 90 removed outlier: 3.652A pdb=" N TRP Q 89 " --> pdb=" O SER Q 86 " (cutoff:3.500A) Processing helix chain 'Q' and resid 100 through 112 Processing helix chain 'Q' and resid 155 through 164 removed outlier: 3.514A pdb=" N HIS Q 164 " --> pdb=" O TYR Q 160 " (cutoff:3.500A) Processing helix chain 'Q' and resid 170 through 179 removed outlier: 4.213A pdb=" N GLU Q 177 " --> pdb=" O GLN Q 173 " (cutoff:3.500A) Processing helix chain 'Q' and resid 188 through 198 Processing helix chain 'Q' and resid 205 through 207 No H-bonds generated for 'chain 'Q' and resid 205 through 207' Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13 removed outlier: 6.076A pdb=" N ARG A 18 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N THR A 198 " --> pdb=" O ARG A 18 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLN A 20 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL A 196 " --> pdb=" O GLN A 20 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N VAL A 22 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU A 194 " --> pdb=" O VAL A 22 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLU A 24 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N LEU A 192 " --> pdb=" O GLU A 24 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASP A 195 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL A 174 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLU A 197 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 3.936A pdb=" N LEU A 138 " --> pdb=" O MET A 95 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER A 53 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLU A 141 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N VAL A 51 " --> pdb=" O GLU A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 removed outlier: 6.720A pdb=" N GLY A 103 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N THR A 127 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL A 105 " --> pdb=" O ILE A 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 15 removed outlier: 3.581A pdb=" N GLU B 24 " --> pdb=" O THR B 8 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ARG B 18 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N THR B 198 " --> pdb=" O ARG B 18 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N GLN B 20 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL B 196 " --> pdb=" O GLN B 20 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N VAL B 22 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LEU B 194 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N GLU B 24 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N LEU B 192 " --> pdb=" O GLU B 24 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 97 removed outlier: 6.749A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 87 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 removed outlier: 5.849A pdb=" N GLY B 103 " --> pdb=" O THR B 127 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N THR B 127 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL B 105 " --> pdb=" O ILE B 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB2, first strand: chain 'C' and resid 96 through 97 removed outlier: 4.470A pdb=" N LEU C 105 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE C 140 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N PHE C 107 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLU C 138 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ASP C 109 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR C 136 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY C 155 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL C 135 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N PHE C 153 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA C 137 " --> pdb=" O THR C 151 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N THR C 151 " --> pdb=" O ALA C 137 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB4, first strand: chain 'C' and resid 376 through 379 removed outlier: 3.698A pdb=" N VAL C 180 " --> pdb=" O ARG C 377 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N SER C 177 " --> pdb=" O SER C 456 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 184 through 191 removed outlier: 4.860A pdb=" N HIS C 200 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE C 214 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL C 204 " --> pdb=" O LEU C 212 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N LEU C 212 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 354 through 355 removed outlier: 3.531A pdb=" N VAL C 363 " --> pdb=" O MET C 355 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 505 through 506 removed outlier: 6.643A pdb=" N ILE C 512 " --> pdb=" O LEU C 531 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LEU C 531 " --> pdb=" O ILE C 512 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N THR C 514 " --> pdb=" O VAL C 529 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL C 529 " --> pdb=" O THR C 514 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N TYR C 516 " --> pdb=" O GLU C 527 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N GLU C 527 " --> pdb=" O TYR C 516 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS C 518 " --> pdb=" O SER C 525 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 505 through 506 Processing sheet with id=AB9, first strand: chain 'C' and resid 559 through 562 Processing sheet with id=AC1, first strand: chain 'C' and resid 626 through 627 Processing sheet with id=AC2, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.261A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 667 through 671 Processing sheet with id=AC4, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC5, first strand: chain 'C' and resid 717 through 720 removed outlier: 5.973A pdb=" N ILE C 735 " --> pdb=" O LYS C 897 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 749 through 760 removed outlier: 3.976A pdb=" N SER C 749 " --> pdb=" O ARG C 877 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ASN C 866 " --> pdb=" O SER C 854 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N SER C 854 " --> pdb=" O ASN C 866 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU C 868 " --> pdb=" O VAL C 852 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL C 852 " --> pdb=" O LEU C 868 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ARG C 870 " --> pdb=" O ILE C 850 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ILE C 850 " --> pdb=" O ARG C 870 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TYR C 872 " --> pdb=" O ILE C 848 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 784 through 785 removed outlier: 3.803A pdb=" N ILE C 789 " --> pdb=" O ASP C 785 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 801 through 803 removed outlier: 6.625A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 806 through 808 Processing sheet with id=AD1, first strand: chain 'C' and resid 944 through 945 Processing sheet with id=AD2, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 6.089A pdb=" N CYS D 441 " --> pdb=" O MET D 515 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL D 517 " --> pdb=" O CYS D 441 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N LEU D 443 " --> pdb=" O VAL D 517 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 7.990A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEU D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL D 431 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1066 through 1068 Processing sheet with id=AD5, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AD6, first strand: chain 'D' and resid 93 through 102 removed outlier: 10.094A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.022A pdb=" N ALA D 99 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ALA D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 234 through 235 removed outlier: 5.083A pdb=" N ILE D 136 " --> pdb=" O ALA D 255 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ALA D 255 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 328 through 329 Processing sheet with id=AD9, first strand: chain 'D' and resid 635 through 637 Processing sheet with id=AE1, first strand: chain 'D' and resid 886 through 888 Processing sheet with id=AE2, first strand: chain 'D' and resid 897 through 899 Processing sheet with id=AE3, first strand: chain 'D' and resid 929 through 930 removed outlier: 6.107A pdb=" N ALA D 929 " --> pdb=" O ILE D 937 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1051 through 1056 removed outlier: 5.455A pdb=" N ILE D1064 " --> pdb=" O ASP D1078 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASP D1078 " --> pdb=" O ILE D1064 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE D1066 " --> pdb=" O VAL D1076 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N VAL D1076 " --> pdb=" O ILE D1066 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1181 through 1182 Processing sheet with id=AE6, first strand: chain 'D' and resid 1273 through 1274 Processing sheet with id=AE7, first strand: chain 'O' and resid 26 through 30 removed outlier: 3.793A pdb=" N ALA O 45 " --> pdb=" O GLU O 3 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU O 5 " --> pdb=" O ALA O 45 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP O 49 " --> pdb=" O LEU O 7 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL O 46 " --> pdb=" O LEU O 74 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N VAL O 76 " --> pdb=" O VAL O 46 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL O 48 " --> pdb=" O VAL O 76 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL O 73 " --> pdb=" O GLU O 93 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N LEU O 95 " --> pdb=" O VAL O 73 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ALA O 75 " --> pdb=" O LEU O 95 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 126 through 129 Processing sheet with id=AE9, first strand: chain 'O' and resid 209 through 212 Processing sheet with id=AF1, first strand: chain 'P' and resid 26 through 30 removed outlier: 6.149A pdb=" N LEU P 4 " --> pdb=" O ARG P 28 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ALA P 30 " --> pdb=" O LEU P 4 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N LEU P 6 " --> pdb=" O ALA P 30 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N GLU P 3 " --> pdb=" O ALA P 45 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU P 47 " --> pdb=" O GLU P 3 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N LEU P 5 " --> pdb=" O LEU P 47 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ASP P 49 " --> pdb=" O LEU P 5 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU P 7 " --> pdb=" O ASP P 49 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL P 46 " --> pdb=" O LEU P 74 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N VAL P 76 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL P 48 " --> pdb=" O VAL P 76 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N LEU P 95 " --> pdb=" O VAL P 73 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ALA P 75 " --> pdb=" O LEU P 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'P' and resid 132 through 135 removed outlier: 3.832A pdb=" N THR P 140 " --> pdb=" O ASP P 135 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'P' and resid 209 through 212 Processing sheet with id=AF4, first strand: chain 'N' and resid 26 through 30 removed outlier: 6.658A pdb=" N LEU N 4 " --> pdb=" O ARG N 28 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA N 30 " --> pdb=" O LEU N 4 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU N 6 " --> pdb=" O ALA N 30 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLU N 3 " --> pdb=" O ALA N 45 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N LEU N 47 " --> pdb=" O GLU N 3 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU N 5 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ASP N 49 " --> pdb=" O LEU N 5 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LEU N 7 " --> pdb=" O ASP N 49 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N VAL N 46 " --> pdb=" O LEU N 74 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL N 76 " --> pdb=" O VAL N 46 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL N 48 " --> pdb=" O VAL N 76 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N VAL N 73 " --> pdb=" O GLU N 93 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N LEU N 95 " --> pdb=" O VAL N 73 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA N 75 " --> pdb=" O LEU N 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'N' and resid 126 through 129 Processing sheet with id=AF6, first strand: chain 'N' and resid 169 through 170 removed outlier: 4.079A pdb=" N PHE N 169 " --> pdb=" O TYR N 217 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR N 217 " --> pdb=" O PHE N 169 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Q' and resid 26 through 30 removed outlier: 3.910A pdb=" N ASP Q 49 " --> pdb=" O LEU Q 7 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N VAL Q 46 " --> pdb=" O LEU Q 74 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N VAL Q 76 " --> pdb=" O VAL Q 46 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL Q 48 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL Q 73 " --> pdb=" O GLU Q 93 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU Q 95 " --> pdb=" O VAL Q 73 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ALA Q 75 " --> pdb=" O LEU Q 95 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Q' and resid 133 through 135 removed outlier: 3.753A pdb=" N THR Q 140 " --> pdb=" O ASP Q 135 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Q' and resid 209 through 210 1281 hydrogen bonds defined for protein. 3540 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 147 hydrogen bonds 294 hydrogen bond angles 0 basepair planarities 58 basepair parallelities 99 stacking parallelities Total time for adding SS restraints: 9.19 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.55: 35439 1.55 - 1.88: 527 1.88 - 2.21: 0 2.21 - 2.54: 0 2.54 - 2.87: 1 Bond restraints: 35967 Sorted by residual: bond pdb=" C LYS D1090 " pdb=" N ARG D1097 " ideal model delta sigma weight residual 1.332 2.868 -1.535 1.40e-02 5.10e+03 1.20e+04 bond pdb=" C3' DA L 21 " pdb=" C2' DA L 21 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.25e+01 bond pdb=" C3' DG K 38 " pdb=" C2' DG K 38 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C1' DT L 60 " pdb=" N1 DT L 60 " ideal model delta sigma weight residual 1.468 1.514 -0.046 1.40e-02 5.10e+03 1.08e+01 bond pdb=" C1' DT L 53 " pdb=" N1 DT L 53 " ideal model delta sigma weight residual 1.468 1.511 -0.043 1.40e-02 5.10e+03 9.25e+00 ... (remaining 35962 not shown) Histogram of bond angle deviations from ideal: 0.00 - 15.21: 49430 15.21 - 30.42: 1 30.42 - 45.62: 0 45.62 - 60.83: 0 60.83 - 76.04: 1 Bond angle restraints: 49432 Sorted by residual: angle pdb=" O LYS D1090 " pdb=" C LYS D1090 " pdb=" N ARG D1097 " ideal model delta sigma weight residual 122.59 46.55 76.04 1.33e+00 5.65e-01 3.27e+03 angle pdb=" C LYS D1090 " pdb=" N ARG D1097 " pdb=" CA ARG D1097 " ideal model delta sigma weight residual 121.54 140.43 -18.89 1.91e+00 2.74e-01 9.79e+01 angle pdb=" O4' DA K 35 " pdb=" C4' DA K 35 " pdb=" C3' DA K 35 " ideal model delta sigma weight residual 106.00 102.82 3.18 6.00e-01 2.78e+00 2.81e+01 angle pdb=" C SER P 66 " pdb=" N THR P 67 " pdb=" CA THR P 67 " ideal model delta sigma weight residual 120.79 127.76 -6.97 1.39e+00 5.18e-01 2.51e+01 angle pdb=" C ASP P 182 " pdb=" N PHE P 183 " pdb=" CA PHE P 183 " ideal model delta sigma weight residual 121.70 130.49 -8.79 1.80e+00 3.09e-01 2.38e+01 ... (remaining 49427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.63: 20389 34.63 - 69.27: 1015 69.27 - 103.90: 49 103.90 - 138.53: 5 138.53 - 173.16: 6 Dihedral angle restraints: 21464 sinusoidal: 9569 harmonic: 11895 Sorted by residual: dihedral pdb=" CA LYS D1090 " pdb=" C LYS D1090 " pdb=" N ARG D1097 " pdb=" CA ARG D1097 " ideal model delta harmonic sigma weight residual -180.00 -138.74 -41.26 0 5.00e+00 4.00e-02 6.81e+01 dihedral pdb=" CA LEU P 64 " pdb=" C LEU P 64 " pdb=" N SER P 65 " pdb=" CA SER P 65 " ideal model delta harmonic sigma weight residual -180.00 -152.72 -27.28 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA ILE C1106 " pdb=" C ILE C1106 " pdb=" N VAL C1107 " pdb=" CA VAL C1107 " ideal model delta harmonic sigma weight residual 180.00 152.76 27.24 0 5.00e+00 4.00e-02 2.97e+01 ... (remaining 21461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 4320 0.049 - 0.099: 1029 0.099 - 0.148: 292 0.148 - 0.197: 71 0.197 - 0.246: 4 Chirality restraints: 5716 Sorted by residual: chirality pdb=" CB THR O 8 " pdb=" CA THR O 8 " pdb=" OG1 THR O 8 " pdb=" CG2 THR O 8 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" C3' DG K 66 " pdb=" C4' DG K 66 " pdb=" O3' DG K 66 " pdb=" C2' DG K 66 " both_signs ideal model delta sigma weight residual False -2.73 -2.51 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" C1' DG L 74 " pdb=" O4' DG L 74 " pdb=" C2' DG L 74 " pdb=" N9 DG L 74 " both_signs ideal model delta sigma weight residual False 2.43 2.21 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 5713 not shown) Planarity restraints: 5909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D1090 " 0.174 2.00e-02 2.50e+03 2.72e-01 7.38e+02 pdb=" C LYS D1090 " -0.434 2.00e-02 2.50e+03 pdb=" O LYS D1090 " 0.277 2.00e-02 2.50e+03 pdb=" N ARG D1097 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C1014 " -0.021 2.00e-02 2.50e+03 4.35e-02 1.89e+01 pdb=" C ARG C1014 " 0.075 2.00e-02 2.50e+03 pdb=" O ARG C1014 " -0.029 2.00e-02 2.50e+03 pdb=" N SER C1015 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 110 " -0.061 5.00e-02 4.00e+02 9.06e-02 1.31e+01 pdb=" N PRO D 111 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO D 111 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO D 111 " -0.051 5.00e-02 4.00e+02 ... (remaining 5906 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 533 2.53 - 3.12: 30518 3.12 - 3.72: 60066 3.72 - 4.31: 83563 4.31 - 4.90: 128278 Nonbonded interactions: 302958 Sorted by model distance: nonbonded pdb=" OP2 DT L 53 " pdb=" C7 DT L 53 " model vdw 1.940 3.460 nonbonded pdb=" O GLN O 121 " pdb=" NE2 GLN O 121 " model vdw 2.002 3.120 nonbonded pdb=" N2 DG L 18 " pdb=" O6 DG L 19 " model vdw 2.042 3.120 nonbonded pdb=" NE2 GLN D1109 " pdb=" O GLN D1110 " model vdw 2.077 3.120 nonbonded pdb=" OD1 ASP D 485 " pdb=" N VAL D 486 " model vdw 2.188 3.120 ... (remaining 302953 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 52 or (resid 153 through 154 and (name N or name CA or name C or name O or name \ CB )) or resid 155 through 157 or (resid 158 and (name N or name CA or name C or \ name O or name CB )) or resid 159 through 160 or (resid 161 and (name N or name \ CA or name C or name O or name CB )) or resid 162 through 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 through 223 o \ r (resid 224 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 25 through 226)) selection = (chain 'B' and resid 2 through 226) } ncs_group { reference = (chain 'N' and (resid 1 through 68 or (resid 69 and (name N or name CA or name C \ or name O or name CB )) or resid 70 through 113 or resid 124 through 128 or (re \ sid 129 and (name N or name CA or name C or name O or name CB )) or resid 130 th \ rough 135 or (resid 136 and (name N or name CA or name C or name O or name CB or \ name CG or name CD )) or resid 137 or (resid 138 and (name N or name CA or name \ C or name O or name CB )) or resid 139 or (resid 140 through 141 and (name N or \ name CA or name C or name O or name CB )) or (resid 142 through 143 and (name N \ or name CA or name C or name O or name CB or name CG )) or (resid 144 through 1 \ 46 and (name N or name CA or name C or name O or name CB )) or resid 147 or (res \ id 148 and (name N or name CA or name C or name O or name CB or name CG or name \ CD1)) or resid 149 or (resid 150 and (name N or name CA or name C or name O or n \ ame CB )) or resid 151 through 158 or (resid 159 and (name N or name CA or name \ C or name O or name CB )) or resid 160 through 162 or (resid 163 and (name N or \ name CA or name C or name O or name CB )) or resid 164 through 176 or (resid 177 \ and (name N or name CA or name C or name O or name CB or name CG )) or resid 17 \ 8 through 182 or (resid 183 through 184 and (name N or name CA or name C or name \ O or name CB )) or resid 185 through 219 or (resid 220 and (name N or name CA o \ r name C or name O or name CB or name CG1)) or (resid 221 through 223 and (name \ N or name CA or name C or name O or name CB )))) selection = (chain 'O' and (resid 1 through 68 or (resid 69 and (name N or name CA or name C \ or name O or name CB )) or resid 70 through 113 or resid 124 through 128 or (re \ sid 129 and (name N or name CA or name C or name O or name CB )) or resid 130 th \ rough 135 or (resid 136 and (name N or name CA or name C or name O or name CB or \ name CG or name CD )) or resid 137 or (resid 138 and (name N or name CA or name \ C or name O or name CB )) or resid 139 or (resid 140 through 141 and (name N or \ name CA or name C or name O or name CB )) or (resid 142 through 143 and (name N \ or name CA or name C or name O or name CB or name CG )) or (resid 144 through 1 \ 46 and (name N or name CA or name C or name O or name CB )) or resid 147 or (res \ id 148 and (name N or name CA or name C or name O or name CB or name CG or name \ CD1)) or resid 149 or (resid 150 and (name N or name CA or name C or name O or n \ ame CB )) or resid 151 through 158 or (resid 159 and (name N or name CA or name \ C or name O or name CB )) or resid 160 through 162 or (resid 163 and (name N or \ name CA or name C or name O or name CB )) or resid 164 through 166 or (resid 167 \ and (name N or name CA or name C or name O or name CB )) or resid 168 through 1 \ 72 or (resid 173 and (name N or name CA or name C or name O or name CB or name C \ G or name CD )) or resid 174 through 176 or (resid 177 and (name N or name CA or \ name C or name O or name CB or name CG )) or resid 178 through 183 or (resid 18 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 185 through \ 220 or (resid 221 through 223 and (name N or name CA or name C or name O or name \ CB )))) selection = (chain 'P' and (resid 1 through 128 or (resid 129 and (name N or name CA or name \ C or name O or name CB )) or resid 130 through 141 or (resid 142 through 143 an \ d (name N or name CA or name C or name O or name CB or name CG )) or resid 144 t \ hrough 153 or (resid 154 and (name N or name CA or name C or name O or name CB ) \ ) or resid 155 through 158 or (resid 159 and (name N or name CA or name C or nam \ e O or name CB )) or resid 160 through 166 or (resid 167 and (name N or name CA \ or name C or name O or name CB )) or resid 168 through 172 or (resid 173 and (na \ me N or name CA or name C or name O or name CB or name CG or name CD )) or resid \ 174 through 181 or (resid 182 through 184 and (name N or name CA or name C or n \ ame O or name CB )) or resid 185 through 211 or (resid 212 and (name N or name C \ A or name C or name O or name CB or name CG2)) or (resid 213 and (name N or name \ CA or name C or name O or name CB )) or resid 214 through 219 or (resid 220 and \ (name N or name CA or name C or name O or name CB or name CG1)) or resid 221 th \ rough 223)) selection = (chain 'Q' and (resid 1 through 68 or (resid 69 and (name N or name CA or name C \ or name O or name CB )) or resid 70 through 141 or (resid 142 through 143 and ( \ name N or name CA or name C or name O or name CB or name CG )) or (resid 144 thr \ ough 146 and (name N or name CA or name C or name O or name CB )) or resid 147 t \ hrough 153 or (resid 154 and (name N or name CA or name C or name O or name CB ) \ ) or resid 155 through 166 or (resid 167 and (name N or name CA or name C or nam \ e O or name CB )) or resid 168 through 172 or (resid 173 and (name N or name CA \ or name C or name O or name CB or name CG or name CD )) or resid 174 through 181 \ or (resid 182 through 184 and (name N or name CA or name C or name O or name CB \ )) or resid 185 through 211 or (resid 212 and (name N or name CA or name C or n \ ame O or name CB or name CG2)) or (resid 213 and (name N or name CA or name C or \ name O or name CB )) or resid 214 through 219 or (resid 220 and (name N or name \ CA or name C or name O or name CB or name CG1)) or resid 221 through 223)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 38.360 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4626 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 : 0.010 1.535 35973 Z= 0.671 Angle : 0.892 76.038 49438 Z= 0.587 Chirality : 0.049 0.246 5716 Planarity : 0.008 0.272 5909 Dihedral : 18.648 173.164 13816 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 21.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.32 % Favored : 90.63 % Rotamer: Outliers : 0.44 % Allowed : 1.95 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.93 (0.12), residues: 4129 helix: -1.55 (0.12), residues: 1457 sheet: -1.92 (0.24), residues: 409 loop : -2.24 (0.12), residues: 2263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P 109 TYR 0.019 0.002 TYR C1027 PHE 0.017 0.002 PHE D 226 TRP 0.018 0.002 TRP D 223 HIS 0.006 0.002 HIS D1150 Details of bonding type rmsd/Z covalent geometry : bond 0.00963 / 0.67 (35967) covalent geometry : angle 0.89080 / 0.59 (49432) hydrogen bonds : bond 0.21437 / 14.86 ( 1422) hydrogen bonds : angle 8.52927 / 5.87 ( 3834) metal coordination : bond 0.00775 / 0.42 ( 6) metal coordination : angle 4.61245 / 2.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8258 Ramachandran restraints generated. 4129 Oldfield, 0 Emsley, 4129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8258 Ramachandran restraints generated. 4129 Oldfield, 0 Emsley, 4129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 917 residues out of total 3491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 902 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 PHE cc_start: 0.6251 (m-80) cc_final: 0.5888 (m-80) REVERT: A 59 VAL cc_start: 0.5066 (t) cc_final: 0.4690 (p) REVERT: A 83 LEU cc_start: 0.6301 (mt) cc_final: 0.5635 (mm) REVERT: A 84 VAL cc_start: 0.4403 (t) cc_final: 0.3701 (t) REVERT: A 151 GLN cc_start: 0.6187 (mm110) cc_final: 0.5754 (mp10) REVERT: A 224 GLU cc_start: 0.5413 (tp30) cc_final: 0.4970 (mt-10) REVERT: B 43 LEU cc_start: 0.7537 (mp) cc_final: 0.7116 (mt) REVERT: B 44 SER cc_start: 0.6488 (m) cc_final: 0.6158 (p) REVERT: B 112 PRO cc_start: 0.4168 (Cg_endo) cc_final: 0.3670 (Cg_exo) REVERT: B 225 LEU cc_start: 0.6520 (mt) cc_final: 0.6133 (tp) REVERT: C 62 GLU cc_start: 0.6501 (mm-30) cc_final: 0.6268 (mt-10) REVERT: C 88 GLU cc_start: 0.6841 (tt0) cc_final: 0.6379 (tt0) REVERT: C 181 ARG cc_start: 0.5562 (mtt90) cc_final: 0.5362 (mpt-90) REVERT: C 258 MET cc_start: 0.3061 (mmm) cc_final: 0.2540 (mpp) REVERT: C 300 PHE cc_start: 0.4390 (m-80) cc_final: 0.4106 (m-10) REVERT: C 305 ARG cc_start: 0.3203 (mtt-85) cc_final: 0.2545 (ttm-80) REVERT: C 328 ILE cc_start: 0.5362 (mt) cc_final: 0.4844 (mm) REVERT: C 342 ILE cc_start: 0.5249 (mt) cc_final: 0.5033 (tt) REVERT: C 355 MET cc_start: 0.2479 (tmm) cc_final: 0.0750 (tmm) REVERT: C 405 THR cc_start: 0.5855 (m) cc_final: 0.5561 (p) REVERT: C 440 MET cc_start: 0.5153 (tpt) cc_final: 0.4947 (tpt) REVERT: C 597 LEU cc_start: 0.6293 (tp) cc_final: 0.5947 (tp) REVERT: C 616 VAL cc_start: 0.6454 (t) cc_final: 0.6070 (m) REVERT: C 650 ILE cc_start: 0.5770 (mm) cc_final: 0.5517 (mm) REVERT: C 740 ARG cc_start: 0.3591 (mtt180) cc_final: 0.3349 (ttp80) REVERT: C 748 THR cc_start: 0.4705 (m) cc_final: 0.4246 (t) REVERT: C 756 GLU cc_start: 0.6756 (tt0) cc_final: 0.6337 (tp30) REVERT: C 809 LYS cc_start: 0.4484 (tttt) cc_final: 0.4221 (ttpt) REVERT: C 841 HIS cc_start: 0.5622 (m-70) cc_final: 0.5147 (m-70) REVERT: C 865 VAL cc_start: 0.4514 (t) cc_final: 0.4140 (p) REVERT: C 889 HIS cc_start: 0.5395 (m-70) cc_final: 0.4918 (m90) REVERT: C 891 ASN cc_start: 0.4662 (p0) cc_final: 0.4414 (p0) REVERT: C 1007 LYS cc_start: 0.5781 (mtmt) cc_final: 0.5349 (mmmm) REVERT: C 1024 THR cc_start: 0.4512 (m) cc_final: 0.3693 (m) REVERT: C 1060 LYS cc_start: 0.4233 (tttm) cc_final: 0.4012 (tptt) REVERT: C 1094 ASP cc_start: 0.4702 (m-30) cc_final: 0.3840 (m-30) REVERT: D 6 PHE cc_start: 0.4008 (t80) cc_final: 0.3683 (t80) REVERT: D 34 ILE cc_start: 0.7362 (mm) cc_final: 0.7011 (mt) REVERT: D 70 PHE cc_start: 0.5228 (m-80) cc_final: 0.4955 (m-80) REVERT: D 106 TYR cc_start: 0.5556 (m-80) cc_final: 0.5217 (m-80) REVERT: D 137 THR cc_start: 0.5582 (m) cc_final: 0.5338 (m) REVERT: D 155 MET cc_start: 0.5082 (tpp) cc_final: 0.3680 (tmm) REVERT: D 210 ASP cc_start: 0.5737 (t0) cc_final: 0.5275 (m-30) REVERT: D 219 LEU cc_start: 0.5078 (tt) cc_final: 0.4853 (mt) REVERT: D 222 ILE cc_start: 0.4774 (tt) cc_final: 0.4529 (tt) REVERT: D 236 VAL cc_start: 0.5535 (m) cc_final: 0.4934 (m) REVERT: D 273 GLU cc_start: 0.5807 (tt0) cc_final: 0.5363 (tp30) REVERT: D 278 ARG cc_start: 0.5167 (mpt-90) cc_final: 0.4898 (mtt90) REVERT: D 315 ASP cc_start: 0.4956 (p0) cc_final: 0.4519 (t0) REVERT: D 360 LEU cc_start: 0.6049 (tp) cc_final: 0.5672 (mt) REVERT: D 363 PRO cc_start: 0.6681 (Cg_endo) cc_final: 0.6277 (Cg_exo) REVERT: D 373 MET cc_start: 0.6442 (mtm) cc_final: 0.6115 (mtm) REVERT: D 407 LYS cc_start: 0.5473 (mtmt) cc_final: 0.5272 (tttm) REVERT: D 409 LYS cc_start: 0.3689 (mttm) cc_final: 0.3119 (tttt) REVERT: D 457 MET cc_start: 0.4985 (tpp) cc_final: 0.4705 (mmt) REVERT: D 503 THR cc_start: 0.6031 (p) cc_final: 0.4946 (p) REVERT: D 505 HIS cc_start: 0.5543 (p90) cc_final: 0.5156 (p-80) REVERT: D 523 GLN cc_start: 0.6360 (mt0) cc_final: 0.5791 (mm-40) REVERT: D 537 ASP cc_start: 0.5867 (p0) cc_final: 0.5664 (p0) REVERT: D 550 GLU cc_start: 0.6610 (mt-10) cc_final: 0.6153 (mt-10) REVERT: D 568 PRO cc_start: 0.5476 (Cg_endo) cc_final: 0.5265 (Cg_exo) REVERT: D 583 THR cc_start: 0.6858 (m) cc_final: 0.6474 (p) REVERT: D 641 ARG cc_start: 0.5659 (ttt180) cc_final: 0.5364 (ttt-90) REVERT: D 732 SER cc_start: 0.4819 (t) cc_final: 0.4556 (p) REVERT: D 757 GLU cc_start: 0.5477 (tp30) cc_final: 0.5222 (mt-10) REVERT: D 820 MET cc_start: 0.5043 (ttt) cc_final: 0.4719 (tpp) REVERT: D 862 ASP cc_start: 0.5171 (m-30) cc_final: 0.4952 (m-30) REVERT: D 883 ASP cc_start: 0.6983 (m-30) cc_final: 0.6762 (t70) REVERT: D 983 MET cc_start: 0.3850 (mmp) cc_final: 0.3432 (mmm) REVERT: D 1077 TYR cc_start: 0.3909 (m-80) cc_final: 0.3234 (m-10) REVERT: D 1111 LEU cc_start: 0.5327 (mt) cc_final: 0.4730 (mp) REVERT: D 1208 MET cc_start: 0.5478 (pmm) cc_final: 0.5056 (pmm) REVERT: E 64 ILE cc_start: 0.5971 (mt) cc_final: 0.5715 (mt) REVERT: F 210 GLU cc_start: 0.3014 (tm-30) cc_final: 0.2722 (tp30) REVERT: F 240 LEU cc_start: 0.5477 (mt) cc_final: 0.5034 (tt) REVERT: F 242 ASN cc_start: 0.4958 (p0) cc_final: 0.4652 (p0) REVERT: F 263 MET cc_start: 0.5133 (tmm) cc_final: 0.4911 (tpp) REVERT: F 283 TRP cc_start: 0.5685 (t60) cc_final: 0.5414 (t60) REVERT: F 285 CYS cc_start: 0.4079 (m) cc_final: 0.3532 (m) REVERT: F 296 LEU cc_start: 0.6357 (mt) cc_final: 0.5933 (mt) REVERT: F 308 LYS cc_start: 0.6858 (ptpt) cc_final: 0.6603 (mttt) REVERT: F 343 PHE cc_start: 0.5145 (t80) cc_final: 0.4658 (t80) REVERT: F 425 GLN cc_start: 0.4637 (pt0) cc_final: 0.4302 (pt0) REVERT: F 453 PHE cc_start: 0.4909 (t80) cc_final: 0.4617 (t80) REVERT: O 146 ARG cc_start: 0.4450 (ptp90) cc_final: 0.4219 (ptt-90) REVERT: O 191 ASP cc_start: 0.6364 (m-30) cc_final: 0.5876 (m-30) REVERT: P 93 GLU cc_start: 0.1034 (mm-30) cc_final: 0.0760 (mp0) REVERT: P 169 PHE cc_start: 0.4993 (m-10) cc_final: 0.4427 (m-80) REVERT: N 193 HIS cc_start: 0.2730 (m-70) cc_final: 0.2260 (t-90) outliers start: 15 outliers final: 3 residues processed: 913 average time/residue: 0.2477 time to fit residues: 347.2408 Evaluate side-chains 424 residues out of total 3491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 421 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain O residue 220 VAL Chi-restraints excluded: chain P residue 148 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 9.9990 chunk 401 optimal weight: 7.9990 chunk 424 optimal weight: 6.9990 chunk 155 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 ASN B 124 HIS C 247 GLN C 375 ASN C 386 GLN C 603 ASN C 680 HIS C 700 GLN ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 920 HIS C 941 HIS ** C 981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 687 GLN D 854 HIS D1110 GLN D1131 GLN E 63 GLN F 261 GLN F 294 HIS F 299 ASN F 461 GLN P 42 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.134957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.108610 restraints weight = 125668.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.106344 restraints weight = 94445.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.107224 restraints weight = 90092.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.107563 restraints weight = 69482.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.107551 restraints weight = 62389.526| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5493 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 35973 Z= 0.250 Angle : 0.870 14.415 49438 Z= 0.460 Chirality : 0.054 0.335 5716 Planarity : 0.008 0.086 5909 Dihedral : 19.992 177.087 6219 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.54 % Favored : 93.44 % Rotamer: Outliers : 2.69 % Allowed : 13.80 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.12), residues: 4131 helix: -1.10 (0.12), residues: 1552 sheet: -1.97 (0.23), residues: 437 loop : -2.13 (0.12), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 482 TYR 0.026 0.003 TYR C 480 PHE 0.029 0.003 PHE D 252 TRP 0.019 0.003 TRP D 223 HIS 0.013 0.003 HIS C 479 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.25 (35967) covalent geometry : angle 0.87001 / 0.46 (49432) hydrogen bonds : bond 0.06435 / 4.28 ( 1422) hydrogen bonds : angle 6.37163 / 4.36 ( 3834) metal coordination : bond 0.00498 / 0.25 ( 6) metal coordination : angle 2.65753 / 1.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8262 Ramachandran restraints generated. 4131 Oldfield, 0 Emsley, 4131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8262 Ramachandran restraints generated. 4131 Oldfield, 0 Emsley, 4131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 3491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 471 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.5185 (mt-10) cc_final: 0.4985 (pm20) REVERT: A 151 GLN cc_start: 0.5444 (mm110) cc_final: 0.5174 (mm110) REVERT: A 217 GLU cc_start: 0.4846 (mm-30) cc_final: 0.4516 (mm-30) REVERT: B 162 ILE cc_start: 0.6002 (mp) cc_final: 0.5504 (tt) REVERT: B 168 TYR cc_start: 0.6934 (m-10) cc_final: 0.6691 (m-80) REVERT: B 225 LEU cc_start: 0.6723 (mt) cc_final: 0.6460 (mt) REVERT: C 57 GLN cc_start: 0.6819 (mm110) cc_final: 0.6619 (mm-40) REVERT: C 124 ASP cc_start: 0.5144 (t70) cc_final: 0.4859 (t0) REVERT: C 258 MET cc_start: 0.3097 (mmm) cc_final: 0.2710 (mmt) REVERT: C 300 PHE cc_start: 0.4393 (m-80) cc_final: 0.3874 (m-10) REVERT: C 305 ARG cc_start: 0.2959 (mtt-85) cc_final: 0.2330 (ttm-80) REVERT: C 307 ASP cc_start: 0.3026 (OUTLIER) cc_final: 0.2751 (m-30) REVERT: C 355 MET cc_start: 0.1561 (tmm) cc_final: 0.0420 (tmm) REVERT: C 404 MET cc_start: 0.4814 (ttm) cc_final: 0.4570 (tpp) REVERT: C 440 MET cc_start: 0.7287 (tpt) cc_final: 0.6625 (tpt) REVERT: C 496 LEU cc_start: 0.8025 (mp) cc_final: 0.7773 (mp) REVERT: C 593 MET cc_start: 0.6749 (mtt) cc_final: 0.6508 (mtt) REVERT: C 618 LEU cc_start: 0.6855 (mt) cc_final: 0.6449 (mp) REVERT: C 747 LEU cc_start: 0.7523 (tt) cc_final: 0.7033 (tp) REVERT: C 809 LYS cc_start: 0.4609 (tttt) cc_final: 0.4192 (tmmt) REVERT: C 839 VAL cc_start: 0.4068 (t) cc_final: 0.3825 (t) REVERT: C 846 LYS cc_start: 0.6112 (mmtp) cc_final: 0.5130 (mmtp) REVERT: C 1009 MET cc_start: 0.3691 (OUTLIER) cc_final: 0.3316 (mpp) REVERT: C 1042 HIS cc_start: 0.5904 (t70) cc_final: 0.5529 (t70) REVERT: C 1124 LEU cc_start: 0.3047 (tp) cc_final: 0.2650 (tp) REVERT: D 6 PHE cc_start: 0.4694 (t80) cc_final: 0.4272 (t80) REVERT: D 155 MET cc_start: 0.5347 (tpp) cc_final: 0.4641 (tmm) REVERT: D 211 ARG cc_start: 0.3959 (mmt-90) cc_final: 0.2750 (mtm-85) REVERT: D 223 TRP cc_start: 0.4286 (t-100) cc_final: 0.4062 (t-100) REVERT: D 383 ASP cc_start: 0.5831 (t70) cc_final: 0.5547 (t0) REVERT: D 409 LYS cc_start: 0.5538 (mttm) cc_final: 0.3716 (tttt) REVERT: D 440 GLN cc_start: 0.8108 (mt0) cc_final: 0.7521 (mt0) REVERT: D 450 GLU cc_start: 0.6921 (tp30) cc_final: 0.6334 (tp30) REVERT: D 505 HIS cc_start: 0.6959 (p90) cc_final: 0.6755 (p90) REVERT: D 541 MET cc_start: 0.7543 (OUTLIER) cc_final: 0.7086 (mmm) REVERT: D 665 GLU cc_start: 0.6107 (pm20) cc_final: 0.5863 (pt0) REVERT: D 688 MET cc_start: 0.7293 (mmp) cc_final: 0.6912 (mmt) REVERT: D 862 ASP cc_start: 0.6092 (m-30) cc_final: 0.5254 (m-30) REVERT: D 1005 GLU cc_start: 0.6374 (tm-30) cc_final: 0.6165 (tt0) REVERT: D 1077 TYR cc_start: 0.4804 (m-80) cc_final: 0.4169 (m-10) REVERT: E 67 TYR cc_start: 0.6906 (t80) cc_final: 0.6632 (t80) REVERT: F 242 ASN cc_start: 0.4493 (p0) cc_final: 0.4265 (p0) REVERT: F 248 GLU cc_start: 0.6520 (tt0) cc_final: 0.6201 (mt-10) REVERT: F 263 MET cc_start: 0.5453 (tmm) cc_final: 0.5253 (tpp) REVERT: F 297 GLU cc_start: 0.6887 (mt-10) cc_final: 0.6591 (mt-10) REVERT: F 453 PHE cc_start: 0.6035 (t80) cc_final: 0.5759 (t80) REVERT: F 456 LEU cc_start: 0.7030 (mt) cc_final: 0.6732 (tp) REVERT: O 139 TYR cc_start: 0.5391 (t80) cc_final: 0.4697 (t80) REVERT: O 146 ARG cc_start: 0.4736 (ptp90) cc_final: 0.4514 (ptt-90) REVERT: O 155 PHE cc_start: 0.6174 (t80) cc_final: 0.5674 (t80) REVERT: P 169 PHE cc_start: 0.4695 (m-10) cc_final: 0.4404 (m-80) REVERT: N 107 ARG cc_start: 0.0548 (mmt-90) cc_final: 0.0204 (mmt180) REVERT: N 146 ARG cc_start: 0.0091 (pmt-80) cc_final: -0.1029 (ptt-90) REVERT: N 193 HIS cc_start: 0.3034 (m-70) cc_final: 0.2786 (m90) outliers start: 91 outliers final: 54 residues processed: 538 average time/residue: 0.2192 time to fit residues: 188.4776 Evaluate side-chains 371 residues out of total 3491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 314 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 383 GLU Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 754 GLU Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 930 GLN Chi-restraints excluded: chain C residue 1009 MET Chi-restraints excluded: chain C residue 1120 SER Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 879 ASP Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 919 SER Chi-restraints excluded: chain D residue 965 VAL Chi-restraints excluded: chain D residue 1041 ARG Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain D residue 1254 ILE Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 501 GLU Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 192 VAL Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 215 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 361 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 365 optimal weight: 6.9990 chunk 246 optimal weight: 0.0270 chunk 28 optimal weight: 0.0040 chunk 45 optimal weight: 0.9980 chunk 57 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 chunk 12 optimal weight: 0.0040 chunk 264 optimal weight: 6.9990 chunk 223 optimal weight: 4.9990 overall best weight: 1.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 438 GLN C 612 GLN C 679 ASN C 718 ASN C 775 ASN C 875 GLN C 981 GLN D 262 GLN D 375 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 674 ASN D1139 GLN ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 164 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.135437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.108663 restraints weight = 124991.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.107081 restraints weight = 89625.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.107912 restraints weight = 75950.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.108079 restraints weight = 64932.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.108300 restraints weight = 55170.073| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5475 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 35973 Z= 0.140 Angle : 0.682 13.229 49438 Z= 0.361 Chirality : 0.047 0.358 5716 Planarity : 0.005 0.058 5909 Dihedral : 19.659 176.957 6218 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.16 % Allowed : 16.25 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.12), residues: 4131 helix: -0.66 (0.13), residues: 1575 sheet: -1.78 (0.23), residues: 443 loop : -1.86 (0.13), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 159 TYR 0.025 0.001 TYR F 231 PHE 0.025 0.001 PHE D 252 TRP 0.031 0.002 TRP N 179 HIS 0.008 0.001 HIS N 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 (35967) covalent geometry : angle 0.68200 / 0.36 (49432) hydrogen bonds : bond 0.05059 / 3.41 ( 1422) hydrogen bonds : angle 5.80522 / 4.00 ( 3834) metal coordination : bond 0.00124 / 0.06 ( 6) metal coordination : angle 1.72890 / 0.63 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8262 Ramachandran restraints generated. 4131 Oldfield, 0 Emsley, 4131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8262 Ramachandran restraints generated. 4131 Oldfield, 0 Emsley, 4131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 3491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 401 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 GLU cc_start: 0.4770 (mm-30) cc_final: 0.4440 (mm-30) REVERT: B 133 LYS cc_start: 0.2524 (tptt) cc_final: 0.2317 (mttt) REVERT: C 103 MET cc_start: 0.3239 (OUTLIER) cc_final: 0.2997 (ptt) REVERT: C 189 GLU cc_start: 0.5297 (pt0) cc_final: 0.5091 (pt0) REVERT: C 300 PHE cc_start: 0.4340 (m-80) cc_final: 0.3814 (m-10) REVERT: C 305 ARG cc_start: 0.3257 (mtt-85) cc_final: 0.3026 (mtp85) REVERT: C 342 ILE cc_start: 0.5563 (mm) cc_final: 0.4994 (tp) REVERT: C 355 MET cc_start: 0.1632 (tmm) cc_final: 0.0819 (tmm) REVERT: C 440 MET cc_start: 0.7411 (tpt) cc_final: 0.6687 (tpt) REVERT: C 474 ASP cc_start: 0.5771 (OUTLIER) cc_final: 0.5284 (m-30) REVERT: C 519 VAL cc_start: 0.0528 (OUTLIER) cc_final: 0.0203 (p) REVERT: C 528 ILE cc_start: 0.7094 (mm) cc_final: 0.6888 (mm) REVERT: C 579 MET cc_start: 0.4087 (ppp) cc_final: 0.3886 (ppp) REVERT: C 618 LEU cc_start: 0.6607 (mt) cc_final: 0.6140 (mp) REVERT: C 636 ILE cc_start: 0.7460 (pt) cc_final: 0.7131 (mt) REVERT: C 809 LYS cc_start: 0.4649 (tttt) cc_final: 0.4133 (ttpt) REVERT: C 846 LYS cc_start: 0.5849 (mmtp) cc_final: 0.5315 (mttp) REVERT: C 875 GLN cc_start: 0.5985 (OUTLIER) cc_final: 0.5651 (pt0) REVERT: C 939 CYS cc_start: 0.3240 (OUTLIER) cc_final: 0.2875 (m) REVERT: C 981 GLN cc_start: 0.5423 (OUTLIER) cc_final: 0.5207 (tm-30) REVERT: C 1042 HIS cc_start: 0.5889 (t70) cc_final: 0.5580 (t70) REVERT: D 6 PHE cc_start: 0.4655 (t80) cc_final: 0.4401 (t80) REVERT: D 155 MET cc_start: 0.5186 (tpp) cc_final: 0.4825 (tmm) REVERT: D 211 ARG cc_start: 0.3424 (mmt-90) cc_final: 0.3003 (mtm-85) REVERT: D 368 ASN cc_start: 0.5939 (m-40) cc_final: 0.5714 (m110) REVERT: D 383 ASP cc_start: 0.5785 (t70) cc_final: 0.5537 (t0) REVERT: D 409 LYS cc_start: 0.4666 (mttm) cc_final: 0.3548 (tttt) REVERT: D 414 ARG cc_start: 0.6455 (mtp-110) cc_final: 0.6242 (mtp-110) REVERT: D 440 GLN cc_start: 0.8186 (mt0) cc_final: 0.7653 (mt0) REVERT: D 450 GLU cc_start: 0.7146 (tp30) cc_final: 0.6579 (tp30) REVERT: D 505 HIS cc_start: 0.6810 (p90) cc_final: 0.6583 (p90) REVERT: D 541 MET cc_start: 0.7356 (OUTLIER) cc_final: 0.7046 (mmm) REVERT: D 630 ARG cc_start: 0.7030 (ptm160) cc_final: 0.6567 (mtm180) REVERT: D 663 MET cc_start: 0.5863 (tpp) cc_final: 0.4993 (mmm) REVERT: D 688 MET cc_start: 0.7474 (mmp) cc_final: 0.7206 (mmt) REVERT: D 862 ASP cc_start: 0.5943 (m-30) cc_final: 0.4823 (m-30) REVERT: D 1077 TYR cc_start: 0.4889 (m-80) cc_final: 0.4274 (m-10) REVERT: D 1085 ARG cc_start: 0.5525 (mtp-110) cc_final: 0.5161 (mtp180) REVERT: E 55 ILE cc_start: 0.7604 (mm) cc_final: 0.7279 (mm) REVERT: E 70 GLN cc_start: 0.3478 (pt0) cc_final: 0.3240 (mt0) REVERT: F 240 LEU cc_start: 0.4156 (mt) cc_final: 0.3688 (tt) REVERT: F 263 MET cc_start: 0.5024 (tmm) cc_final: 0.4821 (tpp) REVERT: F 283 TRP cc_start: 0.5794 (t60) cc_final: 0.5559 (t60) REVERT: F 297 GLU cc_start: 0.6830 (mt-10) cc_final: 0.6583 (mt-10) REVERT: F 392 ARG cc_start: 0.4048 (ttp80) cc_final: 0.3829 (tmm160) REVERT: F 453 PHE cc_start: 0.6116 (t80) cc_final: 0.5386 (t80) REVERT: O 146 ARG cc_start: 0.4753 (ptp90) cc_final: 0.4543 (ptt-90) REVERT: O 155 PHE cc_start: 0.5984 (t80) cc_final: 0.5325 (t80) REVERT: P 169 PHE cc_start: 0.4601 (m-10) cc_final: 0.4391 (m-80) REVERT: P 188 ARG cc_start: 0.5107 (ptm160) cc_final: 0.3935 (ttp80) REVERT: N 107 ARG cc_start: 0.0559 (mmt-90) cc_final: 0.0245 (mmt180) REVERT: N 146 ARG cc_start: 0.0166 (pmt-80) cc_final: -0.0798 (ptt-90) outliers start: 107 outliers final: 47 residues processed: 478 average time/residue: 0.2426 time to fit residues: 186.2555 Evaluate side-chains 365 residues out of total 3491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 311 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 383 GLU Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 630 MET Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 718 ASN Chi-restraints excluded: chain C residue 754 GLU Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 875 GLN Chi-restraints excluded: chain C residue 939 CYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 981 GLN Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 730 THR Chi-restraints excluded: chain D residue 879 ASP Chi-restraints excluded: chain D residue 916 ILE Chi-restraints excluded: chain D residue 919 SER Chi-restraints excluded: chain D residue 1041 ARG Chi-restraints excluded: chain D residue 1106 GLU Chi-restraints excluded: chain D residue 1194 VAL Chi-restraints excluded: chain D residue 1254 ILE Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 192 VAL Chi-restraints excluded: chain N residue 158 LEU Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 215 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 249 optimal weight: 0.3980 chunk 355 optimal weight: 20.0000 chunk 340 optimal weight: 50.0000 chunk 242 optimal weight: 20.0000 chunk 372 optimal weight: 30.0000 chunk 38 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 45 optimal weight: 20.0000 chunk 176 optimal weight: 10.0000 chunk 172 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 overall best weight: 6.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 79 ASN ** C 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 612 GLN C 679 ASN C 981 GLN ** C1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 639 GLN D 767 HIS D1269 ASN ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 25 HIS ** N 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 193 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.132560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.105353 restraints weight = 123595.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.103852 restraints weight = 90995.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.104230 restraints weight = 74319.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.104496 restraints weight = 67416.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.104732 restraints weight = 56787.291| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5598 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.151 35973 Z= 0.240 Angle : 0.833 11.893 49438 Z= 0.439 Chirality : 0.052 0.357 5716 Planarity : 0.007 0.068 5909 Dihedral : 19.758 179.394 6218 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.19 % Favored : 92.76 % Rotamer: Outliers : 4.70 % Allowed : 19.03 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.12), residues: 4131 helix: -0.87 (0.12), residues: 1587 sheet: -1.83 (0.23), residues: 454 loop : -1.97 (0.13), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 480 TYR 0.032 0.003 TYR F 346 PHE 0.035 0.003 PHE F 335 TRP 0.046 0.003 TRP O 179 HIS 0.013 0.002 HIS C 479 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.24 (35967) covalent geometry : angle 0.83249 / 0.44 (49432) hydrogen bonds : bond 0.05521 / 3.72 ( 1422) hydrogen bonds : angle 5.85339 / 4.04 ( 3834) metal coordination : bond 0.00515 / 0.30 ( 6) metal coordination : angle 1.93798 / 0.82 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8262 Ramachandran restraints generated. 4131 Oldfield, 0 Emsley, 4131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8262 Ramachandran restraints generated. 4131 Oldfield, 0 Emsley, 4131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 3491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 349 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.5062 (mt-10) cc_final: 0.4586 (mt-10) REVERT: A 95 MET cc_start: 0.7086 (mtm) cc_final: 0.6884 (ttm) REVERT: A 151 GLN cc_start: 0.6125 (mm110) cc_final: 0.5519 (mp10) REVERT: B 46 ILE cc_start: 0.7015 (mm) cc_final: 0.6397 (mt) REVERT: B 60 LEU cc_start: 0.4421 (tp) cc_final: 0.4219 (tt) REVERT: B 85 VAL cc_start: 0.6650 (OUTLIER) cc_final: 0.6313 (p) REVERT: C 300 PHE cc_start: 0.4777 (m-80) cc_final: 0.4240 (m-10) REVERT: C 305 ARG cc_start: 0.3184 (mtt-85) cc_final: 0.2564 (ttm-80) REVERT: C 355 MET cc_start: 0.1640 (tmm) cc_final: 0.0936 (tmm) REVERT: C 440 MET cc_start: 0.7513 (tpt) cc_final: 0.6989 (tpt) REVERT: C 474 ASP cc_start: 0.5946 (OUTLIER) cc_final: 0.5284 (m-30) REVERT: C 500 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7155 (tp) REVERT: C 519 VAL cc_start: 0.1222 (OUTLIER) cc_final: 0.0955 (p) REVERT: C 747 LEU cc_start: 0.7403 (tt) cc_final: 0.6747 (tp) REVERT: C 846 LYS cc_start: 0.6671 (mmtp) cc_final: 0.6108 (mttp) REVERT: C 981 GLN cc_start: 0.6364 (OUTLIER) cc_final: 0.6118 (mm-40) REVERT: C 993 LEU cc_start: 0.4051 (OUTLIER) cc_final: 0.3259 (tt) REVERT: C 1009 MET cc_start: 0.4649 (tmm) cc_final: 0.4287 (pmm) REVERT: C 1042 HIS cc_start: 0.5921 (t70) cc_final: 0.5657 (t70) REVERT: C 1051 MET cc_start: 0.6532 (tpt) cc_final: 0.6210 (tpp) REVERT: D 6 PHE cc_start: 0.5069 (t80) cc_final: 0.4734 (t80) REVERT: D 155 MET cc_start: 0.5108 (tpp) cc_final: 0.4415 (tmm) REVERT: D 211 ARG cc_start: 0.3821 (mmt-90) cc_final: 0.3364 (mtm-85) REVERT: D 383 ASP cc_start: 0.6023 (t70) cc_final: 0.5749 (t0) REVERT: D 407 LYS cc_start: 0.5625 (mtmt) cc_final: 0.5419 (tptm) REVERT: D 450 GLU cc_start: 0.6963 (tp30) cc_final: 0.6541 (tp30) REVERT: D 541 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7206 (mmm) REVERT: D 630 ARG cc_start: 0.7222 (ptm160) cc_final: 0.6761 (mtm180) REVERT: D 688 MET cc_start: 0.7546 (mmp) cc_final: 0.7325 (mmp) REVERT: D 862 ASP cc_start: 0.6482 (m-30) cc_final: 0.6183 (m-30) REVERT: D 1084 GLN cc_start: 0.3701 (mm-40) cc_final: 0.3333 (mt0) REVERT: D 1085 ARG cc_start: 0.5765 (mtp-110) cc_final: 0.5205 (mtp180) REVERT: E 55 ILE cc_start: 0.7697 (mm) cc_final: 0.7386 (mm) REVERT: F 263 MET cc_start: 0.5361 (tmm) cc_final: 0.5154 (tpp) REVERT: F 297 GLU cc_start: 0.6838 (mt-10) cc_final: 0.6384 (mt-10) REVERT: F 359 MET cc_start: 0.6285 (mtp) cc_final: 0.5952 (mtm) REVERT: F 453 PHE cc_start: 0.6474 (t80) cc_final: 0.6269 (t80) REVERT: O 152 TYR cc_start: 0.5536 (t80) cc_final: 0.5239 (t80) REVERT: O 155 PHE cc_start: 0.5884 (t80) cc_final: 0.5322 (t80) REVERT: P 188 ARG cc_start: 0.4897 (ptm160) cc_final: 0.3971 (ttp80) REVERT: N 82 LEU cc_start: 0.1102 (mt) cc_final: 0.0771 (pp) REVERT: N 107 ARG cc_start: 0.0620 (mmt-90) cc_final: 0.0212 (mmt180) REVERT: N 146 ARG cc_start: 0.0229 (pmt-80) cc_final: -0.0959 (ptt-90) REVERT: Q 190 VAL cc_start: 0.1052 (m) cc_final: 0.0746 (m) outliers start: 159 outliers final: 91 residues processed: 486 average time/residue: 0.2299 time to fit residues: 182.6990 Evaluate side-chains 385 residues out of total 3491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 287 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 383 GLU Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 715 LEU Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 770 THR Chi-restraints excluded: chain C residue 832 VAL Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 898 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 981 GLN Chi-restraints excluded: chain C residue 993 LEU Chi-restraints excluded: chain C residue 1100 VAL Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain C residue 1139 SER Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 632 LYS Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 660 ASP Chi-restraints excluded: chain D residue 700 LEU Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 879 ASP Chi-restraints excluded: chain D residue 919 SER Chi-restraints excluded: chain D residue 965 VAL Chi-restraints excluded: chain D residue 1041 ARG Chi-restraints excluded: chain D residue 1124 VAL Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1194 VAL Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain D residue 1254 ILE Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 498 VAL Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 192 VAL Chi-restraints excluded: chain N residue 158 LEU Chi-restraints excluded: chain N residue 170 THR Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 76 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 82 optimal weight: 6.9990 chunk 166 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 350 optimal weight: 0.0670 chunk 235 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 340 optimal weight: 50.0000 chunk 295 optimal weight: 20.0000 chunk 364 optimal weight: 0.7980 chunk 234 optimal weight: 20.0000 chunk 37 optimal weight: 0.8980 overall best weight: 1.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 HIS C 539 HIS C 679 ASN C 718 ASN C 751 HIS D 368 ASN ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1139 GLN ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 294 HIS ** F 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 214 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.133333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.105976 restraints weight = 122409.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.104581 restraints weight = 87609.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.105143 restraints weight = 72035.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.105265 restraints weight = 65987.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.105342 restraints weight = 56920.681| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5582 moved from start: 0.5223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35973 Z= 0.140 Angle : 0.666 13.052 49438 Z= 0.353 Chirality : 0.046 0.357 5716 Planarity : 0.005 0.076 5909 Dihedral : 19.503 177.737 6218 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.43 % Allowed : 21.18 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.12), residues: 4131 helix: -0.48 (0.13), residues: 1588 sheet: -1.66 (0.23), residues: 470 loop : -1.81 (0.13), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 515 TYR 0.025 0.001 TYR F 231 PHE 0.021 0.002 PHE D 252 TRP 0.026 0.002 TRP D 223 HIS 0.010 0.001 HIS F 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (35967) covalent geometry : angle 0.66572 / 0.35 (49432) hydrogen bonds : bond 0.04523 / 3.07 ( 1422) hydrogen bonds : angle 5.44889 / 3.76 ( 3834) metal coordination : bond 0.00297 / 0.15 ( 6) metal coordination : angle 1.13082 / 0.42 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8262 Ramachandran restraints generated. 4131 Oldfield, 0 Emsley, 4131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8262 Ramachandran restraints generated. 4131 Oldfield, 0 Emsley, 4131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 336 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ILE cc_start: 0.7767 (OUTLIER) cc_final: 0.7561 (tt) REVERT: A 151 GLN cc_start: 0.6151 (mm110) cc_final: 0.5517 (mp10) REVERT: B 1 MET cc_start: 0.3611 (tpp) cc_final: 0.3375 (tpp) REVERT: B 26 LEU cc_start: 0.7861 (mt) cc_final: 0.7659 (mt) REVERT: B 46 ILE cc_start: 0.7071 (mm) cc_final: 0.6476 (mt) REVERT: B 56 ILE cc_start: 0.6691 (OUTLIER) cc_final: 0.6426 (tp) REVERT: B 85 VAL cc_start: 0.6524 (OUTLIER) cc_final: 0.6143 (p) REVERT: B 190 ASP cc_start: 0.6233 (p0) cc_final: 0.5593 (p0) REVERT: C 132 PRO cc_start: 0.6419 (Cg_endo) cc_final: 0.5993 (Cg_exo) REVERT: C 146 GLU cc_start: 0.4179 (OUTLIER) cc_final: 0.3274 (tt0) REVERT: C 300 PHE cc_start: 0.4771 (m-80) cc_final: 0.4235 (m-10) REVERT: C 305 ARG cc_start: 0.3215 (mtt-85) cc_final: 0.2651 (ttm-80) REVERT: C 342 ILE cc_start: 0.5796 (mm) cc_final: 0.5164 (tp) REVERT: C 355 MET cc_start: 0.1506 (tmm) cc_final: 0.0889 (tmm) REVERT: C 440 MET cc_start: 0.7446 (tpt) cc_final: 0.6778 (tpt) REVERT: C 474 ASP cc_start: 0.5796 (OUTLIER) cc_final: 0.5194 (m-30) REVERT: C 519 VAL cc_start: 0.1090 (OUTLIER) cc_final: 0.0841 (p) REVERT: C 754 GLU cc_start: 0.6613 (OUTLIER) cc_final: 0.6242 (tt0) REVERT: C 846 LYS cc_start: 0.6578 (mmtp) cc_final: 0.6186 (mttm) REVERT: C 934 THR cc_start: 0.6723 (OUTLIER) cc_final: 0.6400 (m) REVERT: C 981 GLN cc_start: 0.6238 (OUTLIER) cc_final: 0.5879 (tp40) REVERT: C 1009 MET cc_start: 0.4458 (tmm) cc_final: 0.4150 (pmm) REVERT: C 1042 HIS cc_start: 0.5918 (t70) cc_final: 0.5681 (t70) REVERT: D 6 PHE cc_start: 0.4949 (t80) cc_final: 0.4420 (t80) REVERT: D 74 ILE cc_start: 0.7060 (mt) cc_final: 0.6842 (mp) REVERT: D 152 GLU cc_start: 0.6043 (tp30) cc_final: 0.5821 (tp30) REVERT: D 211 ARG cc_start: 0.3738 (mmt-90) cc_final: 0.3404 (mtm-85) REVERT: D 296 LEU cc_start: 0.7578 (tp) cc_final: 0.7339 (tt) REVERT: D 366 ILE cc_start: 0.7121 (mp) cc_final: 0.6896 (mt) REVERT: D 383 ASP cc_start: 0.5938 (t70) cc_final: 0.5641 (t0) REVERT: D 407 LYS cc_start: 0.5529 (mtmt) cc_final: 0.5327 (tptm) REVERT: D 450 GLU cc_start: 0.6887 (tp30) cc_final: 0.6597 (tp30) REVERT: D 630 ARG cc_start: 0.7050 (ptm160) cc_final: 0.6778 (mtm180) REVERT: D 1084 GLN cc_start: 0.3681 (mm-40) cc_final: 0.3417 (mt0) REVERT: D 1085 ARG cc_start: 0.5615 (mtp-110) cc_final: 0.5181 (mtp180) REVERT: E 55 ILE cc_start: 0.7641 (mm) cc_final: 0.7297 (mm) REVERT: F 263 MET cc_start: 0.5124 (tmm) cc_final: 0.4911 (tpp) REVERT: F 283 TRP cc_start: 0.5630 (t60) cc_final: 0.5383 (t60) REVERT: F 297 GLU cc_start: 0.7010 (mt-10) cc_final: 0.6615 (mt-10) REVERT: F 359 MET cc_start: 0.6168 (mtp) cc_final: 0.5816 (mtm) REVERT: F 453 PHE cc_start: 0.6610 (t80) cc_final: 0.6348 (t80) REVERT: O 152 TYR cc_start: 0.5567 (t80) cc_final: 0.5293 (t80) REVERT: O 155 PHE cc_start: 0.5618 (t80) cc_final: 0.5153 (t80) REVERT: P 188 ARG cc_start: 0.5049 (ptm160) cc_final: 0.3888 (ttp80) REVERT: P 215 VAL cc_start: 0.4313 (OUTLIER) cc_final: 0.4100 (m) REVERT: N 107 ARG cc_start: 0.0565 (mmt-90) cc_final: 0.0201 (mpt-90) REVERT: N 146 ARG cc_start: 0.0238 (pmt-80) cc_final: -0.0756 (ptt-90) outliers start: 116 outliers final: 72 residues processed: 431 average time/residue: 0.2269 time to fit residues: 160.6301 Evaluate side-chains 372 residues out of total 3491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 290 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 383 GLU Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 754 GLU Chi-restraints excluded: chain C residue 832 VAL Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 879 ILE Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 934 THR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 981 GLN Chi-restraints excluded: chain C residue 1103 TYR Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain C residue 1139 SER Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 289 LYS Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 632 LYS Chi-restraints excluded: chain D residue 730 THR Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 879 ASP Chi-restraints excluded: chain D residue 898 VAL Chi-restraints excluded: chain D residue 916 ILE Chi-restraints excluded: chain D residue 919 SER Chi-restraints excluded: chain D residue 927 THR Chi-restraints excluded: chain D residue 1041 ARG Chi-restraints excluded: chain D residue 1194 VAL Chi-restraints excluded: chain D residue 1254 ILE Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 498 VAL Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 192 VAL Chi-restraints excluded: chain P residue 215 VAL Chi-restraints excluded: chain N residue 131 GLU Chi-restraints excluded: chain N residue 134 ILE Chi-restraints excluded: chain N residue 158 LEU Chi-restraints excluded: chain N residue 159 LYS Chi-restraints excluded: chain N residue 170 THR Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 76 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 336 optimal weight: 50.0000 chunk 125 optimal weight: 9.9990 chunk 78 optimal weight: 0.6980 chunk 188 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 387 optimal weight: 10.0000 chunk 250 optimal weight: 8.9990 chunk 223 optimal weight: 9.9990 chunk 273 optimal weight: 9.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 ASN C 679 ASN C 700 GLN D 368 ASN ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN D1139 GLN ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.132077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.105235 restraints weight = 121885.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.103240 restraints weight = 90315.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.103758 restraints weight = 80585.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.103893 restraints weight = 66111.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.104153 restraints weight = 59304.620| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5620 moved from start: 0.5693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 35973 Z= 0.173 Angle : 0.700 11.250 49438 Z= 0.368 Chirality : 0.047 0.348 5716 Planarity : 0.006 0.063 5909 Dihedral : 19.493 179.985 6218 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 4.02 % Allowed : 21.89 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.13), residues: 4131 helix: -0.43 (0.13), residues: 1594 sheet: -1.48 (0.24), residues: 437 loop : -1.81 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D1060 TYR 0.021 0.002 TYR P 160 PHE 0.023 0.002 PHE B 219 TRP 0.023 0.002 TRP O 179 HIS 0.010 0.001 HIS P 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (35967) covalent geometry : angle 0.69982 / 0.37 (49432) hydrogen bonds : bond 0.04586 / 3.11 ( 1422) hydrogen bonds : angle 5.35251 / 3.70 ( 3834) metal coordination : bond 0.00414 / 0.23 ( 6) metal coordination : angle 1.88056 / 0.76 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8262 Ramachandran restraints generated. 4131 Oldfield, 0 Emsley, 4131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8262 Ramachandran restraints generated. 4131 Oldfield, 0 Emsley, 4131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 337 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ILE cc_start: 0.7853 (OUTLIER) cc_final: 0.7559 (pt) REVERT: A 151 GLN cc_start: 0.6270 (mm110) cc_final: 0.5672 (mp10) REVERT: B 1 MET cc_start: 0.3788 (tpp) cc_final: 0.3365 (ttt) REVERT: B 46 ILE cc_start: 0.7137 (mm) cc_final: 0.6577 (mt) REVERT: B 56 ILE cc_start: 0.6792 (OUTLIER) cc_final: 0.6504 (tp) REVERT: B 85 VAL cc_start: 0.6468 (OUTLIER) cc_final: 0.6042 (p) REVERT: B 155 SER cc_start: 0.4426 (m) cc_final: 0.4179 (p) REVERT: B 190 ASP cc_start: 0.6157 (p0) cc_final: 0.5554 (p0) REVERT: C 76 GLU cc_start: 0.3208 (pt0) cc_final: 0.2566 (tm-30) REVERT: C 146 GLU cc_start: 0.4186 (OUTLIER) cc_final: 0.3283 (tt0) REVERT: C 300 PHE cc_start: 0.4796 (m-80) cc_final: 0.4216 (m-10) REVERT: C 302 LYS cc_start: 0.5696 (mmmt) cc_final: 0.5260 (tppt) REVERT: C 305 ARG cc_start: 0.2834 (mtt-85) cc_final: 0.2327 (ttm-80) REVERT: C 355 MET cc_start: 0.1523 (tmm) cc_final: 0.0797 (tmm) REVERT: C 440 MET cc_start: 0.7626 (tpt) cc_final: 0.7172 (tpt) REVERT: C 474 ASP cc_start: 0.5881 (OUTLIER) cc_final: 0.5237 (m-30) REVERT: C 519 VAL cc_start: 0.1373 (OUTLIER) cc_final: 0.1140 (p) REVERT: C 846 LYS cc_start: 0.6819 (mmtp) cc_final: 0.6413 (mttm) REVERT: C 1009 MET cc_start: 0.4802 (tmm) cc_final: 0.4235 (mpp) REVERT: C 1042 HIS cc_start: 0.5837 (t70) cc_final: 0.5635 (t70) REVERT: C 1051 MET cc_start: 0.6349 (tpt) cc_final: 0.6034 (tpp) REVERT: C 1072 GLU cc_start: 0.5855 (OUTLIER) cc_final: 0.5455 (mm-30) REVERT: D 6 PHE cc_start: 0.5000 (t80) cc_final: 0.4721 (t80) REVERT: D 152 GLU cc_start: 0.6418 (tp30) cc_final: 0.5973 (tp30) REVERT: D 211 ARG cc_start: 0.3945 (mmt-90) cc_final: 0.3681 (mtm-85) REVERT: D 296 LEU cc_start: 0.7378 (tp) cc_final: 0.7178 (tt) REVERT: D 312 MET cc_start: 0.5553 (OUTLIER) cc_final: 0.5307 (tmt) REVERT: D 383 ASP cc_start: 0.6102 (t70) cc_final: 0.5837 (t0) REVERT: D 407 LYS cc_start: 0.5444 (mtmt) cc_final: 0.5099 (tptm) REVERT: D 447 MET cc_start: 0.7249 (ttm) cc_final: 0.6757 (ttm) REVERT: D 479 GLN cc_start: 0.6207 (mt0) cc_final: 0.5933 (mt0) REVERT: D 630 ARG cc_start: 0.7175 (ptm160) cc_final: 0.6912 (mtm180) REVERT: D 679 LEU cc_start: 0.7167 (tt) cc_final: 0.6703 (mp) REVERT: D 1036 GLU cc_start: 0.5295 (tp30) cc_final: 0.5035 (tp30) REVERT: D 1085 ARG cc_start: 0.5733 (mtp-110) cc_final: 0.5304 (mtp180) REVERT: D 1097 ARG cc_start: 0.3773 (pmt-80) cc_final: 0.3384 (ptt90) REVERT: E 55 ILE cc_start: 0.7648 (mm) cc_final: 0.7439 (mm) REVERT: F 214 GLN cc_start: 0.4643 (tm-30) cc_final: 0.4371 (tm-30) REVERT: F 263 MET cc_start: 0.5461 (tmm) cc_final: 0.5250 (tpp) REVERT: F 297 GLU cc_start: 0.6800 (mt-10) cc_final: 0.6424 (mt-10) REVERT: F 401 LYS cc_start: 0.6293 (tmmt) cc_final: 0.5718 (mtmt) REVERT: F 453 PHE cc_start: 0.6700 (t80) cc_final: 0.6380 (t80) REVERT: O 155 PHE cc_start: 0.5824 (t80) cc_final: 0.5313 (t80) REVERT: P 188 ARG cc_start: 0.4940 (ptm160) cc_final: 0.3568 (ttp80) REVERT: N 146 ARG cc_start: 0.0199 (pmt-80) cc_final: -0.0816 (ptt-90) REVERT: N 159 LYS cc_start: -0.0507 (OUTLIER) cc_final: -0.0744 (ptpt) outliers start: 136 outliers final: 90 residues processed: 448 average time/residue: 0.2275 time to fit residues: 166.3919 Evaluate side-chains 390 residues out of total 3491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 291 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 383 GLU Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 832 VAL Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 879 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1100 VAL Chi-restraints excluded: chain C residue 1103 TYR Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain C residue 1139 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 289 LYS Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 632 LYS Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 653 HIS Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 879 ASP Chi-restraints excluded: chain D residue 893 THR Chi-restraints excluded: chain D residue 919 SER Chi-restraints excluded: chain D residue 965 VAL Chi-restraints excluded: chain D residue 1041 ARG Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1194 VAL Chi-restraints excluded: chain D residue 1254 ILE Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 498 VAL Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 192 VAL Chi-restraints excluded: chain N residue 158 LEU Chi-restraints excluded: chain N residue 159 LYS Chi-restraints excluded: chain N residue 170 THR Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 76 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 241 optimal weight: 7.9990 chunk 400 optimal weight: 8.9990 chunk 202 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 176 optimal weight: 10.0000 chunk 406 optimal weight: 9.9990 chunk 313 optimal weight: 9.9990 chunk 231 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 218 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 247 GLN C 539 HIS ** C 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 679 ASN C1111 ASN D 368 ASN ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN ** F 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.130497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.103381 restraints weight = 121575.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.101703 restraints weight = 86954.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.101866 restraints weight = 78346.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.102065 restraints weight = 66417.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.102190 restraints weight = 59004.729| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5684 moved from start: 0.6356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 35973 Z= 0.217 Angle : 0.779 12.139 49438 Z= 0.407 Chirality : 0.050 0.370 5716 Planarity : 0.006 0.066 5909 Dihedral : 19.595 179.538 6218 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 4.67 % Allowed : 22.48 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.12), residues: 4131 helix: -0.63 (0.13), residues: 1580 sheet: -1.72 (0.23), residues: 464 loop : -1.87 (0.13), residues: 2087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1014 TYR 0.023 0.003 TYR O 152 PHE 0.026 0.003 PHE F 335 TRP 0.029 0.003 TRP N 179 HIS 0.013 0.002 HIS Q 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.22 (35967) covalent geometry : angle 0.77877 / 0.41 (49432) hydrogen bonds : bond 0.04995 / 3.41 ( 1422) hydrogen bonds : angle 5.53706 / 3.83 ( 3834) metal coordination : bond 0.00590 / 0.33 ( 6) metal coordination : angle 2.60067 / 1.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8262 Ramachandran restraints generated. 4131 Oldfield, 0 Emsley, 4131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8262 Ramachandran restraints generated. 4131 Oldfield, 0 Emsley, 4131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 338 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 ILE cc_start: 0.7106 (mm) cc_final: 0.6555 (mt) REVERT: B 85 VAL cc_start: 0.6343 (OUTLIER) cc_final: 0.5909 (p) REVERT: B 190 ASP cc_start: 0.6345 (p0) cc_final: 0.5669 (p0) REVERT: C 76 GLU cc_start: 0.3345 (pt0) cc_final: 0.2622 (tm-30) REVERT: C 88 GLU cc_start: 0.5795 (tt0) cc_final: 0.5319 (mt-10) REVERT: C 124 ASP cc_start: 0.5597 (t0) cc_final: 0.5372 (t70) REVERT: C 146 GLU cc_start: 0.4216 (OUTLIER) cc_final: 0.3415 (tt0) REVERT: C 163 LYS cc_start: 0.6771 (mttp) cc_final: 0.6506 (mtpt) REVERT: C 300 PHE cc_start: 0.4817 (m-80) cc_final: 0.4298 (m-10) REVERT: C 302 LYS cc_start: 0.5869 (mmmt) cc_final: 0.5403 (tppt) REVERT: C 305 ARG cc_start: 0.3120 (mtt-85) cc_final: 0.2665 (ttm-80) REVERT: C 355 MET cc_start: 0.1869 (tmm) cc_final: 0.1282 (tmm) REVERT: C 440 MET cc_start: 0.7247 (tpt) cc_final: 0.6850 (tpt) REVERT: C 474 ASP cc_start: 0.5800 (OUTLIER) cc_final: 0.5039 (m-30) REVERT: C 500 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.7083 (tp) REVERT: C 754 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6822 (tt0) REVERT: C 846 LYS cc_start: 0.6969 (mmtp) cc_final: 0.6647 (mmtt) REVERT: C 1051 MET cc_start: 0.6515 (tpt) cc_final: 0.6205 (tpp) REVERT: C 1072 GLU cc_start: 0.6103 (OUTLIER) cc_final: 0.5580 (mm-30) REVERT: D 6 PHE cc_start: 0.5081 (t80) cc_final: 0.4842 (t80) REVERT: D 89 ARG cc_start: 0.6957 (ttm-80) cc_final: 0.6642 (mtp85) REVERT: D 211 ARG cc_start: 0.3961 (mmt-90) cc_final: 0.3710 (mtm-85) REVERT: D 223 TRP cc_start: 0.4412 (t-100) cc_final: 0.4204 (t-100) REVERT: D 289 LYS cc_start: 0.6874 (OUTLIER) cc_final: 0.6466 (mtpt) REVERT: D 312 MET cc_start: 0.5683 (OUTLIER) cc_final: 0.5142 (tmt) REVERT: D 383 ASP cc_start: 0.6405 (t70) cc_final: 0.6145 (t0) REVERT: D 407 LYS cc_start: 0.5753 (mtmt) cc_final: 0.5536 (tptp) REVERT: D 447 MET cc_start: 0.7436 (ttm) cc_final: 0.6951 (ttm) REVERT: D 479 GLN cc_start: 0.5567 (mt0) cc_final: 0.5355 (mt0) REVERT: D 679 LEU cc_start: 0.7330 (tt) cc_final: 0.6823 (mp) REVERT: D 759 GLN cc_start: 0.5072 (mp10) cc_final: 0.4361 (mt0) REVERT: D 887 ARG cc_start: 0.6551 (mmt90) cc_final: 0.5884 (mmm160) REVERT: D 1025 THR cc_start: 0.0890 (OUTLIER) cc_final: 0.0550 (m) REVERT: D 1084 GLN cc_start: 0.3622 (mm-40) cc_final: 0.3264 (mt0) REVERT: D 1085 ARG cc_start: 0.5475 (mtp-110) cc_final: 0.4972 (mtp180) REVERT: D 1097 ARG cc_start: 0.4291 (pmt-80) cc_final: 0.3868 (ptt90) REVERT: E 55 ILE cc_start: 0.7733 (mm) cc_final: 0.7503 (mm) REVERT: F 214 GLN cc_start: 0.4567 (tm-30) cc_final: 0.4309 (tm-30) REVERT: F 297 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6546 (mt-10) REVERT: F 328 LEU cc_start: 0.6438 (OUTLIER) cc_final: 0.6056 (tp) REVERT: F 352 ARG cc_start: 0.5014 (mtm110) cc_final: 0.4681 (ttp-170) REVERT: F 397 GLU cc_start: 0.4737 (mp0) cc_final: 0.4068 (mm-30) REVERT: F 401 LYS cc_start: 0.6432 (tmmt) cc_final: 0.5815 (mtmt) REVERT: F 453 PHE cc_start: 0.6560 (t80) cc_final: 0.6232 (t80) REVERT: P 152 TYR cc_start: 0.3357 (t80) cc_final: 0.3062 (t80) outliers start: 158 outliers final: 115 residues processed: 472 average time/residue: 0.2292 time to fit residues: 176.3138 Evaluate side-chains 417 residues out of total 3491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 292 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 383 GLU Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 754 GLU Chi-restraints excluded: chain C residue 762 THR Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 832 VAL Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 879 ILE Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 999 ASP Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1100 VAL Chi-restraints excluded: chain C residue 1103 TYR Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain C residue 1139 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 289 LYS Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 632 LYS Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 653 HIS Chi-restraints excluded: chain D residue 660 ASP Chi-restraints excluded: chain D residue 700 LEU Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 893 THR Chi-restraints excluded: chain D residue 918 THR Chi-restraints excluded: chain D residue 927 THR Chi-restraints excluded: chain D residue 965 VAL Chi-restraints excluded: chain D residue 972 THR Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1041 ARG Chi-restraints excluded: chain D residue 1194 VAL Chi-restraints excluded: chain D residue 1254 ILE Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 278 ARG Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 425 GLN Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 498 VAL Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 501 GLU Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 192 VAL Chi-restraints excluded: chain N residue 134 ILE Chi-restraints excluded: chain N residue 158 LEU Chi-restraints excluded: chain N residue 170 THR Chi-restraints excluded: chain N residue 188 ARG Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 76 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 189 optimal weight: 8.9990 chunk 264 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 chunk 381 optimal weight: 9.9990 chunk 378 optimal weight: 9.9990 chunk 220 optimal weight: 0.8980 chunk 255 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 298 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 235 optimal weight: 0.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 ASN ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN ** F 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.130700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.102341 restraints weight = 121520.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.101728 restraints weight = 80312.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.101870 restraints weight = 66145.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.102190 restraints weight = 61416.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.102224 restraints weight = 52547.125| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5683 moved from start: 0.6581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 35973 Z= 0.165 Angle : 0.697 12.044 49438 Z= 0.366 Chirality : 0.047 0.342 5716 Planarity : 0.005 0.067 5909 Dihedral : 19.524 178.253 6218 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.81 % Allowed : 23.57 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.13), residues: 4131 helix: -0.43 (0.13), residues: 1588 sheet: -1.60 (0.24), residues: 456 loop : -1.78 (0.13), residues: 2087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 144 TYR 0.020 0.002 TYR F 231 PHE 0.029 0.002 PHE D 651 TRP 0.023 0.002 TRP O 179 HIS 0.007 0.001 HIS P 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 (35967) covalent geometry : angle 0.69688 / 0.37 (49432) hydrogen bonds : bond 0.04532 / 3.10 ( 1422) hydrogen bonds : angle 5.33378 / 3.70 ( 3834) metal coordination : bond 0.00418 / 0.22 ( 6) metal coordination : angle 2.32753 / 0.92 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8262 Ramachandran restraints generated. 4131 Oldfield, 0 Emsley, 4131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8262 Ramachandran restraints generated. 4131 Oldfield, 0 Emsley, 4131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 326 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ILE cc_start: 0.7927 (OUTLIER) cc_final: 0.7383 (pt) REVERT: A 190 ASP cc_start: 0.5085 (m-30) cc_final: 0.4703 (m-30) REVERT: B 1 MET cc_start: 0.4616 (tpp) cc_final: 0.4390 (ttt) REVERT: B 85 VAL cc_start: 0.6426 (OUTLIER) cc_final: 0.6014 (p) REVERT: C 76 GLU cc_start: 0.3686 (pt0) cc_final: 0.2801 (tm-30) REVERT: C 124 ASP cc_start: 0.5601 (t0) cc_final: 0.5381 (t70) REVERT: C 146 GLU cc_start: 0.4175 (OUTLIER) cc_final: 0.3267 (tt0) REVERT: C 163 LYS cc_start: 0.6529 (mttp) cc_final: 0.6314 (mtpt) REVERT: C 300 PHE cc_start: 0.4789 (m-80) cc_final: 0.4340 (m-10) REVERT: C 302 LYS cc_start: 0.5939 (mmmt) cc_final: 0.5519 (tppt) REVERT: C 305 ARG cc_start: 0.3123 (mtt-85) cc_final: 0.2717 (ttm-80) REVERT: C 333 LEU cc_start: 0.4365 (tp) cc_final: 0.4140 (tp) REVERT: C 355 MET cc_start: 0.2042 (tmm) cc_final: 0.1447 (tmm) REVERT: C 440 MET cc_start: 0.7484 (tpt) cc_final: 0.7068 (tpt) REVERT: C 474 ASP cc_start: 0.5775 (OUTLIER) cc_final: 0.5028 (m-30) REVERT: C 630 MET cc_start: 0.6034 (OUTLIER) cc_final: 0.5693 (ttm) REVERT: C 846 LYS cc_start: 0.6914 (mmtp) cc_final: 0.6523 (mmtt) REVERT: C 1051 MET cc_start: 0.6530 (tpt) cc_final: 0.6248 (tpp) REVERT: C 1072 GLU cc_start: 0.6063 (OUTLIER) cc_final: 0.5567 (mm-30) REVERT: D 6 PHE cc_start: 0.4968 (t80) cc_final: 0.4709 (t80) REVERT: D 116 TYR cc_start: 0.6625 (m-10) cc_final: 0.6387 (m-10) REVERT: D 211 ARG cc_start: 0.3881 (mmt-90) cc_final: 0.3669 (mtm-85) REVERT: D 312 MET cc_start: 0.5357 (ttt) cc_final: 0.5100 (tmt) REVERT: D 383 ASP cc_start: 0.6380 (t70) cc_final: 0.6153 (t0) REVERT: D 407 LYS cc_start: 0.5763 (mtmt) cc_final: 0.5486 (tptp) REVERT: D 447 MET cc_start: 0.7487 (ttm) cc_final: 0.7025 (ttm) REVERT: D 459 ARG cc_start: 0.6722 (tpp-160) cc_final: 0.6444 (tpp80) REVERT: D 479 GLN cc_start: 0.5640 (mt0) cc_final: 0.5413 (mt0) REVERT: D 679 LEU cc_start: 0.7305 (tt) cc_final: 0.6748 (mp) REVERT: D 759 GLN cc_start: 0.5221 (mp10) cc_final: 0.4514 (mt0) REVERT: D 1085 ARG cc_start: 0.5372 (mtp-110) cc_final: 0.4881 (mtp180) REVERT: D 1097 ARG cc_start: 0.4190 (pmt-80) cc_final: 0.3339 (ptt-90) REVERT: E 55 ILE cc_start: 0.7653 (mm) cc_final: 0.7341 (mm) REVERT: F 297 GLU cc_start: 0.6954 (mt-10) cc_final: 0.6594 (mt-10) REVERT: F 328 LEU cc_start: 0.6458 (OUTLIER) cc_final: 0.6157 (tp) REVERT: F 397 GLU cc_start: 0.4801 (mp0) cc_final: 0.4137 (mm-30) REVERT: F 401 LYS cc_start: 0.6400 (tmmt) cc_final: 0.5777 (mtmt) REVERT: F 453 PHE cc_start: 0.6607 (t80) cc_final: 0.6263 (t80) REVERT: P 152 TYR cc_start: 0.3162 (t80) cc_final: 0.2921 (t80) outliers start: 129 outliers final: 97 residues processed: 432 average time/residue: 0.2270 time to fit residues: 160.9847 Evaluate side-chains 398 residues out of total 3491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 294 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 383 GLU Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 630 MET Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 762 THR Chi-restraints excluded: chain C residue 832 VAL Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 879 ILE Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 981 GLN Chi-restraints excluded: chain C residue 999 ASP Chi-restraints excluded: chain C residue 1036 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1103 TYR Chi-restraints excluded: chain C residue 1124 LEU Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain C residue 1139 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 632 LYS Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 653 HIS Chi-restraints excluded: chain D residue 656 TRP Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 893 THR Chi-restraints excluded: chain D residue 918 THR Chi-restraints excluded: chain D residue 927 THR Chi-restraints excluded: chain D residue 1041 ARG Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1194 VAL Chi-restraints excluded: chain D residue 1254 ILE Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 278 ARG Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 498 VAL Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 192 VAL Chi-restraints excluded: chain N residue 134 ILE Chi-restraints excluded: chain N residue 158 LEU Chi-restraints excluded: chain N residue 170 THR Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain Q residue 76 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 260 optimal weight: 10.0000 chunk 275 optimal weight: 9.9990 chunk 282 optimal weight: 0.8980 chunk 208 optimal weight: 9.9990 chunk 181 optimal weight: 20.0000 chunk 278 optimal weight: 7.9990 chunk 244 optimal weight: 9.9990 chunk 389 optimal weight: 20.0000 chunk 8 optimal weight: 7.9990 chunk 143 optimal weight: 20.0000 chunk 359 optimal weight: 9.9990 overall best weight: 7.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 GLN ** C 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 981 GLN D 368 ASN ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 505 HIS ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN ** F 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.129154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.102290 restraints weight = 120797.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.100212 restraints weight = 88446.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.101262 restraints weight = 77097.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.101082 restraints weight = 64306.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.101302 restraints weight = 57416.157| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5696 moved from start: 0.7099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 35973 Z= 0.239 Angle : 0.835 13.243 49438 Z= 0.434 Chirality : 0.051 0.339 5716 Planarity : 0.007 0.070 5909 Dihedral : 19.720 179.857 6218 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 4.25 % Allowed : 23.40 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.12), residues: 4131 helix: -0.79 (0.12), residues: 1573 sheet: -1.71 (0.24), residues: 453 loop : -1.92 (0.13), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 40 TYR 0.022 0.003 TYR C 670 PHE 0.035 0.003 PHE C 214 TRP 0.029 0.003 TRP D 223 HIS 0.011 0.002 HIS Q 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.24 (35967) covalent geometry : angle 0.83390 / 0.43 (49432) hydrogen bonds : bond 0.05286 / 3.61 ( 1422) hydrogen bonds : angle 5.66209 / 3.93 ( 3834) metal coordination : bond 0.00589 / 0.32 ( 6) metal coordination : angle 3.80230 / 1.52 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8262 Ramachandran restraints generated. 4131 Oldfield, 0 Emsley, 4131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8262 Ramachandran restraints generated. 4131 Oldfield, 0 Emsley, 4131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 303 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ASP cc_start: 0.5129 (m-30) cc_final: 0.4882 (m-30) REVERT: C 163 LYS cc_start: 0.6899 (mttp) cc_final: 0.6694 (mtpt) REVERT: C 300 PHE cc_start: 0.4911 (m-80) cc_final: 0.4503 (m-10) REVERT: C 302 LYS cc_start: 0.6061 (mmmt) cc_final: 0.5369 (ttmm) REVERT: C 355 MET cc_start: 0.2289 (tmm) cc_final: 0.1812 (tmm) REVERT: C 418 ILE cc_start: 0.6804 (mt) cc_final: 0.6580 (mt) REVERT: C 440 MET cc_start: 0.7383 (tpt) cc_final: 0.6964 (tpt) REVERT: C 474 ASP cc_start: 0.5903 (OUTLIER) cc_final: 0.5137 (m-30) REVERT: C 500 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.7073 (tp) REVERT: C 846 LYS cc_start: 0.7074 (mmtp) cc_final: 0.6719 (mmtt) REVERT: C 981 GLN cc_start: 0.6232 (OUTLIER) cc_final: 0.5924 (tm-30) REVERT: C 1051 MET cc_start: 0.6574 (tpt) cc_final: 0.6263 (tpp) REVERT: C 1072 GLU cc_start: 0.6196 (OUTLIER) cc_final: 0.5776 (mm-30) REVERT: D 152 GLU cc_start: 0.6815 (tp30) cc_final: 0.6266 (tp30) REVERT: D 155 MET cc_start: 0.5142 (tpp) cc_final: 0.4463 (tpp) REVERT: D 223 TRP cc_start: 0.4691 (t-100) cc_final: 0.4458 (t-100) REVERT: D 312 MET cc_start: 0.5847 (OUTLIER) cc_final: 0.5219 (tmt) REVERT: D 383 ASP cc_start: 0.6444 (t70) cc_final: 0.6120 (t0) REVERT: D 407 LYS cc_start: 0.5885 (mtmt) cc_final: 0.5511 (tptp) REVERT: D 447 MET cc_start: 0.7237 (ttm) cc_final: 0.6771 (ttm) REVERT: D 459 ARG cc_start: 0.6972 (tpp-160) cc_final: 0.6604 (tpp80) REVERT: D 759 GLN cc_start: 0.5187 (mp10) cc_final: 0.4496 (mt0) REVERT: D 887 ARG cc_start: 0.6763 (mmt90) cc_final: 0.6160 (mmm160) REVERT: D 1025 THR cc_start: 0.0756 (OUTLIER) cc_final: 0.0390 (m) REVERT: D 1085 ARG cc_start: 0.5149 (mtp-110) cc_final: 0.4810 (mtp180) REVERT: D 1097 ARG cc_start: 0.3941 (pmt-80) cc_final: 0.3699 (ptt90) REVERT: E 55 ILE cc_start: 0.7690 (mm) cc_final: 0.7420 (mm) REVERT: F 297 GLU cc_start: 0.6917 (mt-10) cc_final: 0.6547 (mt-10) REVERT: F 328 LEU cc_start: 0.6652 (OUTLIER) cc_final: 0.6325 (tp) REVERT: F 397 GLU cc_start: 0.4637 (mp0) cc_final: 0.3774 (mm-30) REVERT: F 401 LYS cc_start: 0.6416 (tmmt) cc_final: 0.5772 (mtmt) REVERT: F 453 PHE cc_start: 0.6708 (t80) cc_final: 0.6449 (t80) REVERT: G 278 ARG cc_start: 0.2271 (mtp180) cc_final: 0.1633 (ttm170) REVERT: P 152 TYR cc_start: 0.3035 (t80) cc_final: 0.2646 (t80) REVERT: P 204 GLU cc_start: 0.5192 (pt0) cc_final: 0.4138 (mm-30) outliers start: 144 outliers final: 113 residues processed: 431 average time/residue: 0.2289 time to fit residues: 161.9069 Evaluate side-chains 403 residues out of total 3491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 283 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 214 PHE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 383 GLU Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 762 THR Chi-restraints excluded: chain C residue 832 VAL Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 879 ILE Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 981 GLN Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1103 TYR Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain C residue 1139 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 632 LYS Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 653 HIS Chi-restraints excluded: chain D residue 700 LEU Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 893 THR Chi-restraints excluded: chain D residue 916 ILE Chi-restraints excluded: chain D residue 918 THR Chi-restraints excluded: chain D residue 919 SER Chi-restraints excluded: chain D residue 965 VAL Chi-restraints excluded: chain D residue 972 THR Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1041 ARG Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1194 VAL Chi-restraints excluded: chain D residue 1254 ILE Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 278 ARG Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 498 VAL Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 175 LEU Chi-restraints excluded: chain P residue 192 VAL Chi-restraints excluded: chain N residue 134 ILE Chi-restraints excluded: chain N residue 158 LEU Chi-restraints excluded: chain N residue 170 THR Chi-restraints excluded: chain N residue 188 ARG Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 83 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 217 optimal weight: 7.9990 chunk 148 optimal weight: 7.9990 chunk 271 optimal weight: 8.9990 chunk 36 optimal weight: 40.0000 chunk 179 optimal weight: 3.9990 chunk 395 optimal weight: 1.9990 chunk 241 optimal weight: 5.9990 chunk 121 optimal weight: 8.9990 chunk 187 optimal weight: 0.0570 chunk 351 optimal weight: 30.0000 chunk 400 optimal weight: 10.0000 overall best weight: 4.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 ASN ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN ** G 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.129743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.102722 restraints weight = 120571.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.100965 restraints weight = 85492.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.101043 restraints weight = 78476.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.101154 restraints weight = 77052.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.101292 restraints weight = 62608.646| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5726 moved from start: 0.7202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 35973 Z= 0.166 Angle : 0.725 12.710 49438 Z= 0.379 Chirality : 0.047 0.344 5716 Planarity : 0.006 0.068 5909 Dihedral : 19.587 178.410 6218 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.60 % Allowed : 23.81 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.13), residues: 4131 helix: -0.56 (0.13), residues: 1585 sheet: -1.63 (0.23), residues: 472 loop : -1.81 (0.13), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 186 TYR 0.026 0.002 TYR D 241 PHE 0.028 0.002 PHE D 651 TRP 0.032 0.002 TRP N 179 HIS 0.007 0.001 HIS P 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (35967) covalent geometry : angle 0.72394 / 0.38 (49432) hydrogen bonds : bond 0.04627 / 3.15 ( 1422) hydrogen bonds : angle 5.41944 / 3.76 ( 3834) metal coordination : bond 0.00450 / 0.23 ( 6) metal coordination : angle 2.87891 / 1.09 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8262 Ramachandran restraints generated. 4131 Oldfield, 0 Emsley, 4131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8262 Ramachandran restraints generated. 4131 Oldfield, 0 Emsley, 4131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 303 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ASP cc_start: 0.5070 (m-30) cc_final: 0.4794 (m-30) REVERT: C 300 PHE cc_start: 0.4860 (m-80) cc_final: 0.4417 (m-10) REVERT: C 302 LYS cc_start: 0.6084 (mmmt) cc_final: 0.5635 (tppt) REVERT: C 355 MET cc_start: 0.2099 (tmm) cc_final: 0.1712 (tmm) REVERT: C 440 MET cc_start: 0.7481 (tpt) cc_final: 0.7077 (tpt) REVERT: C 754 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.6436 (tt0) REVERT: C 846 LYS cc_start: 0.6907 (mmtp) cc_final: 0.6658 (mmtt) REVERT: C 962 GLU cc_start: 0.5924 (tp30) cc_final: 0.5720 (tp30) REVERT: C 964 LEU cc_start: 0.6130 (pt) cc_final: 0.5722 (mp) REVERT: C 1028 MET cc_start: 0.7090 (ttt) cc_final: 0.6843 (mtp) REVERT: C 1051 MET cc_start: 0.6500 (tpt) cc_final: 0.6190 (tpp) REVERT: C 1072 GLU cc_start: 0.6116 (OUTLIER) cc_final: 0.5649 (mm-30) REVERT: D 29 LYS cc_start: 0.6269 (OUTLIER) cc_final: 0.5892 (mttt) REVERT: D 116 TYR cc_start: 0.6595 (m-10) cc_final: 0.6377 (m-10) REVERT: D 152 GLU cc_start: 0.6982 (tp30) cc_final: 0.6403 (tp30) REVERT: D 155 MET cc_start: 0.4831 (tpp) cc_final: 0.4138 (tpp) REVERT: D 310 MET cc_start: 0.5746 (tpp) cc_final: 0.5372 (mmm) REVERT: D 312 MET cc_start: 0.5358 (ttt) cc_final: 0.5011 (tmt) REVERT: D 383 ASP cc_start: 0.6426 (t70) cc_final: 0.6200 (t0) REVERT: D 447 MET cc_start: 0.7182 (ttm) cc_final: 0.6738 (ttm) REVERT: D 759 GLN cc_start: 0.5157 (mp10) cc_final: 0.4469 (mt0) REVERT: D 887 ARG cc_start: 0.6824 (mmt90) cc_final: 0.6263 (mmm160) REVERT: D 1085 ARG cc_start: 0.5194 (mtp-110) cc_final: 0.4849 (mtp180) REVERT: D 1097 ARG cc_start: 0.4039 (pmt-80) cc_final: 0.3813 (ptt90) REVERT: D 1112 MET cc_start: 0.4678 (tpp) cc_final: 0.4385 (tpt) REVERT: E 55 ILE cc_start: 0.7653 (mm) cc_final: 0.7434 (mm) REVERT: F 246 GLU cc_start: 0.5269 (mt-10) cc_final: 0.4949 (mt-10) REVERT: F 297 GLU cc_start: 0.6941 (mt-10) cc_final: 0.6634 (mt-10) REVERT: F 328 LEU cc_start: 0.6711 (OUTLIER) cc_final: 0.6370 (tp) REVERT: F 397 GLU cc_start: 0.4798 (mp0) cc_final: 0.4054 (mm-30) REVERT: F 401 LYS cc_start: 0.6394 (tmmt) cc_final: 0.5807 (mtmt) REVERT: F 453 PHE cc_start: 0.6659 (t80) cc_final: 0.6384 (t80) REVERT: F 501 GLU cc_start: 0.5034 (tt0) cc_final: 0.4781 (pt0) REVERT: P 152 TYR cc_start: 0.3109 (t80) cc_final: 0.2835 (t80) outliers start: 122 outliers final: 101 residues processed: 409 average time/residue: 0.2215 time to fit residues: 150.1764 Evaluate side-chains 390 residues out of total 3491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 285 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 383 GLU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 754 GLU Chi-restraints excluded: chain C residue 762 THR Chi-restraints excluded: chain C residue 832 VAL Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 879 ILE Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1103 TYR Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain C residue 1139 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 632 LYS Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 653 HIS Chi-restraints excluded: chain D residue 700 LEU Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 893 THR Chi-restraints excluded: chain D residue 918 THR Chi-restraints excluded: chain D residue 965 VAL Chi-restraints excluded: chain D residue 1041 ARG Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1194 VAL Chi-restraints excluded: chain D residue 1254 ILE Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 278 ARG Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 498 VAL Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 156 GLU Chi-restraints excluded: chain P residue 175 LEU Chi-restraints excluded: chain P residue 192 VAL Chi-restraints excluded: chain N residue 158 LEU Chi-restraints excluded: chain N residue 170 THR Chi-restraints excluded: chain N residue 188 ARG Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 83 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 357 optimal weight: 7.9990 chunk 347 optimal weight: 20.0000 chunk 187 optimal weight: 9.9990 chunk 296 optimal weight: 0.5980 chunk 364 optimal weight: 0.9980 chunk 375 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 chunk 30 optimal weight: 30.0000 chunk 108 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 545 ASN ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1119 HIS ** D1139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN ** G 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.129997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.103460 restraints weight = 120333.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.100870 restraints weight = 91161.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.101431 restraints weight = 83449.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.101619 restraints weight = 72535.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.101851 restraints weight = 59359.447| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5704 moved from start: 0.7282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 35973 Z= 0.146 Angle : 0.681 11.699 49438 Z= 0.357 Chirality : 0.046 0.349 5716 Planarity : 0.005 0.062 5909 Dihedral : 19.479 178.236 6218 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.19 % Allowed : 24.49 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.13), residues: 4131 helix: -0.37 (0.13), residues: 1588 sheet: -1.50 (0.24), residues: 450 loop : -1.71 (0.13), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 221 TYR 0.021 0.002 TYR D 241 PHE 0.025 0.002 PHE D 651 TRP 0.040 0.002 TRP D 223 HIS 0.007 0.001 HIS P 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (35967) covalent geometry : angle 0.68075 / 0.36 (49432) hydrogen bonds : bond 0.04316 / 2.93 ( 1422) hydrogen bonds : angle 5.24288 / 3.64 ( 3834) metal coordination : bond 0.00352 / 0.18 ( 6) metal coordination : angle 2.63438 / 0.97 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6327.09 seconds wall clock time: 110 minutes 15.07 seconds (6615.07 seconds total)