Starting phenix.real_space_refine on Tue Aug 26 13:59:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hih_34816/08_2025/8hih_34816.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hih_34816/08_2025/8hih_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_34816/08_2025/8hih_34816.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hih_34816/08_2025/8hih_34816.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hih_34816/08_2025/8hih_34816.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hih_34816/08_2025/8hih_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-2.0-5787/lib/python3.9/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: 6.97, per 1000 atoms: 0.20 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: 2.36 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 4.05 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: 7.83 Time building geometry restraints manager: 3.37 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=" N THR P 67 " pdb=" CA THR P 67 " ideal model delta sigma weight residual 1.459 1.490 -0.032 1.16e-02 7.43e+03 7.44e+00 bond pdb=" CA ARG Q 69 " pdb=" C ARG Q 69 " ideal model delta sigma weight residual 1.525 1.577 -0.052 2.10e-02 2.27e+03 6.15e+00 bond pdb=" N GLY E 27 " pdb=" CA GLY E 27 " ideal model delta sigma weight residual 1.451 1.489 -0.038 1.60e-02 3.91e+03 5.57e+00 bond pdb=" C ILE C 723 " pdb=" N MET C 724 " ideal model delta sigma weight residual 1.328 1.295 0.033 1.44e-02 4.82e+03 5.41e+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=" 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 angle pdb=" N ARG C 453 " pdb=" CA ARG C 453 " pdb=" C ARG C 453 " ideal model delta sigma weight residual 112.24 106.01 6.23 1.28e+00 6.10e-01 2.37e+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: 4338 0.049 - 0.099: 1120 0.099 - 0.148: 244 0.148 - 0.197: 12 0.197 - 0.246: 2 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=" 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 2.42 2.21 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA ARG P 69 " pdb=" N ARG P 69 " pdb=" C ARG P 69 " pdb=" CB ARG P 69 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.43e-01 ... (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: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.030 Extract box with map and model: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 35.460 Find NCS groups from input model: 0.420 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4620 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= 0.632 Angle : 0.866 76.038 49438 Z= 0.527 Chirality : 0.045 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 aren 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 covalent geometry : bond 0.00951 (35967) covalent geometry : angle 0.86473 (49432) hydrogen bonds : bond 0.21437 ( 1422) hydrogen bonds : angle 8.52927 ( 3834) metal coordination : bond 0.00775 ( 6) metal coordination : angle 4.61245 ( 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 : 1.353 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: 0.7012 (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: 0.4080 (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: 0.2857 time to fit residues: 396.7094 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 : 1.236 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 17 ASN B 124 HIS C 57 GLN C 375 ASN C 386 GLN C 603 ASN C 700 GLN ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 875 GLN ** C 981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 GLN ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 687 GLN D 854 HIS D1110 GLN ** D1131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1139 GLN F 261 GLN ** F 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 ASN F 461 GLN P 42 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.133699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.106558 restraints weight = 124757.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.104756 restraints weight = 96095.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.105353 restraints weight = 77133.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.105498 restraints weight = 73055.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.105554 restraints weight = 61726.881| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5503 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 35973 Z= 0.249 Angle : 0.838 11.028 49438 Z= 0.443 Chirality : 0.050 0.258 5716 Planarity : 0.007 0.074 5909 Dihedral : 19.765 178.808 6219 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.63 % Favored : 93.32 % Rotamer: Outliers : 2.54 % Allowed : 14.18 % Favored : 83.28 % 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 aren not related in a simple way. whole: -2.40 (0.12), residues: 4131 helix: -0.87 (0.12), residues: 1562 sheet: -1.87 (0.23), residues: 417 loop : -2.09 (0.12), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 517 TYR 0.025 0.003 TYR C 480 PHE 0.027 0.003 PHE D 840 TRP 0.016 0.003 TRP D 105 HIS 0.017 0.002 HIS C 479 Details of bonding type rmsd covalent geometry : bond 0.00561 (35967) covalent geometry : angle 0.83787 (49432) hydrogen bonds : bond 0.05831 ( 1422) hydrogen bonds : angle 6.15078 ( 3834) metal coordination : bond 0.00357 ( 6) metal coordination : angle 2.78170 ( 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 559 residues out of total 3491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 473 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.5150 (mt-10) cc_final: 0.4782 (mt-10) REVERT: A 151 GLN cc_start: 0.5400 (mm110) cc_final: 0.5171 (mm110) REVERT: A 217 GLU cc_start: 0.4933 (mm-30) cc_final: 0.4597 (mm-30) REVERT: B 46 ILE cc_start: 0.6944 (mm) cc_final: 0.6203 (mt) REVERT: B 168 TYR cc_start: 0.6974 (m-10) cc_final: 0.6728 (m-80) REVERT: C 57 GLN cc_start: 0.6744 (mm-40) cc_final: 0.6496 (mm-40) REVERT: C 258 MET cc_start: 0.3140 (mmm) cc_final: 0.2820 (mmt) REVERT: C 300 PHE cc_start: 0.4502 (m-80) cc_final: 0.3979 (m-10) REVERT: C 305 ARG cc_start: 0.3153 (mtt-85) cc_final: 0.2472 (ttm-80) REVERT: C 355 MET cc_start: 0.1744 (tmm) cc_final: 0.0723 (tmm) REVERT: C 404 MET cc_start: 0.4893 (ttm) cc_final: 0.4613 (tpp) REVERT: C 440 MET cc_start: 0.7356 (tpt) cc_final: 0.6494 (tpt) REVERT: C 442 GLN cc_start: 0.4546 (tp-100) cc_final: 0.4339 (tt0) REVERT: C 496 LEU cc_start: 0.8191 (mp) cc_final: 0.7953 (mp) REVERT: C 500 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7242 (tp) REVERT: C 528 ILE cc_start: 0.6940 (mm) cc_final: 0.6629 (mm) REVERT: C 593 MET cc_start: 0.6965 (mtp) cc_final: 0.6703 (mtt) REVERT: C 747 LEU cc_start: 0.7545 (tt) cc_final: 0.6977 (tp) REVERT: C 809 LYS cc_start: 0.4568 (tttt) cc_final: 0.4162 (ttpt) REVERT: C 841 HIS cc_start: 0.4677 (m-70) cc_final: 0.4091 (m-70) REVERT: C 846 LYS cc_start: 0.6459 (mmtp) cc_final: 0.5924 (mttp) REVERT: C 1009 MET cc_start: 0.4155 (OUTLIER) cc_final: 0.3815 (pmm) REVERT: C 1042 HIS cc_start: 0.5955 (t70) cc_final: 0.5724 (t70) REVERT: D 6 PHE cc_start: 0.4666 (t80) cc_final: 0.4380 (t80) REVERT: D 155 MET cc_start: 0.5117 (tpp) cc_final: 0.4487 (tmm) REVERT: D 211 ARG cc_start: 0.3802 (mmt-90) cc_final: 0.3237 (mtm-85) REVERT: D 234 LEU cc_start: 0.6548 (OUTLIER) cc_final: 0.6146 (tt) REVERT: D 363 PRO cc_start: 0.6693 (Cg_endo) cc_final: 0.6434 (Cg_exo) REVERT: D 366 ILE cc_start: 0.7346 (mp) cc_final: 0.7039 (mt) REVERT: D 383 ASP cc_start: 0.6147 (t0) cc_final: 0.5892 (t0) REVERT: D 414 ARG cc_start: 0.6450 (mtp-110) cc_final: 0.6076 (mtp180) REVERT: D 450 GLU cc_start: 0.7024 (tp30) cc_final: 0.6491 (tp30) REVERT: D 523 GLN cc_start: 0.7469 (mt0) cc_final: 0.7168 (mm110) REVERT: D 541 MET cc_start: 0.7628 (OUTLIER) cc_final: 0.7197 (mmm) REVERT: D 634 LYS cc_start: 0.6642 (ttpt) cc_final: 0.6298 (mttm) REVERT: D 862 ASP cc_start: 0.6065 (m-30) cc_final: 0.5163 (m-30) REVERT: D 1085 ARG cc_start: 0.5741 (mtp-110) cc_final: 0.5299 (mtp180) REVERT: D 1111 LEU cc_start: 0.6128 (mt) cc_final: 0.5663 (mm) REVERT: D 1208 MET cc_start: 0.6090 (pmm) cc_final: 0.5890 (pmm) REVERT: E 67 TYR cc_start: 0.7022 (t80) cc_final: 0.6822 (t80) REVERT: F 233 LYS cc_start: 0.6855 (tttp) cc_final: 0.6391 (mmmt) REVERT: F 281 MET cc_start: 0.4699 (mmt) cc_final: 0.4358 (tmm) REVERT: F 283 TRP cc_start: 0.5316 (t60) cc_final: 0.4958 (t60) REVERT: F 285 CYS cc_start: 0.4045 (m) cc_final: 0.3761 (m) REVERT: F 297 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6340 (mt-10) REVERT: F 350 TRP cc_start: 0.6191 (m100) cc_final: 0.5587 (m100) REVERT: F 411 LEU cc_start: 0.6894 (mm) cc_final: 0.6641 (mt) REVERT: F 453 PHE cc_start: 0.6207 (t80) cc_final: 0.5963 (t80) REVERT: F 456 LEU cc_start: 0.7186 (mt) cc_final: 0.6975 (tp) REVERT: O 146 ARG cc_start: 0.5064 (ptp90) cc_final: 0.4850 (ptt-90) REVERT: N 82 LEU cc_start: 0.1198 (mt) cc_final: 0.0863 (pp) REVERT: N 107 ARG cc_start: 0.0609 (mmt-90) cc_final: 0.0262 (mmt180) REVERT: N 146 ARG cc_start: 0.0541 (pmt-80) cc_final: -0.0706 (ptt-90) REVERT: N 193 HIS cc_start: 0.2986 (m-70) cc_final: 0.2635 (m90) outliers start: 86 outliers final: 45 residues processed: 538 average time/residue: 0.2526 time to fit residues: 215.0120 Evaluate side-chains 363 residues out of total 3491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 314 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 176 VAL 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 500 LEU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 1009 MET Chi-restraints excluded: chain C residue 1046 THR Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 234 LEU 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 596 THR Chi-restraints excluded: chain D residue 633 ILE 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 1176 LEU Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain D residue 1254 ILE Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain F residue 228 VAL 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 O residue 215 VAL 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 71 ILE 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: 3.9990 chunk 70 optimal weight: 0.9990 chunk 365 optimal weight: 0.8980 chunk 246 optimal weight: 6.9990 chunk 28 optimal weight: 0.0980 chunk 45 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 12 optimal weight: 0.2980 chunk 264 optimal weight: 20.0000 chunk 223 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 375 ASN ** C 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 775 ASN C 920 HIS C 981 GLN C 986 GLN C1077 GLN D 368 ASN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1131 GLN E 70 GLN P 164 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.134149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.107484 restraints weight = 123341.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.105763 restraints weight = 96242.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.106619 restraints weight = 78762.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.106759 restraints weight = 61841.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.106857 restraints weight = 56805.233| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5453 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 35973 Z= 0.136 Angle : 0.636 9.625 49438 Z= 0.337 Chirality : 0.043 0.217 5716 Planarity : 0.005 0.058 5909 Dihedral : 19.328 179.910 6218 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.75 % Allowed : 16.99 % Favored : 80.27 % 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 aren not related in a simple way. whole: -1.78 (0.12), residues: 4131 helix: -0.33 (0.13), residues: 1585 sheet: -1.60 (0.24), residues: 433 loop : -1.74 (0.13), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 515 TYR 0.042 0.001 TYR O 139 PHE 0.024 0.002 PHE D 252 TRP 0.032 0.002 TRP N 179 HIS 0.004 0.001 HIS C 539 Details of bonding type rmsd covalent geometry : bond 0.00295 (35967) covalent geometry : angle 0.63612 (49432) hydrogen bonds : bond 0.04309 ( 1422) hydrogen bonds : angle 5.33424 ( 3834) metal coordination : bond 0.00145 ( 6) metal coordination : angle 1.07494 ( 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 497 residues out of total 3491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 404 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.7191 (m-80) cc_final: 0.6905 (m-80) REVERT: A 54 ILE cc_start: 0.7718 (OUTLIER) cc_final: 0.7163 (pt) REVERT: A 151 GLN cc_start: 0.5497 (mm110) cc_final: 0.5133 (mm110) REVERT: B 46 ILE cc_start: 0.6994 (mm) cc_final: 0.6304 (mt) REVERT: C 49 GLU cc_start: 0.5921 (pp20) cc_final: 0.5082 (mt-10) REVERT: C 57 GLN cc_start: 0.6699 (mm-40) cc_final: 0.6286 (mm-40) REVERT: C 189 GLU cc_start: 0.5269 (pt0) cc_final: 0.4991 (pt0) REVERT: C 300 PHE cc_start: 0.4464 (m-80) cc_final: 0.3895 (m-10) REVERT: C 305 ARG cc_start: 0.3447 (mtt-85) cc_final: 0.2800 (ttm-80) REVERT: C 307 ASP cc_start: 0.3027 (m-30) cc_final: 0.2736 (m-30) REVERT: C 320 LEU cc_start: 0.7093 (mt) cc_final: 0.6819 (mp) REVERT: C 440 MET cc_start: 0.7606 (tpt) cc_final: 0.6622 (tpt) REVERT: C 474 ASP cc_start: 0.5597 (OUTLIER) cc_final: 0.5092 (m-30) REVERT: C 519 VAL cc_start: 0.0922 (OUTLIER) cc_final: 0.0720 (p) REVERT: C 618 LEU cc_start: 0.6652 (mt) cc_final: 0.6168 (mp) REVERT: C 661 MET cc_start: 0.4512 (tpt) cc_final: 0.3977 (tpt) REVERT: C 740 ARG cc_start: 0.4092 (mtm-85) cc_final: 0.3830 (ttp80) REVERT: C 747 LEU cc_start: 0.7279 (tt) cc_final: 0.6686 (tp) REVERT: C 846 LYS cc_start: 0.6230 (mmtp) cc_final: 0.5611 (mttp) REVERT: C 1009 MET cc_start: 0.3932 (tmm) cc_final: 0.3704 (mpp) REVERT: C 1119 GLU cc_start: 0.1884 (OUTLIER) cc_final: 0.1353 (tp30) REVERT: D 6 PHE cc_start: 0.4951 (t80) cc_final: 0.4509 (t80) REVERT: D 155 MET cc_start: 0.5022 (tpp) cc_final: 0.4785 (tmm) REVERT: D 211 ARG cc_start: 0.3664 (mmt-90) cc_final: 0.3341 (mtm-85) REVERT: D 234 LEU cc_start: 0.6270 (OUTLIER) cc_final: 0.5933 (tp) REVERT: D 383 ASP cc_start: 0.6258 (t0) cc_final: 0.6053 (t0) REVERT: D 409 LYS cc_start: 0.5028 (mttm) cc_final: 0.3526 (tttt) REVERT: D 440 GLN cc_start: 0.8177 (mt0) cc_final: 0.7545 (mt0) REVERT: D 450 GLU cc_start: 0.6923 (tp30) cc_final: 0.6568 (tp30) REVERT: D 523 GLN cc_start: 0.7424 (mt0) cc_final: 0.7117 (mm-40) REVERT: D 541 MET cc_start: 0.7563 (OUTLIER) cc_final: 0.7235 (mmm) REVERT: D 634 LYS cc_start: 0.6477 (ttpt) cc_final: 0.6071 (mttt) REVERT: D 663 MET cc_start: 0.5895 (tpp) cc_final: 0.5178 (mmm) REVERT: D 862 ASP cc_start: 0.6165 (m-30) cc_final: 0.5806 (m-30) REVERT: D 875 ARG cc_start: 0.6862 (tmt-80) cc_final: 0.6651 (ttt-90) REVERT: D 1059 GLU cc_start: 0.5732 (tp30) cc_final: 0.5448 (tp30) REVERT: D 1084 GLN cc_start: 0.3861 (mm-40) cc_final: 0.3640 (mt0) REVERT: D 1085 ARG cc_start: 0.5749 (mtp-110) cc_final: 0.5328 (mtp180) REVERT: E 55 ILE cc_start: 0.7525 (mm) cc_final: 0.7298 (mm) REVERT: F 240 LEU cc_start: 0.4702 (mt) cc_final: 0.4258 (tp) REVERT: F 283 TRP cc_start: 0.5340 (t60) cc_final: 0.5040 (t60) REVERT: F 297 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6635 (mt-10) REVERT: F 359 MET cc_start: 0.6169 (mtm) cc_final: 0.5817 (mtm) REVERT: F 411 LEU cc_start: 0.6720 (mm) cc_final: 0.6385 (mt) REVERT: F 453 PHE cc_start: 0.6384 (t80) cc_final: 0.5877 (t80) REVERT: F 479 PHE cc_start: 0.5424 (m-80) cc_final: 0.5214 (m-80) REVERT: P 160 TYR cc_start: 0.4042 (t80) cc_final: 0.3762 (t80) REVERT: N 107 ARG cc_start: 0.0564 (mmt-90) cc_final: 0.0172 (mmt180) REVERT: N 146 ARG cc_start: 0.0241 (pmt-80) cc_final: -0.0763 (ptt-90) outliers start: 93 outliers final: 43 residues processed: 476 average time/residue: 0.2239 time to fit residues: 169.8379 Evaluate side-chains 348 residues out of total 3491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 299 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain B residue 66 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 48 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 122 CYS 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 660 VAL Chi-restraints excluded: chain C residue 754 GLU Chi-restraints excluded: chain C residue 832 VAL Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 932 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 981 GLN Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain C residue 1103 TYR Chi-restraints excluded: chain C residue 1119 GLU 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 162 VAL Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 234 LEU 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 793 TYR 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 1194 VAL Chi-restraints excluded: chain D residue 1254 ILE Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain F residue 501 GLU 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 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 76 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 249 optimal weight: 0.5980 chunk 355 optimal weight: 9.9990 chunk 340 optimal weight: 30.0000 chunk 242 optimal weight: 7.9990 chunk 372 optimal weight: 5.9990 chunk 38 optimal weight: 20.0000 chunk 78 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 chunk 176 optimal weight: 10.0000 chunk 172 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 375 ASN ** C 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 718 ASN C 751 HIS C 981 GLN D 540 GLN ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN D 767 HIS D1139 GLN D1269 ASN E 63 GLN ** F 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 214 ASN P 25 HIS Q 193 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.131885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.104756 restraints weight = 121312.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.103353 restraints weight = 87614.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.103728 restraints weight = 77870.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.103800 restraints weight = 71670.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.104000 restraints weight = 60723.098| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5543 moved from start: 0.5724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 35973 Z= 0.180 Angle : 0.711 11.589 49438 Z= 0.372 Chirality : 0.045 0.194 5716 Planarity : 0.006 0.061 5909 Dihedral : 19.292 177.018 6218 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 4.37 % Allowed : 18.20 % Favored : 77.43 % 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 aren not related in a simple way. whole: -1.70 (0.12), residues: 4131 helix: -0.28 (0.13), residues: 1594 sheet: -1.27 (0.24), residues: 416 loop : -1.78 (0.13), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 515 TYR 0.035 0.002 TYR O 139 PHE 0.023 0.002 PHE D 252 TRP 0.016 0.002 TRP D 223 HIS 0.008 0.002 HIS C 479 Details of bonding type rmsd covalent geometry : bond 0.00405 (35967) covalent geometry : angle 0.71062 (49432) hydrogen bonds : bond 0.04522 ( 1422) hydrogen bonds : angle 5.31980 ( 3834) metal coordination : bond 0.00514 ( 6) metal coordination : angle 1.90707 ( 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 505 residues out of total 3491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 357 time to evaluate : 1.453 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 83 LEU cc_start: 0.6132 (OUTLIER) cc_final: 0.5657 (mm) REVERT: A 151 GLN cc_start: 0.5509 (mm110) cc_final: 0.5101 (mm110) REVERT: A 226 ASN cc_start: 0.1425 (m-40) cc_final: 0.0790 (t0) REVERT: B 1 MET cc_start: 0.3563 (tpp) cc_final: 0.3179 (ttt) REVERT: B 46 ILE cc_start: 0.7021 (mm) cc_final: 0.6492 (mt) REVERT: B 155 SER cc_start: 0.4433 (m) cc_final: 0.4190 (p) REVERT: C 57 GLN cc_start: 0.6650 (mm-40) cc_final: 0.6153 (mm-40) REVERT: C 76 GLU cc_start: 0.3140 (pt0) cc_final: 0.2568 (tm-30) REVERT: C 88 GLU cc_start: 0.5458 (tt0) cc_final: 0.5194 (mt-10) REVERT: C 146 GLU cc_start: 0.3866 (OUTLIER) cc_final: 0.2846 (tm-30) REVERT: C 147 ILE cc_start: 0.3282 (OUTLIER) cc_final: 0.2831 (tt) REVERT: C 300 PHE cc_start: 0.4590 (m-80) cc_final: 0.4056 (m-10) REVERT: C 302 LYS cc_start: 0.5723 (mmmt) cc_final: 0.5202 (tttt) REVERT: C 440 MET cc_start: 0.7454 (tpt) cc_final: 0.6818 (tpt) REVERT: C 474 ASP cc_start: 0.5526 (OUTLIER) cc_final: 0.4837 (m-30) REVERT: C 618 LEU cc_start: 0.6717 (mt) cc_final: 0.6295 (mp) REVERT: C 630 MET cc_start: 0.5227 (OUTLIER) cc_final: 0.4888 (ppp) REVERT: C 740 ARG cc_start: 0.4638 (mtm-85) cc_final: 0.4417 (ttp80) REVERT: C 741 LEU cc_start: 0.5883 (pp) cc_final: 0.5620 (pp) REVERT: C 939 CYS cc_start: 0.5438 (m) cc_final: 0.5145 (m) REVERT: C 1009 MET cc_start: 0.4677 (OUTLIER) cc_final: 0.4140 (pmm) REVERT: C 1072 GLU cc_start: 0.6002 (OUTLIER) cc_final: 0.5674 (mm-30) REVERT: D 6 PHE cc_start: 0.5023 (t80) cc_final: 0.4659 (t80) REVERT: D 155 MET cc_start: 0.5048 (tpp) cc_final: 0.4419 (tmm) REVERT: D 211 ARG cc_start: 0.3819 (mmt-90) cc_final: 0.3608 (mtm-85) REVERT: D 219 LEU cc_start: 0.6180 (OUTLIER) cc_final: 0.5587 (tt) REVERT: D 289 LYS cc_start: 0.6974 (OUTLIER) cc_final: 0.6640 (mtpt) REVERT: D 327 MET cc_start: 0.5629 (OUTLIER) cc_final: 0.5285 (mtt) REVERT: D 383 ASP cc_start: 0.6465 (t0) cc_final: 0.6245 (t0) REVERT: D 450 GLU cc_start: 0.6809 (tp30) cc_final: 0.6487 (tp30) REVERT: D 541 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.7499 (mmm) REVERT: D 634 LYS cc_start: 0.6657 (ttpt) cc_final: 0.6073 (mttm) REVERT: D 679 LEU cc_start: 0.7253 (tt) cc_final: 0.6780 (mp) REVERT: D 862 ASP cc_start: 0.6479 (m-30) cc_final: 0.6139 (m-30) REVERT: D 1059 GLU cc_start: 0.5907 (tp30) cc_final: 0.5483 (tp30) REVERT: D 1084 GLN cc_start: 0.3849 (mm-40) cc_final: 0.3563 (mt0) REVERT: D 1085 ARG cc_start: 0.5574 (mtp-110) cc_final: 0.5095 (mtp180) REVERT: D 1097 ARG cc_start: 0.4302 (pmt-80) cc_final: 0.3594 (ptt-90) REVERT: E 55 ILE cc_start: 0.7624 (mm) cc_final: 0.7398 (mm) REVERT: F 214 GLN cc_start: 0.4523 (tm-30) cc_final: 0.4227 (pp30) REVERT: F 283 TRP cc_start: 0.5482 (t60) cc_final: 0.4968 (t60) REVERT: F 297 GLU cc_start: 0.6857 (mt-10) cc_final: 0.6442 (mt-10) REVERT: F 411 LEU cc_start: 0.6742 (mm) cc_final: 0.6480 (mt) REVERT: F 453 PHE cc_start: 0.6581 (t80) cc_final: 0.6263 (t80) REVERT: O 191 ASP cc_start: 0.5741 (m-30) cc_final: 0.5371 (m-30) REVERT: O 217 TYR cc_start: 0.5216 (m-80) cc_final: 0.5008 (m-80) REVERT: P 188 ARG cc_start: 0.4531 (OUTLIER) cc_final: 0.3675 (tmm160) REVERT: N 82 LEU cc_start: 0.1160 (mt) cc_final: 0.0728 (pp) REVERT: Q 167 ARG cc_start: 0.0138 (mtt180) cc_final: -0.0073 (mmt180) outliers start: 148 outliers final: 80 residues processed: 474 average time/residue: 0.2476 time to fit residues: 188.4937 Evaluate side-chains 393 residues out of total 3491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 301 time to evaluate : 1.344 ------------------------------------------------------------------------------- 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 83 LEU Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 167 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 110 ILE 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 48 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 339 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 532 THR Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 630 MET Chi-restraints excluded: chain C residue 636 ILE Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 832 VAL Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1009 MET 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 28 VAL Chi-restraints excluded: chain D residue 46 LEU 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 219 LEU 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 327 MET Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 653 HIS Chi-restraints excluded: chain D residue 732 SER 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 927 THR Chi-restraints excluded: chain D residue 965 VAL Chi-restraints excluded: chain D residue 972 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 68 TYR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain F residue 278 ARG Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 501 GLU Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 188 ARG 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 48 VAL Chi-restraints excluded: chain Q residue 70 SER 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: 9.9990 chunk 166 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 350 optimal weight: 20.0000 chunk 235 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 340 optimal weight: 30.0000 chunk 295 optimal weight: 20.0000 chunk 364 optimal weight: 0.9980 chunk 234 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 overall best weight: 3.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 HIS C 543 GLN ** C 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 ASN C 700 GLN C 718 ASN D 262 GLN D 368 ASN ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.131169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.104193 restraints weight = 121068.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.102698 restraints weight = 84146.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.103076 restraints weight = 73905.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.103332 restraints weight = 62941.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.103426 restraints weight = 55915.046| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5558 moved from start: 0.6251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 35973 Z= 0.164 Angle : 0.669 11.326 49438 Z= 0.351 Chirality : 0.044 0.200 5716 Planarity : 0.005 0.078 5909 Dihedral : 19.210 178.467 6218 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.14 % Allowed : 20.56 % Favored : 75.30 % 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 aren not related in a simple way. whole: -1.66 (0.13), residues: 4131 helix: -0.22 (0.13), residues: 1602 sheet: -1.51 (0.23), residues: 456 loop : -1.71 (0.13), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 153 TYR 0.036 0.002 TYR O 139 PHE 0.017 0.002 PHE C1121 TRP 0.021 0.002 TRP D 223 HIS 0.007 0.001 HIS P 164 Details of bonding type rmsd covalent geometry : bond 0.00375 (35967) covalent geometry : angle 0.66828 (49432) hydrogen bonds : bond 0.04217 ( 1422) hydrogen bonds : angle 5.18722 ( 3834) metal coordination : bond 0.00388 ( 6) metal coordination : angle 1.97617 ( 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 477 residues out of total 3491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 337 time to evaluate : 1.362 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 18 ARG cc_start: 0.7208 (mtp85) cc_final: 0.6917 (ttm170) REVERT: A 110 ILE cc_start: 0.7599 (OUTLIER) cc_final: 0.7337 (tt) REVERT: A 151 GLN cc_start: 0.5634 (mm110) cc_final: 0.5200 (mm110) REVERT: A 172 LEU cc_start: 0.7544 (tp) cc_final: 0.7339 (tp) REVERT: B 1 MET cc_start: 0.3799 (tpp) cc_final: 0.3309 (ttt) REVERT: B 84 VAL cc_start: 0.5590 (OUTLIER) cc_final: 0.5367 (m) REVERT: C 57 GLN cc_start: 0.6523 (mm-40) cc_final: 0.6027 (mm-40) REVERT: C 76 GLU cc_start: 0.3300 (pt0) cc_final: 0.2548 (tm-30) REVERT: C 96 ILE cc_start: 0.6462 (mt) cc_final: 0.6129 (pt) REVERT: C 146 GLU cc_start: 0.3910 (OUTLIER) cc_final: 0.3052 (tm-30) REVERT: C 300 PHE cc_start: 0.4673 (m-80) cc_final: 0.4158 (m-10) REVERT: C 302 LYS cc_start: 0.5989 (mmmt) cc_final: 0.5488 (tppt) REVERT: C 440 MET cc_start: 0.7414 (tpt) cc_final: 0.6843 (tpt) REVERT: C 474 ASP cc_start: 0.5763 (OUTLIER) cc_final: 0.5030 (m-30) REVERT: C 556 GLU cc_start: 0.3005 (pt0) cc_final: 0.2752 (tp30) REVERT: C 557 PRO cc_start: 0.4940 (Cg_endo) cc_final: 0.4019 (Cg_exo) REVERT: C 618 LEU cc_start: 0.6842 (mt) cc_final: 0.6251 (mp) REVERT: C 630 MET cc_start: 0.6014 (OUTLIER) cc_final: 0.5095 (ttm) REVERT: C 710 ASP cc_start: 0.4992 (t0) cc_final: 0.4627 (t0) REVERT: C 754 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6647 (tt0) REVERT: C 846 LYS cc_start: 0.6922 (mmtp) cc_final: 0.6454 (mttp) REVERT: C 939 CYS cc_start: 0.6222 (m) cc_final: 0.5579 (m) REVERT: C 1051 MET cc_start: 0.6475 (tpt) cc_final: 0.6172 (tpp) REVERT: C 1072 GLU cc_start: 0.6055 (OUTLIER) cc_final: 0.5669 (mm-30) REVERT: D 6 PHE cc_start: 0.5027 (t80) cc_final: 0.4780 (t80) REVERT: D 223 TRP cc_start: 0.4245 (t-100) cc_final: 0.3951 (t-100) REVERT: D 450 GLU cc_start: 0.6746 (tp30) cc_final: 0.6492 (tp30) REVERT: D 477 GLU cc_start: 0.7124 (mm-30) cc_final: 0.6795 (mm-30) REVERT: D 541 MET cc_start: 0.7661 (OUTLIER) cc_final: 0.7397 (mmm) REVERT: D 634 LYS cc_start: 0.6532 (ttpt) cc_final: 0.6126 (mttm) REVERT: D 679 LEU cc_start: 0.7353 (tt) cc_final: 0.6812 (mp) REVERT: D 948 GLU cc_start: 0.6530 (mp0) cc_final: 0.6131 (mp0) REVERT: D 1059 GLU cc_start: 0.6030 (tp30) cc_final: 0.5563 (tp30) REVERT: D 1085 ARG cc_start: 0.5674 (mtp-110) cc_final: 0.5270 (ttm-80) REVERT: D 1097 ARG cc_start: 0.4238 (pmt-80) cc_final: 0.3621 (ptt-90) REVERT: E 55 ILE cc_start: 0.7627 (mm) cc_final: 0.7412 (mm) REVERT: F 283 TRP cc_start: 0.5160 (t60) cc_final: 0.4942 (t60) REVERT: F 297 GLU cc_start: 0.6910 (mt-10) cc_final: 0.6554 (mt-10) REVERT: F 411 LEU cc_start: 0.6682 (mm) cc_final: 0.6397 (mt) REVERT: F 453 PHE cc_start: 0.6638 (t80) cc_final: 0.6318 (t80) REVERT: O 152 TYR cc_start: 0.5430 (t80) cc_final: 0.5053 (t80) REVERT: N 82 LEU cc_start: 0.1164 (mt) cc_final: 0.0782 (pp) REVERT: N 159 LYS cc_start: -0.0531 (OUTLIER) cc_final: -0.0875 (ptpp) outliers start: 140 outliers final: 88 residues processed: 454 average time/residue: 0.2395 time to fit residues: 174.7606 Evaluate side-chains 388 residues out of total 3491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 291 time to evaluate : 1.317 ------------------------------------------------------------------------------- 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 110 ILE Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 84 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 39 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 115 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 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 514 THR 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 630 MET Chi-restraints excluded: chain C residue 636 ILE Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 687 CYS 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 868 LEU Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 945 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1046 THR 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 D residue 1 MET Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 46 LEU 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 358 ILE 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 541 MET Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 870 SER Chi-restraints excluded: chain D residue 879 ASP Chi-restraints excluded: chain D residue 927 THR Chi-restraints excluded: chain D residue 965 VAL 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 68 TYR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain F residue 278 ARG Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 393 GLU 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 F residue 501 GLU Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain P residue 143 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 46 VAL Chi-restraints excluded: chain Q residue 48 VAL 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: 20.0000 chunk 125 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 188 optimal weight: 9.9990 chunk 51 optimal weight: 30.0000 chunk 43 optimal weight: 9.9990 chunk 131 optimal weight: 0.9980 chunk 387 optimal weight: 30.0000 chunk 250 optimal weight: 20.0000 chunk 223 optimal weight: 9.9990 chunk 273 optimal weight: 5.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 438 GLN C 545 ASN C 603 ASN C1054 GLN ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 505 HIS ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 767 HIS ** D1139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 193 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 = 0.4287 r_free = 0.4287 target = 0.129209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.102028 restraints weight = 120036.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.100470 restraints weight = 87535.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.101131 restraints weight = 74641.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.101069 restraints weight = 68198.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.101196 restraints weight = 56696.629| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5632 moved from start: 0.7147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 35973 Z= 0.211 Angle : 0.759 12.001 49438 Z= 0.398 Chirality : 0.047 0.308 5716 Planarity : 0.006 0.064 5909 Dihedral : 19.398 178.231 6218 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 4.28 % Allowed : 21.95 % Favored : 73.77 % 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 aren not related in a simple way. whole: -1.87 (0.12), residues: 4131 helix: -0.49 (0.13), residues: 1589 sheet: -1.41 (0.24), residues: 437 loop : -1.80 (0.13), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 166 TYR 0.026 0.002 TYR O 139 PHE 0.024 0.003 PHE C 214 TRP 0.033 0.003 TRP O 179 HIS 0.011 0.002 HIS Q 164 Details of bonding type rmsd covalent geometry : bond 0.00477 (35967) covalent geometry : angle 0.75858 (49432) hydrogen bonds : bond 0.04869 ( 1422) hydrogen bonds : angle 5.46546 ( 3834) metal coordination : bond 0.00490 ( 6) metal coordination : angle 3.11220 ( 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 466 residues out of total 3491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 321 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.5956 (OUTLIER) cc_final: 0.5717 (mm) REVERT: A 110 ILE cc_start: 0.7770 (OUTLIER) cc_final: 0.7433 (tt) REVERT: A 151 GLN cc_start: 0.5510 (mm110) cc_final: 0.5070 (mm110) REVERT: A 190 ASP cc_start: 0.5003 (m-30) cc_final: 0.4742 (m-30) REVERT: C 146 GLU cc_start: 0.3890 (OUTLIER) cc_final: 0.3021 (tm-30) REVERT: C 212 LEU cc_start: -0.0472 (OUTLIER) cc_final: -0.0672 (pp) REVERT: C 300 PHE cc_start: 0.4968 (m-80) cc_final: 0.4496 (m-10) REVERT: C 302 LYS cc_start: 0.6091 (mmmt) cc_final: 0.5676 (tppt) REVERT: C 352 GLN cc_start: 0.4599 (tm-30) cc_final: 0.4204 (tm-30) REVERT: C 355 MET cc_start: 0.2480 (mtp) cc_final: 0.2153 (ttt) REVERT: C 440 MET cc_start: 0.7393 (tpt) cc_final: 0.7107 (tpt) REVERT: C 630 MET cc_start: 0.5745 (OUTLIER) cc_final: 0.4768 (ttm) REVERT: C 789 ILE cc_start: 0.6648 (OUTLIER) cc_final: 0.6444 (mm) REVERT: C 1028 MET cc_start: 0.6991 (ttt) cc_final: 0.6757 (mtp) REVERT: C 1051 MET cc_start: 0.6541 (tpt) cc_final: 0.6257 (tpp) REVERT: C 1072 GLU cc_start: 0.6108 (OUTLIER) cc_final: 0.5823 (mm-30) REVERT: D 6 PHE cc_start: 0.5026 (t80) cc_final: 0.4824 (t80) REVERT: D 89 ARG cc_start: 0.6951 (ttm-80) cc_final: 0.6587 (mtp85) REVERT: D 152 GLU cc_start: 0.6504 (tp30) cc_final: 0.6250 (tp30) REVERT: D 155 MET cc_start: 0.4789 (tpp) cc_final: 0.4496 (tpp) REVERT: D 296 LEU cc_start: 0.7350 (tp) cc_final: 0.7114 (tt) REVERT: D 312 MET cc_start: 0.5386 (ttt) cc_final: 0.4929 (ttt) REVERT: D 450 GLU cc_start: 0.6725 (tp30) cc_final: 0.6512 (tp30) REVERT: D 477 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7070 (mt-10) REVERT: D 634 LYS cc_start: 0.6532 (ttpt) cc_final: 0.6161 (mttt) REVERT: D 688 MET cc_start: 0.7276 (OUTLIER) cc_final: 0.7021 (mmt) REVERT: D 759 GLN cc_start: 0.5334 (mp10) cc_final: 0.4635 (mt0) REVERT: D 1097 ARG cc_start: 0.4166 (pmt-80) cc_final: 0.3823 (ptt90) REVERT: E 55 ILE cc_start: 0.7706 (mm) cc_final: 0.7396 (mm) REVERT: F 297 GLU cc_start: 0.6894 (mt-10) cc_final: 0.6535 (mt-10) REVERT: F 397 GLU cc_start: 0.4785 (mp0) cc_final: 0.4172 (mm-30) REVERT: F 411 LEU cc_start: 0.6791 (mm) cc_final: 0.6527 (mt) REVERT: G 278 ARG cc_start: 0.2501 (mtp180) cc_final: 0.1900 (ttm170) REVERT: O 152 TYR cc_start: 0.5412 (t80) cc_final: 0.4430 (t80) REVERT: O 155 PHE cc_start: 0.6501 (t80) cc_final: 0.5841 (t80) REVERT: O 197 LEU cc_start: 0.6197 (OUTLIER) cc_final: 0.5987 (mp) REVERT: P 152 TYR cc_start: 0.3019 (t80) cc_final: 0.2784 (t80) REVERT: P 188 ARG cc_start: 0.4637 (OUTLIER) cc_final: 0.3738 (tmm160) REVERT: N 159 LYS cc_start: -0.0635 (OUTLIER) cc_final: -0.0950 (ptpp) outliers start: 145 outliers final: 94 residues processed: 446 average time/residue: 0.2341 time to fit residues: 169.4202 Evaluate side-chains 376 residues out of total 3491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 271 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 83 LEU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 64 THR 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 39 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 115 VAL 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 147 ILE Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 320 LEU 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 488 THR Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 514 THR 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 630 MET Chi-restraints excluded: chain C residue 636 ILE 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 762 THR Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 832 VAL Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 945 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1046 THR Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1084 THR Chi-restraints excluded: chain C residue 1103 TYR 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 169 GLU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 462 ASP 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 633 ILE 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 688 MET 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 879 ASP Chi-restraints excluded: chain D residue 965 VAL Chi-restraints excluded: chain D residue 972 THR 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 83 VAL Chi-restraints excluded: chain F residue 278 ARG Chi-restraints excluded: chain F residue 393 GLU 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 F residue 501 GLU Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 143 LEU Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 156 GLU Chi-restraints excluded: chain P residue 188 ARG 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 Q residue 62 ARG Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 215 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 241 optimal weight: 9.9990 chunk 400 optimal weight: 20.0000 chunk 202 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 176 optimal weight: 9.9990 chunk 406 optimal weight: 20.0000 chunk 313 optimal weight: 10.0000 chunk 231 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 218 optimal weight: 30.0000 chunk 24 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN A 185 GLN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 GLN ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 193 HIS ** 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 = 0.4296 r_free = 0.4296 target = 0.129711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.103160 restraints weight = 120834.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.101000 restraints weight = 96088.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.101996 restraints weight = 77923.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.102018 restraints weight = 64868.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.102149 restraints weight = 56519.647| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5596 moved from start: 0.7366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35973 Z= 0.150 Angle : 0.655 11.031 49438 Z= 0.344 Chirality : 0.043 0.194 5716 Planarity : 0.005 0.070 5909 Dihedral : 19.244 178.807 6218 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.57 % Allowed : 22.66 % Favored : 73.77 % 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 aren not related in a simple way. whole: -1.58 (0.13), residues: 4131 helix: -0.20 (0.13), residues: 1588 sheet: -1.21 (0.25), residues: 435 loop : -1.69 (0.13), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 478 TYR 0.020 0.002 TYR O 139 PHE 0.016 0.002 PHE D1061 TRP 0.034 0.002 TRP D 223 HIS 0.007 0.001 HIS N 193 Details of bonding type rmsd covalent geometry : bond 0.00342 (35967) covalent geometry : angle 0.65400 (49432) hydrogen bonds : bond 0.04126 ( 1422) hydrogen bonds : angle 5.12212 ( 3834) metal coordination : bond 0.00340 ( 6) metal coordination : angle 2.91383 ( 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 433 residues out of total 3491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 312 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.7452 (mtp85) cc_final: 0.7052 (ttm170) REVERT: A 83 LEU cc_start: 0.6142 (OUTLIER) cc_final: 0.5740 (mm) REVERT: A 110 ILE cc_start: 0.7497 (OUTLIER) cc_final: 0.7213 (tt) REVERT: A 190 ASP cc_start: 0.5107 (m-30) cc_final: 0.4815 (m-30) REVERT: B 1 MET cc_start: 0.4007 (tpp) cc_final: 0.3753 (tpt) REVERT: B 168 TYR cc_start: 0.6602 (m-10) cc_final: 0.6383 (m-80) REVERT: B 190 ASP cc_start: 0.6462 (p0) cc_final: 0.5942 (p0) REVERT: C 300 PHE cc_start: 0.5110 (m-80) cc_final: 0.4626 (m-10) REVERT: C 313 ARG cc_start: 0.5927 (mmm160) cc_final: 0.5623 (tpp80) REVERT: C 373 PHE cc_start: 0.7206 (OUTLIER) cc_final: 0.6216 (m-10) REVERT: C 418 ILE cc_start: 0.7042 (mt) cc_final: 0.6466 (mm) REVERT: C 440 MET cc_start: 0.7464 (tpt) cc_final: 0.6861 (tpt) REVERT: C 570 TYR cc_start: 0.3924 (OUTLIER) cc_final: 0.3132 (m-10) REVERT: C 754 GLU cc_start: 0.6797 (OUTLIER) cc_final: 0.6408 (tt0) REVERT: C 1028 MET cc_start: 0.7026 (ttt) cc_final: 0.6732 (mtp) REVERT: C 1051 MET cc_start: 0.6530 (tpt) cc_final: 0.6308 (tpp) REVERT: C 1072 GLU cc_start: 0.6098 (OUTLIER) cc_final: 0.5828 (mm-30) REVERT: C 1086 GLN cc_start: 0.6678 (OUTLIER) cc_final: 0.6406 (tt0) REVERT: C 1103 TYR cc_start: 0.6071 (OUTLIER) cc_final: 0.5100 (m-80) REVERT: D 6 PHE cc_start: 0.5017 (t80) cc_final: 0.4789 (t80) REVERT: D 155 MET cc_start: 0.4865 (tpp) cc_final: 0.4171 (tpp) REVERT: D 234 LEU cc_start: 0.6308 (OUTLIER) cc_final: 0.5980 (tt) REVERT: D 312 MET cc_start: 0.5131 (ttt) cc_final: 0.4766 (ttt) REVERT: D 450 GLU cc_start: 0.6703 (tp30) cc_final: 0.6475 (tp30) REVERT: D 634 LYS cc_start: 0.6567 (ttpt) cc_final: 0.6123 (mttt) REVERT: D 759 GLN cc_start: 0.5411 (mp10) cc_final: 0.4711 (mt0) REVERT: D 887 ARG cc_start: 0.6788 (mmt90) cc_final: 0.6280 (mmm160) REVERT: D 948 GLU cc_start: 0.6875 (mp0) cc_final: 0.6528 (mp0) REVERT: D 1097 ARG cc_start: 0.4130 (OUTLIER) cc_final: 0.3305 (ptt-90) REVERT: E 55 ILE cc_start: 0.7668 (mm) cc_final: 0.7344 (mm) REVERT: F 240 LEU cc_start: 0.5512 (mt) cc_final: 0.4393 (tt) REVERT: F 297 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6784 (mt-10) REVERT: F 397 GLU cc_start: 0.4707 (mp0) cc_final: 0.4354 (mm-30) REVERT: F 401 LYS cc_start: 0.6391 (ttmt) cc_final: 0.5796 (mtmt) REVERT: F 411 LEU cc_start: 0.6742 (mm) cc_final: 0.6535 (mt) REVERT: O 152 TYR cc_start: 0.5560 (t80) cc_final: 0.5226 (t80) REVERT: O 155 PHE cc_start: 0.6491 (t80) cc_final: 0.5353 (t80) REVERT: P 63 LEU cc_start: 0.2217 (mt) cc_final: 0.1900 (tt) REVERT: P 152 TYR cc_start: 0.3240 (t80) cc_final: 0.3006 (t80) REVERT: N 159 LYS cc_start: -0.0455 (OUTLIER) cc_final: -0.0809 (ptpp) REVERT: N 206 GLU cc_start: 0.1584 (pt0) cc_final: 0.1352 (mt-10) outliers start: 121 outliers final: 82 residues processed: 415 average time/residue: 0.2299 time to fit residues: 155.3219 Evaluate side-chains 363 residues out of total 3491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 270 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 83 LEU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain B residue 64 THR 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 39 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 257 ILE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 383 GLU Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 581 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 754 GLU Chi-restraints excluded: chain C residue 762 THR Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 832 VAL Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 945 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1046 THR Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1086 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 46 LEU 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 358 ILE Chi-restraints excluded: chain D residue 392 THR 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 633 ILE Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 653 HIS Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 846 VAL 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 1097 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 68 TYR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain F residue 278 ARG Chi-restraints excluded: chain F residue 393 GLU 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 501 GLU Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain O residue 127 VAL Chi-restraints excluded: chain O residue 201 LEU Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 143 LEU Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 156 GLU Chi-restraints excluded: chain P residue 192 VAL 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 46 VAL Chi-restraints excluded: chain Q residue 62 ARG Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 215 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: 0.6980 chunk 50 optimal weight: 7.9990 chunk 381 optimal weight: 10.0000 chunk 378 optimal weight: 20.0000 chunk 220 optimal weight: 9.9990 chunk 255 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 298 optimal weight: 6.9990 chunk 19 optimal weight: 30.0000 chunk 235 optimal weight: 2.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 ASN ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 767 HIS ** D1139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 193 HIS ** 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 = 0.4276 r_free = 0.4276 target = 0.128552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.102038 restraints weight = 120659.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.099710 restraints weight = 86657.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.100064 restraints weight = 77636.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.100443 restraints weight = 64588.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.100485 restraints weight = 55490.892| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5663 moved from start: 0.7772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 35973 Z= 0.192 Angle : 0.727 11.829 49438 Z= 0.380 Chirality : 0.046 0.230 5716 Planarity : 0.006 0.064 5909 Dihedral : 19.298 177.394 6218 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 3.96 % Allowed : 22.92 % Favored : 73.12 % 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 aren not related in a simple way. whole: -1.72 (0.13), residues: 4131 helix: -0.37 (0.13), residues: 1580 sheet: -1.37 (0.25), residues: 445 loop : -1.68 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 153 TYR 0.020 0.002 TYR D 248 PHE 0.021 0.002 PHE D1061 TRP 0.046 0.003 TRP D 223 HIS 0.008 0.002 HIS Q 164 Details of bonding type rmsd covalent geometry : bond 0.00440 (35967) covalent geometry : angle 0.72535 (49432) hydrogen bonds : bond 0.04620 ( 1422) hydrogen bonds : angle 5.31215 ( 3834) metal coordination : bond 0.00481 ( 6) metal coordination : angle 4.20746 ( 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 429 residues out of total 3491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 295 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.6109 (OUTLIER) cc_final: 0.5708 (mm) REVERT: A 110 ILE cc_start: 0.7615 (OUTLIER) cc_final: 0.7334 (tt) REVERT: A 190 ASP cc_start: 0.5484 (m-30) cc_final: 0.5211 (m-30) REVERT: B 1 MET cc_start: 0.4404 (tpp) cc_final: 0.3928 (tpt) REVERT: B 168 TYR cc_start: 0.6643 (m-10) cc_final: 0.6338 (m-80) REVERT: B 190 ASP cc_start: 0.6178 (p0) cc_final: 0.5734 (p0) REVERT: C 163 LYS cc_start: 0.6848 (mttp) cc_final: 0.6487 (mtpt) REVERT: C 300 PHE cc_start: 0.5212 (m-80) cc_final: 0.4695 (m-10) REVERT: C 373 PHE cc_start: 0.7212 (OUTLIER) cc_final: 0.6112 (m-10) REVERT: C 440 MET cc_start: 0.7179 (tpt) cc_final: 0.6660 (tpt) REVERT: C 1028 MET cc_start: 0.7119 (ttt) cc_final: 0.6851 (mtp) REVERT: C 1051 MET cc_start: 0.6616 (tpt) cc_final: 0.6240 (tpp) REVERT: C 1072 GLU cc_start: 0.6168 (OUTLIER) cc_final: 0.5889 (mm-30) REVERT: C 1103 TYR cc_start: 0.6172 (OUTLIER) cc_final: 0.5247 (m-80) REVERT: D 6 PHE cc_start: 0.5177 (t80) cc_final: 0.4957 (t80) REVERT: D 155 MET cc_start: 0.4590 (tpp) cc_final: 0.4058 (tpp) REVERT: D 312 MET cc_start: 0.5462 (ttt) cc_final: 0.4966 (ttt) REVERT: D 450 GLU cc_start: 0.6828 (tp30) cc_final: 0.6507 (tp30) REVERT: D 580 ASP cc_start: 0.7176 (OUTLIER) cc_final: 0.6782 (t0) REVERT: D 634 LYS cc_start: 0.6523 (ttpt) cc_final: 0.6095 (mttt) REVERT: D 660 ASP cc_start: 0.5188 (OUTLIER) cc_final: 0.4839 (m-30) REVERT: D 759 GLN cc_start: 0.5265 (mp10) cc_final: 0.4577 (mt0) REVERT: D 887 ARG cc_start: 0.6634 (mmt90) cc_final: 0.6298 (mmm160) REVERT: D 1097 ARG cc_start: 0.4256 (OUTLIER) cc_final: 0.3509 (ptt-90) REVERT: E 55 ILE cc_start: 0.7681 (mm) cc_final: 0.7380 (mm) REVERT: F 240 LEU cc_start: 0.5351 (mt) cc_final: 0.4659 (tt) REVERT: F 268 GLU cc_start: 0.3938 (OUTLIER) cc_final: 0.3178 (pp20) REVERT: F 297 GLU cc_start: 0.7100 (mt-10) cc_final: 0.6812 (mt-10) REVERT: F 397 GLU cc_start: 0.5164 (mp0) cc_final: 0.4563 (mm-30) REVERT: F 401 LYS cc_start: 0.6508 (ttmt) cc_final: 0.5947 (mtmt) REVERT: G 278 ARG cc_start: 0.2384 (mtp180) cc_final: 0.1705 (ttm170) REVERT: O 152 TYR cc_start: 0.5470 (t80) cc_final: 0.5143 (t80) REVERT: O 155 PHE cc_start: 0.6623 (t80) cc_final: 0.5486 (t80) REVERT: P 63 LEU cc_start: 0.2393 (mt) cc_final: 0.2103 (tt) REVERT: P 188 ARG cc_start: 0.4390 (OUTLIER) cc_final: 0.3575 (tmm160) REVERT: N 159 LYS cc_start: -0.0557 (OUTLIER) cc_final: -0.0886 (ptpp) REVERT: N 206 GLU cc_start: 0.2359 (pt0) cc_final: 0.2049 (mm-30) outliers start: 134 outliers final: 103 residues processed: 415 average time/residue: 0.2136 time to fit residues: 144.8630 Evaluate side-chains 374 residues out of total 3491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 260 time to evaluate : 1.296 ------------------------------------------------------------------------------- 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 83 LEU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 136 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 39 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 69 ARG 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 257 ILE Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 383 GLU Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 520 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 636 ILE 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 689 ILE 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 868 LEU Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 945 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1046 THR Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1084 THR 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 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 280 VAL Chi-restraints excluded: chain D residue 289 LYS Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 633 ILE 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 708 VAL 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 870 SER Chi-restraints excluded: chain D residue 879 ASP 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 1097 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 268 GLU Chi-restraints excluded: chain F residue 278 ARG Chi-restraints excluded: chain F residue 393 GLU Chi-restraints excluded: chain F residue 395 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 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 201 LEU Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 143 LEU Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 156 GLU Chi-restraints excluded: chain P residue 188 ARG Chi-restraints excluded: chain P residue 192 VAL Chi-restraints excluded: chain N residue 159 LYS Chi-restraints excluded: chain N residue 170 THR Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 62 ARG Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain Q residue 215 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 260 optimal weight: 8.9990 chunk 275 optimal weight: 5.9990 chunk 282 optimal weight: 9.9990 chunk 208 optimal weight: 9.9990 chunk 181 optimal weight: 9.9990 chunk 278 optimal weight: 10.0000 chunk 244 optimal weight: 0.0980 chunk 389 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 143 optimal weight: 9.9990 chunk 359 optimal weight: 0.8980 overall best weight: 4.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN C 150 GLN ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 679 ASN ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 193 HIS ** 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 = 0.4274 r_free = 0.4274 target = 0.128411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.101107 restraints weight = 120258.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.099909 restraints weight = 82516.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.100063 restraints weight = 70651.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.100260 restraints weight = 70146.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.100348 restraints weight = 55540.628| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5665 moved from start: 0.8065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 35973 Z= 0.180 Angle : 0.705 12.557 49438 Z= 0.368 Chirality : 0.045 0.202 5716 Planarity : 0.006 0.064 5909 Dihedral : 19.244 177.446 6218 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.84 % Allowed : 23.57 % 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 aren not related in a simple way. whole: -1.67 (0.13), residues: 4131 helix: -0.33 (0.13), residues: 1564 sheet: -1.28 (0.25), residues: 442 loop : -1.65 (0.13), residues: 2125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 313 TYR 0.024 0.002 TYR A 176 PHE 0.020 0.002 PHE C1011 TRP 0.049 0.002 TRP D 223 HIS 0.008 0.002 HIS D1150 Details of bonding type rmsd covalent geometry : bond 0.00413 (35967) covalent geometry : angle 0.70311 (49432) hydrogen bonds : bond 0.04433 ( 1422) hydrogen bonds : angle 5.25998 ( 3834) metal coordination : bond 0.00435 ( 6) metal coordination : angle 4.28855 ( 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 433 residues out of total 3491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 303 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.6087 (OUTLIER) cc_final: 0.5685 (mm) REVERT: B 1 MET cc_start: 0.4527 (tpp) cc_final: 0.4062 (tpt) REVERT: B 168 TYR cc_start: 0.6635 (m-10) cc_final: 0.6349 (m-80) REVERT: B 190 ASP cc_start: 0.6053 (p0) cc_final: 0.5794 (p0) REVERT: B 215 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7098 (tt) REVERT: C 163 LYS cc_start: 0.6808 (mttp) cc_final: 0.6430 (mtpt) REVERT: C 300 PHE cc_start: 0.5234 (m-80) cc_final: 0.4818 (m-10) REVERT: C 373 PHE cc_start: 0.7274 (OUTLIER) cc_final: 0.6215 (m-10) REVERT: C 398 ARG cc_start: 0.5427 (mtp180) cc_final: 0.5010 (mmm-85) REVERT: C 440 MET cc_start: 0.7166 (tpt) cc_final: 0.6532 (tpt) REVERT: C 500 LEU cc_start: 0.7200 (OUTLIER) cc_final: 0.6866 (tp) REVERT: C 570 TYR cc_start: 0.4201 (OUTLIER) cc_final: 0.3497 (m-10) REVERT: C 786 GLU cc_start: 0.5309 (tm-30) cc_final: 0.4718 (mp0) REVERT: C 1028 MET cc_start: 0.7034 (ttt) cc_final: 0.6757 (mtp) REVERT: C 1051 MET cc_start: 0.6597 (tpt) cc_final: 0.6267 (tpp) REVERT: C 1072 GLU cc_start: 0.6146 (OUTLIER) cc_final: 0.5904 (mm-30) REVERT: C 1103 TYR cc_start: 0.5872 (OUTLIER) cc_final: 0.5104 (m-80) REVERT: D 155 MET cc_start: 0.4542 (tpp) cc_final: 0.4127 (tpp) REVERT: D 312 MET cc_start: 0.5497 (ttt) cc_final: 0.5027 (ttt) REVERT: D 450 GLU cc_start: 0.6781 (tp30) cc_final: 0.6496 (tp30) REVERT: D 580 ASP cc_start: 0.7191 (OUTLIER) cc_final: 0.6795 (t0) REVERT: D 634 LYS cc_start: 0.6536 (ttpt) cc_final: 0.6116 (mttt) REVERT: D 660 ASP cc_start: 0.4918 (OUTLIER) cc_final: 0.4666 (m-30) REVERT: D 759 GLN cc_start: 0.5349 (mp10) cc_final: 0.4719 (mt0) REVERT: D 887 ARG cc_start: 0.6616 (mmt90) cc_final: 0.6295 (mmm160) REVERT: D 1085 ARG cc_start: 0.5694 (mtp-110) cc_final: 0.4656 (mtt90) REVERT: E 55 ILE cc_start: 0.7617 (mm) cc_final: 0.7332 (mm) REVERT: E 106 HIS cc_start: 0.6269 (p90) cc_final: 0.5704 (p90) REVERT: F 240 LEU cc_start: 0.5870 (mt) cc_final: 0.4676 (tt) REVERT: F 268 GLU cc_start: 0.4166 (OUTLIER) cc_final: 0.3342 (pp20) REVERT: F 297 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6863 (mt-10) REVERT: F 397 GLU cc_start: 0.5343 (mp0) cc_final: 0.4661 (mm-30) REVERT: G 278 ARG cc_start: 0.2521 (mtp180) cc_final: 0.1847 (ttm170) REVERT: O 152 TYR cc_start: 0.5536 (t80) cc_final: 0.5216 (t80) REVERT: O 155 PHE cc_start: 0.6520 (t80) cc_final: 0.5341 (t80) REVERT: P 63 LEU cc_start: 0.2560 (mt) cc_final: 0.2272 (tt) REVERT: P 188 ARG cc_start: 0.4217 (OUTLIER) cc_final: 0.3568 (tmm160) REVERT: N 107 ARG cc_start: 0.0874 (mmt-90) cc_final: 0.0394 (mmt-90) REVERT: N 159 LYS cc_start: -0.0649 (OUTLIER) cc_final: -0.0965 (ptpp) outliers start: 130 outliers final: 95 residues processed: 413 average time/residue: 0.2092 time to fit residues: 141.6213 Evaluate side-chains 382 residues out of total 3491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 275 time to evaluate : 1.128 ------------------------------------------------------------------------------- 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 83 LEU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 136 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 B residue 215 LEU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 115 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 185 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 383 GLU Chi-restraints excluded: chain C residue 488 THR 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 529 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 636 ILE 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 689 ILE 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 868 LEU Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1046 THR Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1084 THR Chi-restraints excluded: chain C residue 1103 TYR Chi-restraints excluded: chain C residue 1125 LEU 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 150 THR 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 317 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 633 ILE 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 708 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 870 SER Chi-restraints excluded: chain D residue 879 ASP Chi-restraints excluded: chain D residue 965 VAL Chi-restraints excluded: chain D residue 972 THR 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 268 GLU Chi-restraints excluded: chain F residue 278 ARG Chi-restraints excluded: chain F residue 393 GLU Chi-restraints excluded: chain F residue 395 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 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 201 LEU Chi-restraints excluded: chain P residue 143 LEU Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 156 GLU Chi-restraints excluded: chain P residue 188 ARG Chi-restraints excluded: chain P residue 192 VAL Chi-restraints excluded: chain N residue 159 LYS Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 62 ARG Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain Q residue 215 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 217 optimal weight: 10.0000 chunk 148 optimal weight: 9.9990 chunk 271 optimal weight: 7.9990 chunk 36 optimal weight: 30.0000 chunk 179 optimal weight: 5.9990 chunk 395 optimal weight: 6.9990 chunk 241 optimal weight: 8.9990 chunk 121 optimal weight: 8.9990 chunk 187 optimal weight: 0.8980 chunk 351 optimal weight: 10.0000 chunk 400 optimal weight: 0.0980 overall best weight: 4.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN B 119 HIS ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 ASN ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 193 HIS ** 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 = 0.4273 r_free = 0.4273 target = 0.128181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.099971 restraints weight = 120023.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.099473 restraints weight = 79489.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.099278 restraints weight = 61451.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.099541 restraints weight = 67081.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.099693 restraints weight = 51475.821| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5682 moved from start: 0.8303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 35973 Z= 0.173 Angle : 0.703 12.672 49438 Z= 0.367 Chirality : 0.045 0.217 5716 Planarity : 0.005 0.051 5909 Dihedral : 19.176 177.160 6218 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 3.72 % Allowed : 23.72 % Favored : 72.56 % 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 aren not related in a simple way. whole: -1.68 (0.13), residues: 4131 helix: -0.32 (0.13), residues: 1577 sheet: -1.41 (0.25), residues: 449 loop : -1.66 (0.13), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 313 TYR 0.025 0.002 TYR A 176 PHE 0.026 0.002 PHE C1011 TRP 0.059 0.002 TRP D 223 HIS 0.011 0.002 HIS N 193 Details of bonding type rmsd covalent geometry : bond 0.00395 (35967) covalent geometry : angle 0.70123 (49432) hydrogen bonds : bond 0.04395 ( 1422) hydrogen bonds : angle 5.21775 ( 3834) metal coordination : bond 0.00457 ( 6) metal coordination : angle 4.47555 ( 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: 126 poor density : 299 time to evaluate : 1.447 Fit side-chains revert: symmetry clash REVERT: A 83 LEU cc_start: 0.6070 (OUTLIER) cc_final: 0.5673 (mm) REVERT: A 153 ARG cc_start: 0.4989 (tpt90) cc_final: 0.4619 (mmp-170) REVERT: B 1 MET cc_start: 0.4531 (tpp) cc_final: 0.4057 (tpt) REVERT: B 168 TYR cc_start: 0.6605 (m-10) cc_final: 0.6323 (m-80) REVERT: B 190 ASP cc_start: 0.6410 (p0) cc_final: 0.5939 (p0) REVERT: B 215 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.7100 (tt) REVERT: C 163 LYS cc_start: 0.6644 (mttp) cc_final: 0.6180 (mtpt) REVERT: C 300 PHE cc_start: 0.5317 (m-80) cc_final: 0.4930 (m-10) REVERT: C 373 PHE cc_start: 0.7244 (OUTLIER) cc_final: 0.6183 (m-10) REVERT: C 440 MET cc_start: 0.7162 (tpt) cc_final: 0.6571 (tpt) REVERT: C 441 ASP cc_start: 0.6637 (t0) cc_final: 0.6279 (t0) REVERT: C 500 LEU cc_start: 0.7186 (OUTLIER) cc_final: 0.6846 (tp) REVERT: C 539 HIS cc_start: 0.6740 (m-70) cc_final: 0.6290 (m-70) REVERT: C 570 TYR cc_start: 0.4127 (OUTLIER) cc_final: 0.3645 (m-10) REVERT: C 578 TYR cc_start: 0.7096 (m-80) cc_final: 0.6678 (t80) REVERT: C 754 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.6659 (tt0) REVERT: C 779 GLU cc_start: 0.1824 (tt0) cc_final: 0.1277 (pt0) REVERT: C 786 GLU cc_start: 0.5490 (tm-30) cc_final: 0.4941 (mp0) REVERT: C 1028 MET cc_start: 0.7055 (ttt) cc_final: 0.6785 (mtp) REVERT: C 1051 MET cc_start: 0.6639 (tpt) cc_final: 0.6332 (tpp) REVERT: C 1072 GLU cc_start: 0.6094 (OUTLIER) cc_final: 0.5836 (mm-30) REVERT: C 1103 TYR cc_start: 0.5689 (OUTLIER) cc_final: 0.4910 (m-80) REVERT: C 1125 LEU cc_start: 0.5383 (OUTLIER) cc_final: 0.5173 (mt) REVERT: D 155 MET cc_start: 0.4694 (tpp) cc_final: 0.4441 (tpp) REVERT: D 252 PHE cc_start: 0.5270 (OUTLIER) cc_final: 0.5036 (p90) REVERT: D 312 MET cc_start: 0.5489 (ttt) cc_final: 0.4980 (ttt) REVERT: D 450 GLU cc_start: 0.6779 (tp30) cc_final: 0.6492 (tp30) REVERT: D 634 LYS cc_start: 0.6522 (ttpt) cc_final: 0.6095 (mttt) REVERT: D 660 ASP cc_start: 0.4938 (OUTLIER) cc_final: 0.4730 (m-30) REVERT: D 759 GLN cc_start: 0.5267 (mp10) cc_final: 0.4610 (mt0) REVERT: D 1085 ARG cc_start: 0.5561 (mtp-110) cc_final: 0.4479 (mtt90) REVERT: D 1155 GLU cc_start: 0.6639 (mt-10) cc_final: 0.6414 (pt0) REVERT: E 55 ILE cc_start: 0.7662 (mm) cc_final: 0.7378 (mm) REVERT: E 106 HIS cc_start: 0.6260 (p90) cc_final: 0.5704 (p90) REVERT: F 297 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6944 (mt-10) REVERT: F 397 GLU cc_start: 0.5441 (mp0) cc_final: 0.4604 (mm-30) REVERT: G 278 ARG cc_start: 0.2521 (mtp180) cc_final: 0.1710 (ttm170) REVERT: O 152 TYR cc_start: 0.5565 (t80) cc_final: 0.5199 (t80) REVERT: O 155 PHE cc_start: 0.6491 (t80) cc_final: 0.5307 (t80) REVERT: P 63 LEU cc_start: 0.2480 (mt) cc_final: 0.2228 (tt) REVERT: P 188 ARG cc_start: 0.4225 (OUTLIER) cc_final: 0.3580 (tmm160) REVERT: N 107 ARG cc_start: 0.0779 (mmt-90) cc_final: 0.0311 (mmt-90) REVERT: N 159 LYS cc_start: -0.0645 (OUTLIER) cc_final: -0.0849 (ptpp) outliers start: 126 outliers final: 101 residues processed: 407 average time/residue: 0.2297 time to fit residues: 154.6731 Evaluate side-chains 381 residues out of total 3491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 267 time to evaluate : 1.357 ------------------------------------------------------------------------------- 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 83 LEU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 136 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 B residue 215 LEU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 383 GLU Chi-restraints excluded: chain C residue 488 THR 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 520 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 636 ILE 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 689 ILE 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 868 LEU Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1046 THR Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1084 THR Chi-restraints excluded: chain C residue 1103 TYR Chi-restraints excluded: chain C residue 1125 LEU 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 150 THR Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 486 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 633 ILE 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 708 VAL Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 870 SER Chi-restraints excluded: chain D residue 879 ASP Chi-restraints excluded: chain D residue 965 VAL Chi-restraints excluded: chain D residue 972 THR 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 278 ARG Chi-restraints excluded: chain F residue 393 GLU Chi-restraints excluded: chain F residue 395 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 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 201 LEU Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 143 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 188 ARG Chi-restraints excluded: chain P residue 192 VAL Chi-restraints excluded: chain N residue 159 LYS Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 62 ARG Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain Q residue 215 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 357 optimal weight: 9.9990 chunk 347 optimal weight: 1.9990 chunk 187 optimal weight: 0.7980 chunk 296 optimal weight: 9.9990 chunk 364 optimal weight: 20.0000 chunk 375 optimal weight: 0.0000 chunk 41 optimal weight: 6.9990 chunk 136 optimal weight: 9.9990 chunk 30 optimal weight: 20.0000 chunk 108 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 overall best weight: 2.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 679 ASN D 349 ASN ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 674 ASN ** D1139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 516 HIS ** G 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 193 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 = 0.128909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.101329 restraints weight = 119316.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.099495 restraints weight = 79333.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.099622 restraints weight = 72751.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.099908 restraints weight = 66951.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.100030 restraints weight = 54460.405| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5680 moved from start: 0.8373 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= 0.135 Angle : 0.647 11.695 49438 Z= 0.337 Chirality : 0.043 0.220 5716 Planarity : 0.005 0.057 5909 Dihedral : 18.985 179.222 6218 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.13 % Allowed : 24.58 % Favored : 72.29 % 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 aren not related in a simple way. whole: -1.39 (0.13), residues: 4131 helix: -0.03 (0.13), residues: 1567 sheet: -1.29 (0.25), residues: 452 loop : -1.51 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 313 TYR 0.027 0.001 TYR A 176 PHE 0.024 0.002 PHE C1011 TRP 0.053 0.002 TRP D 223 HIS 0.008 0.001 HIS N 193 Details of bonding type rmsd covalent geometry : bond 0.00305 (35967) covalent geometry : angle 0.64551 (49432) hydrogen bonds : bond 0.03922 ( 1422) hydrogen bonds : angle 5.00836 ( 3834) metal coordination : bond 0.00361 ( 6) metal coordination : angle 3.34724 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6412.09 seconds wall clock time: 111 minutes 35.33 seconds (6695.33 seconds total)