Starting phenix.real_space_refine on Wed Nov 19 21:11:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6bzo_7319/11_2025/6bzo_7319_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6bzo_7319/11_2025/6bzo_7319.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6bzo_7319/11_2025/6bzo_7319.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6bzo_7319/11_2025/6bzo_7319.map" model { file = "/net/cci-nas-00/data/ceres_data/6bzo_7319/11_2025/6bzo_7319_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6bzo_7319/11_2025/6bzo_7319_neut_trim.cif" } resolution = 3.38 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= 0.011 sd= 0.105 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 55 5.49 5 Mg 1 5.21 5 S 98 5.16 5 Cl 2 4.86 5 C 16922 2.51 5 N 4841 2.21 5 O 5341 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27262 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1724 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 211} Chain: "B" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1775 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 220} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 8556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1111, 8556 Classifications: {'peptide': 1111} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 60, 'TRANS': 1046} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 5, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 53 Chain: "D" Number of atoms: 9857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1263, 9857 Classifications: {'peptide': 1263} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 57, 'TRANS': 1201} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 649 Classifications: {'peptide': 83} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 76} Chain: "F" Number of atoms: 2588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2588 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 316} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "J" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 872 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "O" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 634 Classifications: {'DNA': 31} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 30} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 526 Classifications: {'DNA': 26} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 25} Chain: "C" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 72 Unusual residues: {'FI8': 1} Classifications: {'undetermined': 1} 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} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19086 SG CYS D 891 110.212 96.606 106.836 1.00 81.66 S ATOM 19653 SG CYS D 968 106.169 96.391 105.314 1.00 77.99 S ATOM 19695 SG CYS D 975 107.660 94.511 107.869 1.00 72.31 S ATOM 19713 SG CYS D 978 107.803 97.672 108.917 1.00 71.90 S ATOM 12528 SG CYS D 60 74.249 55.490 67.937 1.00 82.81 S ATOM 12546 SG CYS D 62 73.167 54.920 64.739 1.00 82.09 S ATOM 12655 SG CYS D 75 76.507 55.093 64.395 1.00 84.36 S ATOM 12681 SG CYS D 78 74.819 58.045 64.898 1.00 81.78 S Time building chain proxies: 6.31, per 1000 atoms: 0.23 Number of scatterers: 27262 At special positions: 0 Unit cell: (130.9, 157.3, 194.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 Cl 2 17.00 S 98 16.00 P 55 15.00 Mg 1 11.99 O 5341 8.00 N 4841 7.00 C 16922 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: 2.58 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1401 " pdb="ZN ZN D1401 " - pdb=" SG CYS D 978 " pdb="ZN ZN D1401 " - pdb=" SG CYS D 968 " pdb="ZN ZN D1401 " - pdb=" SG CYS D 891 " pdb="ZN ZN D1401 " - pdb=" SG CYS D 975 " pdb=" ZN D1402 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 60 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 78 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 75 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 62 " Number of angles added : 12 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6180 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 39 sheets defined 40.7% alpha, 13.7% beta 26 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 3.05 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 removed outlier: 3.563A pdb=" N THR A 41 " --> pdb=" O SER A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 203 through 220 removed outlier: 3.694A pdb=" N LEU A 218 " --> pdb=" O THR A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'B' and resid 30 through 45 removed outlier: 3.645A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 81 removed outlier: 3.931A pdb=" N ILE B 77 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N LEU B 78 " --> pdb=" O THR B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 208 through 224 removed outlier: 3.866A pdb=" N LEU B 218 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LEU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 56 removed outlier: 4.230A pdb=" N VAL C 56 " --> pdb=" O LEU C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 67 through 77 removed outlier: 3.764A pdb=" N ARG C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 94 removed outlier: 4.019A pdb=" N GLU C 92 " --> pdb=" O GLU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 125 Processing helix chain 'C' and resid 225 through 229 removed outlier: 3.568A pdb=" N ARG C 228 " --> pdb=" O ARG C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 241 removed outlier: 3.604A pdb=" N LEU C 237 " --> pdb=" O PRO C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 252 removed outlier: 3.817A pdb=" N VAL C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 264 removed outlier: 3.997A pdb=" N SER C 260 " --> pdb=" O GLU C 256 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR C 261 " --> pdb=" O ILE C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 282 removed outlier: 4.418A pdb=" N ASP C 276 " --> pdb=" O GLU C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 294 Processing helix chain 'C' and resid 295 through 299 removed outlier: 3.676A pdb=" N LEU C 299 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 321 removed outlier: 3.813A pdb=" N ASN C 317 " --> pdb=" O ARG C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 349 removed outlier: 3.668A pdb=" N VAL C 338 " --> pdb=" O THR C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 397 removed outlier: 3.762A pdb=" N ARG C 395 " --> pdb=" O VAL C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 removed outlier: 3.621A pdb=" N LEU C 417 " --> pdb=" O THR C 413 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE C 418 " --> pdb=" O PRO C 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 413 through 418' Processing helix chain 'C' and resid 420 through 432 removed outlier: 3.703A pdb=" N VAL C 424 " --> pdb=" O ILE C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 452 removed outlier: 3.540A pdb=" N LYS C 452 " --> pdb=" O GLY C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 538 removed outlier: 4.247A pdb=" N ASP C 537 " --> pdb=" O ALA C 533 " (cutoff:3.500A) removed outlier: 4.234A 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 590 through 594 removed outlier: 3.905A pdb=" N MET C 593 " --> pdb=" O ALA C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 611 Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 815 through 823 removed outlier: 3.561A pdb=" N LEU C 821 " --> pdb=" O GLU C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 858 No H-bonds generated for 'chain 'C' and resid 856 through 858' Processing helix chain 'C' and resid 922 through 927 removed outlier: 3.562A pdb=" N ARG C 925 " --> pdb=" O VAL C 922 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN C 927 " --> pdb=" O ARG C 924 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 943 removed outlier: 3.824A pdb=" N THR C 934 " --> pdb=" O GLN C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 953 through 957 removed outlier: 3.607A pdb=" N ALA C 957 " --> pdb=" O ASP C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 989 removed outlier: 4.119A pdb=" N GLN C 986 " --> pdb=" O GLU C 982 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLY C 987 " --> pdb=" O ALA C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 1036 through 1041 removed outlier: 3.642A pdb=" N LYS C1040 " --> pdb=" O LEU C1036 " (cutoff:3.500A) Processing helix chain 'C' and resid 1070 through 1080 Processing helix chain 'C' and resid 1081 through 1090 removed outlier: 3.527A pdb=" N LEU C1085 " --> pdb=" O ALA C1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 1095 through 1109 removed outlier: 3.609A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS C1101 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA C1105 " --> pdb=" O LYS C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1122 removed outlier: 3.560A pdb=" N PHE C1121 " --> pdb=" O PRO C1118 " (cutoff:3.500A) Processing helix chain 'C' and resid 1123 through 1130 Processing helix chain 'D' and resid 16 through 24 removed outlier: 3.996A pdb=" N ARG D 21 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN D 22 " --> pdb=" O GLU D 18 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER D 24 " --> pdb=" O ILE D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 90 removed outlier: 3.705A pdb=" N ARG D 88 " --> pdb=" O ALA D 85 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG D 89 " --> pdb=" O LYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.762A pdb=" N PHE D 107 " --> pdb=" O HIS D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 118 Processing helix chain 'D' and resid 121 through 130 removed outlier: 4.011A pdb=" N LYS D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE D 128 " --> pdb=" O ASP D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 147 Processing helix chain 'D' and resid 147 through 185 removed outlier: 3.597A pdb=" N GLN D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU D 170 " --> pdb=" O ARG D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 228 removed outlier: 3.667A pdb=" N GLU D 215 " --> pdb=" O ARG D 211 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS D 228 " --> pdb=" O SER D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 247 Processing helix chain 'D' and resid 248 through 250 No H-bonds generated for 'chain 'D' and resid 248 through 250' Processing helix chain 'D' and resid 256 through 267 removed outlier: 3.780A pdb=" N SER D 260 " --> pdb=" O MET D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 284 Processing helix chain 'D' and resid 289 through 305 removed outlier: 3.610A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 339 through 361 removed outlier: 3.546A pdb=" N LEU D 343 " --> pdb=" O ASP D 339 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP D 359 " --> pdb=" O LYS D 355 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU D 360 " --> pdb=" O ARG D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 removed outlier: 3.531A pdb=" N VAL D 367 " --> pdb=" O PRO D 363 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN D 369 " --> pdb=" O ILE D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 406 Processing helix chain 'D' and resid 407 through 411 removed outlier: 3.958A pdb=" N GLN D 410 " --> pdb=" O LYS D 407 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY D 411 " --> pdb=" O GLY D 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 407 through 411' Processing helix chain 'D' and resid 445 through 452 Processing helix chain 'D' and resid 452 through 463 removed outlier: 3.875A pdb=" N VAL D 461 " --> pdb=" O MET D 457 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP D 462 " --> pdb=" O LYS D 458 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU D 463 " --> pdb=" O ARG D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 482 through 492 removed outlier: 3.811A pdb=" N VAL D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU D 488 " --> pdb=" O TRP D 484 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA D 492 " --> pdb=" O GLU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 527 No H-bonds generated for 'chain 'D' and resid 525 through 527' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 560 through 564 removed outlier: 3.664A pdb=" N ASN D 563 " --> pdb=" O LEU D 560 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN D 564 " --> pdb=" O SER D 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 560 through 564' Processing helix chain 'D' and resid 578 through 590 removed outlier: 3.667A pdb=" N THR D 583 " --> pdb=" O LEU D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 624 removed outlier: 3.752A pdb=" N ARG D 624 " --> pdb=" O MET D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 643 through 651 removed outlier: 3.852A pdb=" N GLU D 649 " --> pdb=" O GLU D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 675 removed outlier: 3.956A pdb=" N VAL D 671 " --> pdb=" O THR D 667 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 704 Processing helix chain 'D' and resid 705 through 726 removed outlier: 3.999A pdb=" N VAL D 709 " --> pdb=" O PRO D 705 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA D 710 " --> pdb=" O MET D 706 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN D 711 " --> pdb=" O ILE D 707 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG D 726 " --> pdb=" O TYR D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 763 removed outlier: 3.957A pdb=" N ILE D 745 " --> pdb=" O ARG D 741 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 793 Processing helix chain 'D' and resid 797 through 805 removed outlier: 4.557A pdb=" N VAL D 803 " --> pdb=" O ILE D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 810 through 818 removed outlier: 3.737A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 881 removed outlier: 4.113A pdb=" N HIS D 854 " --> pdb=" O PHE D 850 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU D 860 " --> pdb=" O ALA D 856 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY D 871 " --> pdb=" O THR D 867 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N TYR D 872 " --> pdb=" O ALA D 868 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU D 873 " --> pdb=" O ASP D 869 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 956 Processing helix chain 'D' and resid 964 through 968 removed outlier: 3.676A pdb=" N CYS D 968 " --> pdb=" O VAL D 965 " (cutoff:3.500A) Processing helix chain 'D' and resid 975 through 980 Processing helix chain 'D' and resid 994 through 1005 removed outlier: 3.623A pdb=" N VAL D 998 " --> pdb=" O ALA D 994 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA D 999 " --> pdb=" O VAL D 995 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE D1003 " --> pdb=" O ALA D 999 " (cutoff:3.500A) Processing helix chain 'D' and resid 1006 through 1010 Processing helix chain 'D' and resid 1027 through 1036 removed outlier: 3.502A pdb=" N VAL D1031 " --> pdb=" O GLY D1027 " (cutoff:3.500A) Processing helix chain 'D' and resid 1117 through 1126 removed outlier: 3.504A pdb=" N VAL D1121 " --> pdb=" O ASP D1117 " (cutoff:3.500A) Processing helix chain 'D' and resid 1126 through 1144 removed outlier: 3.563A pdb=" N VAL D1130 " --> pdb=" O GLY D1126 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE D1132 " --> pdb=" O ARG D1128 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL D1141 " --> pdb=" O GLU D1137 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1159 removed outlier: 4.131A pdb=" N ILE D1154 " --> pdb=" O HIS D1150 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1191 removed outlier: 3.545A pdb=" N ASN D1190 " --> pdb=" O PHE D1186 " (cutoff:3.500A) Processing helix chain 'D' and resid 1209 through 1216 removed outlier: 3.967A pdb=" N ALA D1216 " --> pdb=" O LYS D1212 " (cutoff:3.500A) Processing helix chain 'D' and resid 1219 through 1225 Processing helix chain 'D' and resid 1228 through 1237 removed outlier: 4.253A pdb=" N ASP D1235 " --> pdb=" O ARG D1231 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA D1236 " --> pdb=" O VAL D1232 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1255 Processing helix chain 'D' and resid 1260 through 1263 Processing helix chain 'D' and resid 1264 through 1269 Processing helix chain 'D' and resid 1275 through 1282 removed outlier: 3.929A pdb=" N ALA D1281 " --> pdb=" O GLU D1277 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA D1282 " --> pdb=" O ALA D1278 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 37 Processing helix chain 'E' and resid 49 through 70 removed outlier: 3.540A pdb=" N LEU E 53 " --> pdb=" O SER E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'F' and resid 207 through 226 removed outlier: 3.945A pdb=" N GLN F 214 " --> pdb=" O GLU F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 237 removed outlier: 4.226A pdb=" N ALA F 230 " --> pdb=" O ASP F 226 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS F 237 " --> pdb=" O LYS F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 270 removed outlier: 3.579A pdb=" N LYS F 251 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR F 264 " --> pdb=" O THR F 260 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU F 265 " --> pdb=" O GLN F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 308 removed outlier: 4.122A pdb=" N MET F 281 " --> pdb=" O GLN F 277 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ARG F 301 " --> pdb=" O GLU F 297 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N LEU F 302 " --> pdb=" O ALA F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 334 Processing helix chain 'F' and resid 342 through 362 removed outlier: 3.698A pdb=" N TYR F 346 " --> pdb=" O LYS F 342 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N TRP F 349 " --> pdb=" O THR F 345 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TRP F 350 " --> pdb=" O TYR F 346 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE F 355 " --> pdb=" O ILE F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 391 removed outlier: 3.527A pdb=" N VAL F 375 " --> pdb=" O HIS F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 403 Processing helix chain 'F' and resid 406 through 418 removed outlier: 3.633A pdb=" N ARG F 418 " --> pdb=" O GLN F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 437 Processing helix chain 'F' and resid 446 through 465 removed outlier: 3.998A pdb=" N THR F 454 " --> pdb=" O ALA F 450 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU F 455 " --> pdb=" O VAL F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 468 through 480 removed outlier: 3.666A pdb=" N ALA F 472 " --> pdb=" O SER F 468 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLY F 473 " --> pdb=" O GLU F 469 " (cutoff:3.500A) Processing helix chain 'F' and resid 488 through 497 removed outlier: 3.778A pdb=" N GLY F 493 " --> pdb=" O LEU F 489 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR F 496 " --> pdb=" O ILE F 492 " (cutoff:3.500A) Processing helix chain 'F' and resid 499 through 515 removed outlier: 4.145A pdb=" N ILE F 506 " --> pdb=" O ARG F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 516 through 524 removed outlier: 4.377A pdb=" N VAL F 522 " --> pdb=" O SER F 518 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU F 523 " --> pdb=" O ARG F 519 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 89 removed outlier: 3.688A pdb=" N ARG J 88 " --> pdb=" O MET J 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 107 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 15 removed outlier: 3.776A pdb=" N GLU A 24 " --> pdb=" O THR A 8 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 14 " --> pdb=" O ARG A 18 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ARG A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ASP A 195 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL A 174 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLU A 197 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 100 removed outlier: 7.973A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A 50 " --> pdb=" O GLU A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AA4, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA5, first strand: chain 'B' and resid 8 through 10 removed outlier: 3.517A pdb=" N VAL B 22 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL B 22 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU B 194 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N GLU B 24 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N LEU B 192 " --> pdb=" O GLU B 24 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE B 193 " --> pdb=" O TYR B 176 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N TYR B 176 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASP B 195 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL B 174 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLU B 197 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 93 through 99 removed outlier: 7.751A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA8, first strand: chain 'B' and resid 103 through 106 removed outlier: 3.878A pdb=" N ALA B 126 " --> pdb=" O VAL B 105 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 96 through 97 removed outlier: 5.420A pdb=" N LEU C 105 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE C 140 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N PHE C 107 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLU C 138 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ASP C 109 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR C 136 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ALA C 131 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ASP C 156 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU C 133 " --> pdb=" O MET C 154 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS C 148 " --> pdb=" O PHE C 139 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB2, first strand: chain 'C' and resid 376 through 379 removed outlier: 6.895A pdb=" N SER C 177 " --> pdb=" O SER C 456 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 184 through 191 Processing sheet with id=AB4, first strand: chain 'C' and resid 354 through 357 removed outlier: 5.549A pdb=" N VAL C 357 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N VAL C 361 " --> pdb=" O VAL C 357 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 505 through 506 removed outlier: 5.110A pdb=" N GLU C 527 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL C 520 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N SER C 525 " --> pdb=" O VAL C 520 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 505 through 506 Processing sheet with id=AB7, first strand: chain 'C' and resid 558 through 560 Processing sheet with id=AB8, first strand: chain 'C' and resid 626 through 627 removed outlier: 3.626A pdb=" N GLY C 627 " --> pdb=" O VAL C 972 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.664A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N CYS C 687 " --> pdb=" O ASP C 704 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 648 through 653 removed outlier: 6.819A pdb=" N THR C 659 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N VAL C 653 " --> pdb=" O TYR C 657 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TYR C 657 " --> pdb=" O VAL C 653 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 7.263A pdb=" N ILE C 735 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ILE C 898 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU C 737 " --> pdb=" O ILE C 898 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 749 through 759 removed outlier: 3.710A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC5, first strand: chain 'C' and resid 801 through 803 removed outlier: 6.860A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 3.541A pdb=" N ARG D 427 " --> pdb=" O HIS C1042 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N CYS D 441 " --> pdb=" O MET D 515 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL D 517 " --> pdb=" O CYS D 441 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LEU D 443 " --> pdb=" O VAL D 517 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 3.541A pdb=" N ARG D 427 " --> pdb=" O HIS C1042 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LEU D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL D 431 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1066 through 1068 Processing sheet with id=AC9, first strand: chain 'C' and resid 1136 through 1138 removed outlier: 3.764A pdb=" N LEU C1138 " --> pdb=" O GLU D 9 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 93 through 102 removed outlier: 10.047A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.859A pdb=" N ALA D 99 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ALA D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 234 through 235 removed outlier: 6.616A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 421 through 422 removed outlier: 6.653A pdb=" N PHE D 335 " --> pdb=" O ILE F 421 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU F 440 " --> pdb=" O LEU J 6 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 392 through 393 removed outlier: 3.934A pdb=" N ARG D 397 " --> pdb=" O GLY D 393 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 633 through 637 removed outlier: 3.701A pdb=" N LEU D 637 " --> pdb=" O TRP D 662 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 897 through 899 removed outlier: 3.543A pdb=" N VAL D 899 " --> pdb=" O VAL D 960 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL D 960 " --> pdb=" O VAL D 899 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N THR D 924 " --> pdb=" O ARG D 963 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 929 through 930 Processing sheet with id=AD8, first strand: chain 'D' and resid 1051 through 1055 Processing sheet with id=AD9, first strand: chain 'D' and resid 1180 through 1182 removed outlier: 4.636A pdb=" N ARG D1164 " --> pdb=" O VAL D1206 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ALA D1202 " --> pdb=" O ILE D1168 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 1271 through 1274 removed outlier: 3.595A pdb=" N GLN D1273 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU E 105 " --> pdb=" O GLN D1273 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 27 through 33 Processing sheet with id=AE3, first strand: chain 'J' and resid 53 through 55 1002 hydrogen bonds defined for protein. 2805 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 61 hydrogen bonds 122 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 6.28 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 4609 1.29 - 1.42: 6697 1.42 - 1.55: 16236 1.55 - 1.68: 116 1.68 - 1.81: 175 Bond restraints: 27833 Sorted by residual: bond pdb=" C ARG J 10 " pdb=" O ARG J 10 " ideal model delta sigma weight residual 1.234 1.161 0.073 1.07e-02 8.73e+03 4.66e+01 bond pdb=" CA ARG J 10 " pdb=" C ARG J 10 " ideal model delta sigma weight residual 1.528 1.443 0.085 1.34e-02 5.57e+03 4.01e+01 bond pdb=" C2 FI8 C1201 " pdb=" O1 FI8 C1201 " ideal model delta sigma weight residual 1.326 1.427 -0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" C49 FI8 C1201 " pdb=" O17 FI8 C1201 " ideal model delta sigma weight residual 1.332 1.426 -0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" CA ARG J 10 " pdb=" CB ARG J 10 " ideal model delta sigma weight residual 1.526 1.461 0.066 1.44e-02 4.82e+03 2.08e+01 ... (remaining 27828 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 37497 2.15 - 4.30: 411 4.30 - 6.45: 35 6.45 - 8.60: 9 8.60 - 10.75: 3 Bond angle restraints: 37955 Sorted by residual: angle pdb=" C PHE C 254 " pdb=" N SER C 255 " pdb=" CA SER C 255 " ideal model delta sigma weight residual 121.70 131.37 -9.67 1.80e+00 3.09e-01 2.89e+01 angle pdb=" C ARG J 10 " pdb=" CA ARG J 10 " pdb=" CB ARG J 10 " ideal model delta sigma weight residual 113.33 102.58 10.75 2.26e+00 1.96e-01 2.26e+01 angle pdb=" N ASP D 140 " pdb=" CA ASP D 140 " pdb=" C ASP D 140 " ideal model delta sigma weight residual 109.62 116.54 -6.92 1.50e+00 4.44e-01 2.13e+01 angle pdb=" N ARG J 10 " pdb=" CA ARG J 10 " pdb=" CB ARG J 10 " ideal model delta sigma weight residual 110.45 104.40 6.05 1.44e+00 4.82e-01 1.77e+01 angle pdb=" C LYS C 229 " pdb=" N ARG C 230 " pdb=" CA ARG C 230 " ideal model delta sigma weight residual 121.54 129.06 -7.52 1.91e+00 2.74e-01 1.55e+01 ... (remaining 37950 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.95: 16398 32.95 - 65.91: 537 65.91 - 98.86: 22 98.86 - 131.81: 0 131.81 - 164.76: 5 Dihedral angle restraints: 16962 sinusoidal: 7356 harmonic: 9606 Sorted by residual: dihedral pdb=" CA GLN D 600 " pdb=" C GLN D 600 " pdb=" N PRO D 601 " pdb=" CA PRO D 601 " ideal model delta harmonic sigma weight residual -180.00 -139.69 -40.31 0 5.00e+00 4.00e-02 6.50e+01 dihedral pdb=" CA PHE C 61 " pdb=" C PHE C 61 " pdb=" N GLU C 62 " pdb=" CA GLU C 62 " ideal model delta harmonic sigma weight residual 180.00 142.47 37.53 0 5.00e+00 4.00e-02 5.64e+01 dihedral pdb=" CA VAL D1194 " pdb=" C VAL D1194 " pdb=" N ALA D1195 " pdb=" CA ALA D1195 " ideal model delta harmonic sigma weight residual -180.00 -147.14 -32.86 0 5.00e+00 4.00e-02 4.32e+01 ... (remaining 16959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3806 0.060 - 0.121: 497 0.121 - 0.181: 17 0.181 - 0.241: 2 0.241 - 0.301: 2 Chirality restraints: 4324 Sorted by residual: chirality pdb=" CA PHE C 254 " pdb=" N PHE C 254 " pdb=" C PHE C 254 " pdb=" CB PHE C 254 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA LEU D 910 " pdb=" N LEU D 910 " pdb=" C LEU D 910 " pdb=" CB LEU D 910 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA VAL D1098 " pdb=" N VAL D1098 " pdb=" C VAL D1098 " pdb=" CB VAL D1098 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.75e-01 ... (remaining 4321 not shown) Planarity restraints: 4797 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 959 " -0.066 5.00e-02 4.00e+02 9.98e-02 1.59e+01 pdb=" N PRO C 960 " 0.173 5.00e-02 4.00e+02 pdb=" CA PRO C 960 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO C 960 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG D1087 " 0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C ARG D1087 " -0.056 2.00e-02 2.50e+03 pdb=" O ARG D1087 " 0.021 2.00e-02 2.50e+03 pdb=" N VAL D1088 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN D 600 " 0.049 5.00e-02 4.00e+02 7.44e-02 8.85e+00 pdb=" N PRO D 601 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO D 601 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 601 " 0.041 5.00e-02 4.00e+02 ... (remaining 4794 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 209 2.48 - 3.08: 21450 3.08 - 3.69: 39642 3.69 - 4.29: 57950 4.29 - 4.90: 95879 Nonbonded interactions: 215130 Sorted by model distance: nonbonded pdb=" NH1 ARG C 633 " pdb=" OD2 ASP C 637 " model vdw 1.869 3.120 nonbonded pdb=" OE2 GLU D 323 " pdb=" O HOH D1501 " model vdw 1.934 3.040 nonbonded pdb=" OE2 GLU D 750 " pdb=" NZ LYS D 837 " model vdw 1.964 3.120 nonbonded pdb=" NZ LYS C 163 " pdb=" O GLY C 639 " model vdw 1.969 3.120 nonbonded pdb=" OG1 THR D 970 " pdb=" O GLY D 973 " model vdw 1.972 3.040 ... (remaining 215125 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 1 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 \ 83 or (resid 184 and (name N or name CA or name C or name O or name CB )) or res \ id 185 or (resid 186 and (name N or name CA or name C or name O or name CB )) or \ resid 187 through 223 or (resid 224 and (name N or name CA or name C or name O \ or name CB )) or resid 225 through 226)) selection = (chain 'B' and resid 1 through 226) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 31.610 Find NCS groups from input model: 0.250 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:1.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 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 : 0.003 0.101 27841 Z= 0.173 Angle : 0.631 25.985 37967 Z= 0.325 Chirality : 0.039 0.301 4324 Planarity : 0.004 0.100 4797 Dihedral : 14.705 164.764 10782 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 39.31 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.13 % Favored : 89.51 % Rotamer: Outliers : 7.27 % Allowed : 9.78 % Favored : 82.95 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.16 % Twisted Proline : 0.58 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.07 (0.12), residues: 3335 helix: -1.75 (0.13), residues: 1172 sheet: -2.58 (0.24), residues: 357 loop : -3.52 (0.12), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D1097 TYR 0.007 0.001 TYR A 168 PHE 0.024 0.001 PHE C 254 TRP 0.013 0.001 TRP C 63 HIS 0.003 0.000 HIS C 200 Details of bonding type rmsd covalent geometry : bond 0.00315 (27833) covalent geometry : angle 0.54849 (37955) hydrogen bonds : bond 0.15722 ( 1058) hydrogen bonds : angle 6.70726 ( 2927) metal coordination : bond 0.04352 ( 8) metal coordination : angle 17.52467 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 256 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLN cc_start: 0.7773 (mm-40) cc_final: 0.6915 (mm-40) REVERT: A 153 ARG cc_start: 0.7187 (ttp80) cc_final: 0.6825 (ptm160) REVERT: A 221 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8832 (pt) REVERT: B 27 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8097 (pp20) REVERT: B 206 ASP cc_start: 0.7846 (m-30) cc_final: 0.7492 (t0) REVERT: C 407 GLN cc_start: 0.7123 (mm110) cc_final: 0.6787 (tt0) REVERT: C 795 GLU cc_start: 0.7644 (tp30) cc_final: 0.7363 (tp30) REVERT: C 833 ARG cc_start: 0.7962 (mtp85) cc_final: 0.7294 (ttm110) REVERT: D 1012 MET cc_start: 0.5975 (OUTLIER) cc_final: 0.5073 (mtt) REVERT: D 1080 ILE cc_start: 0.8113 (mt) cc_final: 0.7391 (mt) REVERT: D 1176 LEU cc_start: 0.8690 (mp) cc_final: 0.8315 (tp) REVERT: D 1208 MET cc_start: 0.8893 (ptt) cc_final: 0.8687 (ptm) REVERT: F 206 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.8005 (tm-30) REVERT: F 207 ASP cc_start: 0.7123 (OUTLIER) cc_final: 0.6402 (t0) REVERT: F 258 TYR cc_start: 0.8352 (t80) cc_final: 0.7790 (t80) REVERT: F 353 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.8773 (pp30) REVERT: F 418 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7712 (mtp-110) REVERT: J 7 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7922 (ptm-80) REVERT: J 20 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.7548 (ptp90) REVERT: J 27 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.7615 (ptp-110) REVERT: J 84 MET cc_start: 0.8580 (mtp) cc_final: 0.8373 (mtp) outliers start: 203 outliers final: 111 residues processed: 437 average time/residue: 0.2224 time to fit residues: 145.2517 Evaluate side-chains 276 residues out of total 2837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 155 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 232 GLN Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 709 ASP Chi-restraints excluded: chain C residue 797 ARG Chi-restraints excluded: chain C residue 814 LEU Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 899 LEU Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 965 GLU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1076 MET Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 263 LYS Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 639 GLN Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 741 ARG Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 883 ASP Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 1012 MET Chi-restraints excluded: chain D residue 1057 ASP Chi-restraints excluded: chain D residue 1061 PHE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1096 GLU Chi-restraints excluded: chain D residue 1097 ARG Chi-restraints excluded: chain D residue 1098 VAL Chi-restraints excluded: chain D residue 1099 LEU Chi-restraints excluded: chain D residue 1121 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain F residue 206 GLU Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 282 MET Chi-restraints excluded: chain F residue 286 ARG Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 353 GLN Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 397 GLU Chi-restraints excluded: chain F residue 398 GLU Chi-restraints excluded: chain F residue 418 ARG Chi-restraints excluded: chain F residue 423 LEU Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 461 GLN Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain J residue 4 ARG Chi-restraints excluded: chain J residue 7 ARG Chi-restraints excluded: chain J residue 20 ARG Chi-restraints excluded: chain J residue 27 ARG Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 99 LYS Chi-restraints excluded: chain J residue 103 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 197 optimal weight: 0.0570 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.3980 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 9.9990 overall best weight: 1.0502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 HIS B 5 GLN B 79 ASN B 151 GLN C 57 GLN C 317 ASN C 349 HIS C 388 GLN C 476 HIS C 479 HIS ** C 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 920 HIS C 986 GLN C1066 GLN D 175 GLN D 369 ASN D 439 HIS D 468 ASN D 499 ASN D 505 HIS D 540 GLN D 639 GLN D 687 GLN D1084 GLN D1139 GLN D1145 GLN D1251 ASN E 69 ASN E 106 HIS F 293 ASN F 322 GLN F 353 GLN F 388 GLN F 457 GLN F 516 HIS J 36 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.096101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.069636 restraints weight = 66780.458| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.87 r_work: 0.2995 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27841 Z= 0.137 Angle : 0.676 12.422 37967 Z= 0.342 Chirality : 0.044 0.181 4324 Planarity : 0.005 0.107 4797 Dihedral : 15.738 164.892 4685 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.48 % Favored : 93.31 % Rotamer: Outliers : 4.69 % Allowed : 12.36 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.16 % Twisted Proline : 1.16 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.14), residues: 3335 helix: -0.22 (0.15), residues: 1240 sheet: -1.80 (0.26), residues: 346 loop : -2.58 (0.13), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 182 TYR 0.014 0.001 TYR C 344 PHE 0.016 0.001 PHE B 189 TRP 0.013 0.001 TRP C 955 HIS 0.003 0.001 HIS D 792 Details of bonding type rmsd covalent geometry : bond 0.00309 (27833) covalent geometry : angle 0.67435 (37955) hydrogen bonds : bond 0.04062 ( 1058) hydrogen bonds : angle 4.61958 ( 2927) metal coordination : bond 0.00712 ( 8) metal coordination : angle 3.08594 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 204 time to evaluate : 1.080 Fit side-chains revert: symmetry clash REVERT: A 3 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.7969 (pp) REVERT: A 151 GLN cc_start: 0.8056 (mm-40) cc_final: 0.6885 (tp-100) REVERT: A 153 ARG cc_start: 0.7390 (ttp80) cc_final: 0.7102 (ptm160) REVERT: A 223 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8278 (ttp80) REVERT: B 202 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8829 (pt) REVERT: B 206 ASP cc_start: 0.8466 (m-30) cc_final: 0.7919 (t0) REVERT: C 238 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8677 (tt) REVERT: C 246 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7946 (mm-30) REVERT: C 407 GLN cc_start: 0.7816 (mm110) cc_final: 0.7379 (tt0) REVERT: C 455 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.8953 (mt) REVERT: C 607 MET cc_start: 0.8684 (mtt) cc_final: 0.8404 (mtt) REVERT: C 795 GLU cc_start: 0.8146 (tp30) cc_final: 0.7620 (tt0) REVERT: C 1087 GLU cc_start: 0.8567 (tt0) cc_final: 0.8308 (mt-10) REVERT: D 67 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7454 (mmp80) REVERT: D 160 LYS cc_start: 0.9074 (mmmm) cc_final: 0.8712 (mmtp) REVERT: D 177 LEU cc_start: 0.2241 (OUTLIER) cc_final: 0.1990 (tp) REVERT: D 207 GLN cc_start: 0.7182 (OUTLIER) cc_final: 0.6930 (tm-30) REVERT: D 242 ARG cc_start: 0.8607 (mtt90) cc_final: 0.8174 (ptp-110) REVERT: D 506 ARG cc_start: 0.9396 (OUTLIER) cc_final: 0.8468 (ptt-90) REVERT: D 741 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.6453 (ppp80) REVERT: F 202 PHE cc_start: 0.6403 (t80) cc_final: 0.6129 (t80) REVERT: F 204 TRP cc_start: 0.8446 (p-90) cc_final: 0.8154 (p-90) REVERT: F 206 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8237 (tm-30) REVERT: F 207 ASP cc_start: 0.6536 (OUTLIER) cc_final: 0.6181 (t0) REVERT: F 246 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8362 (pm20) REVERT: F 258 TYR cc_start: 0.8566 (t80) cc_final: 0.8134 (t80) REVERT: F 398 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8232 (tm-30) REVERT: J 7 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8310 (ptm-80) REVERT: J 17 GLU cc_start: 0.7878 (mt-10) cc_final: 0.6701 (mt-10) outliers start: 131 outliers final: 70 residues processed: 318 average time/residue: 0.2062 time to fit residues: 101.0479 Evaluate side-chains 244 residues out of total 2837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 159 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 668 ARG Chi-restraints excluded: chain C residue 686 GLN Chi-restraints excluded: chain C residue 797 ARG Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 928 ILE Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1135 VAL Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 741 ARG Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1057 ASP Chi-restraints excluded: chain D residue 1061 PHE Chi-restraints excluded: chain D residue 1097 ARG Chi-restraints excluded: chain D residue 1098 VAL Chi-restraints excluded: chain D residue 1121 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 206 GLU Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 282 MET Chi-restraints excluded: chain F residue 398 GLU Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 461 GLN Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain F residue 503 ILE Chi-restraints excluded: chain J residue 7 ARG Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 98 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 46 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 314 optimal weight: 9.9990 chunk 193 optimal weight: 5.9990 chunk 241 optimal weight: 0.8980 chunk 88 optimal weight: 7.9990 chunk 135 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 322 optimal weight: 8.9990 chunk 273 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 232 GLN C 442 GLN ** C 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 612 GLN D 657 GLN D1133 HIS E 69 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.090618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.063315 restraints weight = 67886.321| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.67 r_work: 0.2789 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.104 27841 Z= 0.346 Angle : 0.776 12.400 37967 Z= 0.398 Chirality : 0.049 0.200 4324 Planarity : 0.006 0.118 4797 Dihedral : 15.462 164.398 4558 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.34 % Favored : 91.45 % Rotamer: Outliers : 5.37 % Allowed : 14.33 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.16 % Twisted Proline : 1.16 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.14), residues: 3335 helix: -0.08 (0.15), residues: 1240 sheet: -1.31 (0.26), residues: 363 loop : -2.41 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 211 TYR 0.022 0.002 TYR C 278 PHE 0.021 0.002 PHE C 906 TRP 0.014 0.002 TRP C 944 HIS 0.007 0.001 HIS J 81 Details of bonding type rmsd covalent geometry : bond 0.00830 (27833) covalent geometry : angle 0.77320 (37955) hydrogen bonds : bond 0.05404 ( 1058) hydrogen bonds : angle 4.81968 ( 2927) metal coordination : bond 0.01884 ( 8) metal coordination : angle 3.73930 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 160 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7605 (tp-100) REVERT: A 223 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8420 (ttp80) REVERT: B 123 MET cc_start: 0.8276 (ttm) cc_final: 0.7805 (ttm) REVERT: B 206 ASP cc_start: 0.8682 (m-30) cc_final: 0.8132 (t0) REVERT: C 407 GLN cc_start: 0.7621 (mm110) cc_final: 0.7337 (tt0) REVERT: C 440 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8440 (ttp) REVERT: C 455 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9082 (mt) REVERT: C 465 ARG cc_start: 0.7849 (ttm-80) cc_final: 0.7572 (ttm-80) REVERT: C 795 GLU cc_start: 0.8223 (tp30) cc_final: 0.7904 (tp30) REVERT: C 933 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8664 (tt0) REVERT: C 959 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7105 (pp) REVERT: D 154 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8089 (mp0) REVERT: D 207 GLN cc_start: 0.7138 (OUTLIER) cc_final: 0.6905 (tm-30) REVERT: D 357 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8706 (tt) REVERT: D 412 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.7975 (mmt90) REVERT: D 663 MET cc_start: 0.8922 (mmm) cc_final: 0.8611 (mmm) REVERT: D 741 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.6633 (ppp80) REVERT: D 899 VAL cc_start: 0.9055 (OUTLIER) cc_final: 0.8849 (m) REVERT: D 1012 MET cc_start: 0.7240 (mpp) cc_final: 0.6752 (mpp) REVERT: F 202 PHE cc_start: 0.6697 (t80) cc_final: 0.6221 (t80) REVERT: F 207 ASP cc_start: 0.6987 (OUTLIER) cc_final: 0.6768 (m-30) REVERT: F 398 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8137 (tm-30) REVERT: F 423 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8792 (tp) REVERT: J 7 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.8381 (ptm-80) outliers start: 150 outliers final: 97 residues processed: 294 average time/residue: 0.1878 time to fit residues: 88.2089 Evaluate side-chains 254 residues out of total 2837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 142 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 686 GLN Chi-restraints excluded: chain C residue 773 ILE Chi-restraints excluded: chain C residue 797 ARG Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 928 ILE Chi-restraints excluded: chain C residue 933 GLU Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 991 CYS Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1135 VAL Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 154 GLU Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 412 ARG Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 741 ARG Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 899 VAL Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1033 GLU Chi-restraints excluded: chain D residue 1057 ASP Chi-restraints excluded: chain D residue 1061 PHE Chi-restraints excluded: chain D residue 1078 ASP Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1098 VAL Chi-restraints excluded: chain D residue 1121 VAL Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 282 MET Chi-restraints excluded: chain F residue 359 MET Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 398 GLU Chi-restraints excluded: chain F residue 423 LEU Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 461 GLN Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain J residue 7 ARG Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 98 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 14 optimal weight: 4.9990 chunk 150 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 210 optimal weight: 0.8980 chunk 292 optimal weight: 9.9990 chunk 193 optimal weight: 0.8980 chunk 272 optimal weight: 10.0000 chunk 199 optimal weight: 0.9980 chunk 166 optimal weight: 0.7980 chunk 310 optimal weight: 0.2980 chunk 303 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 ASN C 298 ASN ** C 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 325 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.095471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.068996 restraints weight = 66277.423| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.88 r_work: 0.2883 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27841 Z= 0.116 Angle : 0.612 15.281 37967 Z= 0.313 Chirality : 0.042 0.181 4324 Planarity : 0.005 0.109 4797 Dihedral : 14.754 165.416 4544 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.55 % Favored : 94.27 % Rotamer: Outliers : 4.80 % Allowed : 14.91 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.16 % Twisted Proline : 1.16 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.14), residues: 3335 helix: 0.56 (0.15), residues: 1235 sheet: -1.04 (0.28), residues: 360 loop : -2.00 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 153 TYR 0.018 0.001 TYR C 278 PHE 0.011 0.001 PHE C 153 TRP 0.015 0.001 TRP C 63 HIS 0.006 0.001 HIS E 106 Details of bonding type rmsd covalent geometry : bond 0.00254 (27833) covalent geometry : angle 0.61106 (37955) hydrogen bonds : bond 0.03641 ( 1058) hydrogen bonds : angle 4.21230 ( 2927) metal coordination : bond 0.00397 ( 8) metal coordination : angle 2.37912 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 171 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 GLN cc_start: 0.8031 (mm-40) cc_final: 0.6857 (tp-100) REVERT: A 185 GLN cc_start: 0.6911 (pm20) cc_final: 0.6530 (pm20) REVERT: B 34 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8221 (pp) REVERT: B 123 MET cc_start: 0.8394 (ttm) cc_final: 0.7879 (ttm) REVERT: B 206 ASP cc_start: 0.8662 (m-30) cc_final: 0.8148 (t0) REVERT: C 59 ASP cc_start: 0.8735 (t0) cc_final: 0.8374 (t0) REVERT: C 238 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8487 (tt) REVERT: C 246 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7876 (mm-30) REVERT: C 465 ARG cc_start: 0.7764 (ttm-80) cc_final: 0.7519 (ttm-80) REVERT: C 467 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7331 (ppt170) REVERT: C 559 VAL cc_start: 0.8496 (t) cc_final: 0.8099 (m) REVERT: C 630 MET cc_start: 0.8954 (tpp) cc_final: 0.8743 (tpp) REVERT: C 723 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8787 (mm) REVERT: C 795 GLU cc_start: 0.8035 (tp30) cc_final: 0.7757 (tt0) REVERT: C 1087 GLU cc_start: 0.8674 (tt0) cc_final: 0.8474 (mt-10) REVERT: D 67 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7308 (mmp80) REVERT: D 154 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8125 (mp0) REVERT: D 245 VAL cc_start: 0.9035 (t) cc_final: 0.8835 (p) REVERT: D 357 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8526 (tt) REVERT: D 506 ARG cc_start: 0.9443 (OUTLIER) cc_final: 0.8341 (ptt-90) REVERT: D 663 MET cc_start: 0.8830 (mmm) cc_final: 0.8504 (mmm) REVERT: D 679 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8958 (tt) REVERT: D 741 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.6646 (ppp80) REVERT: D 978 CYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8859 (m) REVERT: D 1080 ILE cc_start: 0.7523 (OUTLIER) cc_final: 0.6390 (tp) REVERT: E 73 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7227 (pp20) REVERT: F 202 PHE cc_start: 0.6533 (t80) cc_final: 0.6244 (t80) REVERT: F 204 TRP cc_start: 0.8371 (p-90) cc_final: 0.8145 (p-90) REVERT: F 206 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8133 (tm-30) REVERT: F 207 ASP cc_start: 0.6748 (OUTLIER) cc_final: 0.6138 (t0) REVERT: F 246 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8364 (pm20) REVERT: F 293 ASN cc_start: 0.8536 (m-40) cc_final: 0.7894 (t0) REVERT: J 7 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.8314 (ptm-80) REVERT: J 99 LYS cc_start: 0.8811 (tppt) cc_final: 0.8415 (tptp) outliers start: 134 outliers final: 64 residues processed: 295 average time/residue: 0.1933 time to fit residues: 90.7604 Evaluate side-chains 235 residues out of total 2837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 154 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 686 GLN Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 797 ARG Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 928 ILE Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 991 CYS Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1135 VAL Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 154 GLU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 741 ARG Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 978 CYS Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1033 GLU Chi-restraints excluded: chain D residue 1061 PHE Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain D residue 1098 VAL Chi-restraints excluded: chain D residue 1111 LEU Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 206 GLU Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 282 MET Chi-restraints excluded: chain F residue 310 TYR Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 461 GLN Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain F residue 503 ILE Chi-restraints excluded: chain J residue 7 ARG Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 98 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 29 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 220 optimal weight: 5.9990 chunk 238 optimal weight: 6.9990 chunk 177 optimal weight: 5.9990 chunk 210 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 296 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 267 ASN D1084 GLN E 69 ASN F 459 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.089689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.062170 restraints weight = 67610.761| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.72 r_work: 0.2805 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.106 27841 Z= 0.397 Angle : 0.798 15.397 37967 Z= 0.410 Chirality : 0.050 0.211 4324 Planarity : 0.006 0.122 4797 Dihedral : 15.138 163.623 4519 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.37 % Favored : 91.45 % Rotamer: Outliers : 6.02 % Allowed : 15.34 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.16 % Twisted Proline : 1.16 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.14), residues: 3335 helix: 0.20 (0.15), residues: 1231 sheet: -1.25 (0.28), residues: 361 loop : -2.09 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 888 TYR 0.019 0.002 TYR D1142 PHE 0.024 0.002 PHE C 906 TRP 0.015 0.002 TRP C 944 HIS 0.006 0.001 HIS D 854 Details of bonding type rmsd covalent geometry : bond 0.00956 (27833) covalent geometry : angle 0.79586 (37955) hydrogen bonds : bond 0.05481 ( 1058) hydrogen bonds : angle 4.73529 ( 2927) metal coordination : bond 0.02107 ( 8) metal coordination : angle 3.37432 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 149 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7581 (tp-100) REVERT: A 185 GLN cc_start: 0.7216 (pm20) cc_final: 0.6810 (pm20) REVERT: B 123 MET cc_start: 0.8479 (ttm) cc_final: 0.7839 (ttm) REVERT: B 206 ASP cc_start: 0.8696 (m-30) cc_final: 0.8247 (t0) REVERT: C 59 ASP cc_start: 0.8836 (OUTLIER) cc_final: 0.8493 (t0) REVERT: C 246 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7879 (mm-30) REVERT: C 298 ASN cc_start: 0.8302 (m-40) cc_final: 0.7950 (t0) REVERT: C 465 ARG cc_start: 0.8023 (ttm-80) cc_final: 0.7690 (ttm-80) REVERT: C 467 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7242 (ppt170) REVERT: C 723 ILE cc_start: 0.9356 (OUTLIER) cc_final: 0.9081 (mm) REVERT: C 996 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.7849 (mtm110) REVERT: C 1127 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8639 (tp30) REVERT: D 154 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8064 (mp0) REVERT: D 357 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8782 (tt) REVERT: D 427 ARG cc_start: 0.9093 (OUTLIER) cc_final: 0.8782 (ptp90) REVERT: D 451 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9017 (mp) REVERT: D 741 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.6948 (ppp80) REVERT: D 978 CYS cc_start: 0.9334 (OUTLIER) cc_final: 0.9007 (m) REVERT: D 1012 MET cc_start: 0.7546 (mpp) cc_final: 0.7098 (mpp) REVERT: D 1080 ILE cc_start: 0.7572 (OUTLIER) cc_final: 0.6735 (tp) REVERT: D 1273 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.7666 (pp30) REVERT: E 66 ASP cc_start: 0.8724 (m-30) cc_final: 0.8442 (m-30) REVERT: F 207 ASP cc_start: 0.7041 (OUTLIER) cc_final: 0.6060 (t0) REVERT: F 418 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.7987 (mtp-110) REVERT: J 7 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.8371 (ptm-80) outliers start: 168 outliers final: 115 residues processed: 305 average time/residue: 0.1863 time to fit residues: 91.5156 Evaluate side-chains 274 residues out of total 2837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 144 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 686 GLN Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 773 ILE Chi-restraints excluded: chain C residue 797 ARG Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 928 ILE Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 991 CYS Chi-restraints excluded: chain C residue 996 ARG Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1135 VAL Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 154 GLU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 427 ARG Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 741 ARG Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 825 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 936 VAL Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 978 CYS Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1033 GLU Chi-restraints excluded: chain D residue 1057 ASP Chi-restraints excluded: chain D residue 1061 PHE Chi-restraints excluded: chain D residue 1078 ASP Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1089 PHE Chi-restraints excluded: chain D residue 1098 VAL Chi-restraints excluded: chain D residue 1111 LEU Chi-restraints excluded: chain D residue 1121 VAL Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain D residue 1273 GLN Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 282 MET Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 359 MET Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 418 ARG Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 461 GLN Chi-restraints excluded: chain F residue 463 VAL Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain J residue 7 ARG Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 98 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 222 optimal weight: 0.0170 chunk 17 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 173 optimal weight: 20.0000 chunk 72 optimal weight: 6.9990 chunk 109 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 223 optimal weight: 0.3980 chunk 204 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.094897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.068042 restraints weight = 66459.272| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.90 r_work: 0.2933 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27841 Z= 0.114 Angle : 0.619 15.605 37967 Z= 0.314 Chirality : 0.042 0.189 4324 Planarity : 0.005 0.120 4797 Dihedral : 14.599 165.422 4519 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.79 % Favored : 94.06 % Rotamer: Outliers : 4.01 % Allowed : 17.09 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.16 % Twisted Proline : 1.16 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.14), residues: 3335 helix: 0.73 (0.15), residues: 1234 sheet: -0.96 (0.28), residues: 357 loop : -1.86 (0.14), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 211 TYR 0.012 0.001 TYR E 68 PHE 0.012 0.001 PHE D1089 TRP 0.016 0.001 TRP C 63 HIS 0.006 0.001 HIS E 106 Details of bonding type rmsd covalent geometry : bond 0.00251 (27833) covalent geometry : angle 0.61752 (37955) hydrogen bonds : bond 0.03637 ( 1058) hydrogen bonds : angle 4.15006 ( 2927) metal coordination : bond 0.00393 ( 8) metal coordination : angle 2.23996 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 157 time to evaluate : 1.170 Fit side-chains revert: symmetry clash REVERT: A 185 GLN cc_start: 0.7286 (pm20) cc_final: 0.6834 (pm20) REVERT: B 123 MET cc_start: 0.8449 (ttm) cc_final: 0.7823 (ttm) REVERT: B 206 ASP cc_start: 0.8604 (m-30) cc_final: 0.8175 (t0) REVERT: C 59 ASP cc_start: 0.8659 (t0) cc_final: 0.8362 (t0) REVERT: C 246 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7886 (mm-30) REVERT: C 441 ASP cc_start: 0.8199 (t70) cc_final: 0.7917 (p0) REVERT: C 465 ARG cc_start: 0.7873 (ttm-80) cc_final: 0.7614 (ttm-80) REVERT: C 467 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7334 (ppt170) REVERT: C 723 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8769 (mm) REVERT: C 797 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7723 (ppt-90) REVERT: D 154 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8129 (mp0) REVERT: D 245 VAL cc_start: 0.8983 (t) cc_final: 0.8777 (p) REVERT: D 357 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8617 (tt) REVERT: D 506 ARG cc_start: 0.9450 (OUTLIER) cc_final: 0.8391 (ptt-90) REVERT: D 741 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.6414 (ppp80) REVERT: D 978 CYS cc_start: 0.9220 (OUTLIER) cc_final: 0.8885 (m) REVERT: D 1080 ILE cc_start: 0.7472 (OUTLIER) cc_final: 0.6648 (tp) REVERT: E 73 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7298 (pp20) REVERT: F 204 TRP cc_start: 0.8354 (p-90) cc_final: 0.7787 (p-90) REVERT: F 246 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8226 (pm20) REVERT: F 282 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7590 (mmp) REVERT: J 7 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.8338 (ptm-80) REVERT: J 99 LYS cc_start: 0.8853 (tppt) cc_final: 0.8411 (tptp) outliers start: 112 outliers final: 71 residues processed: 259 average time/residue: 0.1843 time to fit residues: 76.9082 Evaluate side-chains 232 residues out of total 2837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 148 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 686 GLN Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 797 ARG Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 928 ILE Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 991 CYS Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1135 VAL Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 154 GLU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 741 ARG Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 978 CYS Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1033 GLU Chi-restraints excluded: chain D residue 1061 PHE Chi-restraints excluded: chain D residue 1078 ASP Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1089 PHE Chi-restraints excluded: chain D residue 1098 VAL Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 282 MET Chi-restraints excluded: chain F residue 310 TYR Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 461 GLN Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain F residue 503 ILE Chi-restraints excluded: chain J residue 7 ARG Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 98 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 297 optimal weight: 9.9990 chunk 231 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 121 optimal weight: 8.9990 chunk 242 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 179 optimal weight: 8.9990 chunk 305 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 320 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.091581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.065428 restraints weight = 66878.632| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.77 r_work: 0.2809 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 27841 Z= 0.269 Angle : 0.696 15.588 37967 Z= 0.354 Chirality : 0.045 0.203 4324 Planarity : 0.005 0.126 4797 Dihedral : 14.760 163.861 4512 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.35 % Favored : 92.50 % Rotamer: Outliers : 4.55 % Allowed : 16.95 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.16 % Twisted Proline : 1.16 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.14), residues: 3335 helix: 0.61 (0.15), residues: 1232 sheet: -1.03 (0.28), residues: 349 loop : -1.89 (0.14), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 211 TYR 0.022 0.001 TYR E 56 PHE 0.017 0.002 PHE C 906 TRP 0.010 0.001 TRP C 955 HIS 0.005 0.001 HIS E 106 Details of bonding type rmsd covalent geometry : bond 0.00646 (27833) covalent geometry : angle 0.69400 (37955) hydrogen bonds : bond 0.04599 ( 1058) hydrogen bonds : angle 4.38083 ( 2927) metal coordination : bond 0.01411 ( 8) metal coordination : angle 2.84990 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 150 time to evaluate : 1.148 Fit side-chains revert: symmetry clash REVERT: A 185 GLN cc_start: 0.7215 (pm20) cc_final: 0.6720 (pm20) REVERT: B 123 MET cc_start: 0.8462 (ttm) cc_final: 0.7852 (ttm) REVERT: B 206 ASP cc_start: 0.8712 (m-30) cc_final: 0.8343 (t0) REVERT: C 59 ASP cc_start: 0.8784 (t0) cc_final: 0.8435 (t0) REVERT: C 246 GLU cc_start: 0.8388 (tm-30) cc_final: 0.7992 (mm-30) REVERT: C 441 ASP cc_start: 0.8341 (t70) cc_final: 0.8063 (p0) REVERT: C 465 ARG cc_start: 0.7980 (ttm-80) cc_final: 0.7653 (ttm-80) REVERT: C 467 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7281 (ppt170) REVERT: C 559 VAL cc_start: 0.8630 (t) cc_final: 0.8218 (m) REVERT: C 723 ILE cc_start: 0.9311 (OUTLIER) cc_final: 0.9070 (mm) REVERT: C 797 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7733 (ppt-90) REVERT: C 996 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7773 (mtm110) REVERT: D 143 MET cc_start: 0.7915 (mmp) cc_final: 0.7162 (mtm) REVERT: D 154 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8143 (mp0) REVERT: D 357 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8657 (tt) REVERT: D 506 ARG cc_start: 0.9420 (OUTLIER) cc_final: 0.8395 (ptt-90) REVERT: D 741 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.6617 (ppp80) REVERT: D 978 CYS cc_start: 0.9294 (OUTLIER) cc_final: 0.8978 (m) REVERT: D 1012 MET cc_start: 0.7365 (mpp) cc_final: 0.6947 (mpp) REVERT: D 1080 ILE cc_start: 0.7510 (OUTLIER) cc_final: 0.6709 (tp) REVERT: E 73 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7274 (pp20) REVERT: F 204 TRP cc_start: 0.8207 (p-90) cc_final: 0.7747 (p-90) REVERT: F 246 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8190 (pm20) REVERT: J 7 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8354 (ptm-80) outliers start: 127 outliers final: 90 residues processed: 269 average time/residue: 0.1840 time to fit residues: 79.8226 Evaluate side-chains 245 residues out of total 2837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 142 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 686 GLN Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 797 ARG Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 928 ILE Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 991 CYS Chi-restraints excluded: chain C residue 996 ARG Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1135 VAL Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 154 GLU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 741 ARG Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 825 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 936 VAL Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 978 CYS Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1033 GLU Chi-restraints excluded: chain D residue 1061 PHE Chi-restraints excluded: chain D residue 1078 ASP Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1089 PHE Chi-restraints excluded: chain D residue 1098 VAL Chi-restraints excluded: chain D residue 1210 ILE Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 282 MET Chi-restraints excluded: chain F residue 310 TYR Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 461 GLN Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain F residue 503 ILE Chi-restraints excluded: chain J residue 7 ARG Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 98 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 207 optimal weight: 3.9990 chunk 289 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 chunk 188 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 181 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 301 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.093290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.066604 restraints weight = 66613.292| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.85 r_work: 0.2833 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 27841 Z= 0.173 Angle : 0.641 15.420 37967 Z= 0.326 Chirality : 0.043 0.200 4324 Planarity : 0.005 0.123 4797 Dihedral : 14.596 164.472 4512 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.69 % Favored : 93.16 % Rotamer: Outliers : 4.05 % Allowed : 17.27 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.16 % Twisted Proline : 1.16 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.14), residues: 3335 helix: 0.77 (0.15), residues: 1233 sheet: -0.98 (0.28), residues: 351 loop : -1.77 (0.14), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 211 TYR 0.022 0.001 TYR E 56 PHE 0.012 0.001 PHE C 906 TRP 0.013 0.001 TRP C 63 HIS 0.006 0.001 HIS E 106 Details of bonding type rmsd covalent geometry : bond 0.00411 (27833) covalent geometry : angle 0.63920 (37955) hydrogen bonds : bond 0.04052 ( 1058) hydrogen bonds : angle 4.21919 ( 2927) metal coordination : bond 0.00846 ( 8) metal coordination : angle 2.45814 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 149 time to evaluate : 1.130 Fit side-chains revert: symmetry clash REVERT: A 185 GLN cc_start: 0.7292 (pm20) cc_final: 0.6795 (pm20) REVERT: B 123 MET cc_start: 0.8462 (ttm) cc_final: 0.7895 (ttm) REVERT: B 141 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7722 (pm20) REVERT: B 206 ASP cc_start: 0.8681 (m-30) cc_final: 0.8341 (t0) REVERT: C 59 ASP cc_start: 0.8736 (t0) cc_final: 0.8383 (t0) REVERT: C 246 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7937 (mm-30) REVERT: C 465 ARG cc_start: 0.7921 (ttm-80) cc_final: 0.7566 (ttm-80) REVERT: C 467 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7314 (ppt170) REVERT: C 587 VAL cc_start: 0.9364 (OUTLIER) cc_final: 0.9151 (p) REVERT: C 996 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7708 (mtm110) REVERT: D 154 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8033 (mp0) REVERT: D 357 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8603 (tt) REVERT: D 506 ARG cc_start: 0.9448 (OUTLIER) cc_final: 0.8434 (ptt-90) REVERT: D 741 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.6395 (ppp80) REVERT: D 978 CYS cc_start: 0.9267 (OUTLIER) cc_final: 0.8942 (m) REVERT: D 1080 ILE cc_start: 0.7476 (OUTLIER) cc_final: 0.6688 (tp) REVERT: E 79 VAL cc_start: 0.9271 (OUTLIER) cc_final: 0.8966 (m) REVERT: F 204 TRP cc_start: 0.8087 (p-90) cc_final: 0.7649 (p-90) REVERT: F 246 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8185 (pm20) REVERT: J 7 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.8350 (ptm-80) REVERT: J 99 LYS cc_start: 0.8838 (tppt) cc_final: 0.8423 (tptp) outliers start: 113 outliers final: 84 residues processed: 253 average time/residue: 0.1879 time to fit residues: 76.8234 Evaluate side-chains 238 residues out of total 2837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 141 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 928 ILE Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 991 CYS Chi-restraints excluded: chain C residue 996 ARG Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1135 VAL Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 154 GLU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 441 CYS Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 741 ARG Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 890 ASP Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 978 CYS Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1033 GLU Chi-restraints excluded: chain D residue 1061 PHE Chi-restraints excluded: chain D residue 1078 ASP Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1089 PHE Chi-restraints excluded: chain D residue 1098 VAL Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 282 MET Chi-restraints excluded: chain F residue 310 TYR Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 461 GLN Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain F residue 503 ILE Chi-restraints excluded: chain J residue 7 ARG Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 76 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 162 optimal weight: 7.9990 chunk 276 optimal weight: 5.9990 chunk 181 optimal weight: 9.9990 chunk 330 optimal weight: 6.9990 chunk 283 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 289 optimal weight: 4.9990 chunk 261 optimal weight: 0.0570 chunk 260 optimal weight: 8.9990 chunk 99 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 overall best weight: 3.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN F 434 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.091606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.065474 restraints weight = 67058.140| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.75 r_work: 0.2810 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 27841 Z= 0.257 Angle : 0.700 15.403 37967 Z= 0.356 Chirality : 0.046 0.202 4324 Planarity : 0.005 0.126 4797 Dihedral : 14.721 163.700 4506 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.53 % Favored : 92.35 % Rotamer: Outliers : 4.44 % Allowed : 17.02 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.16 % Twisted Proline : 1.16 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.14), residues: 3335 helix: 0.64 (0.15), residues: 1236 sheet: -1.05 (0.28), residues: 351 loop : -1.80 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 211 TYR 0.029 0.001 TYR E 56 PHE 0.018 0.002 PHE C 906 TRP 0.009 0.001 TRP C 955 HIS 0.006 0.001 HIS E 106 Details of bonding type rmsd covalent geometry : bond 0.00616 (27833) covalent geometry : angle 0.69867 (37955) hydrogen bonds : bond 0.04591 ( 1058) hydrogen bonds : angle 4.38009 ( 2927) metal coordination : bond 0.01362 ( 8) metal coordination : angle 2.76821 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 143 time to evaluate : 1.061 Fit side-chains REVERT: A 185 GLN cc_start: 0.7221 (pm20) cc_final: 0.6704 (pm20) REVERT: B 123 MET cc_start: 0.8443 (ttm) cc_final: 0.7858 (ttm) REVERT: B 141 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7673 (pm20) REVERT: B 206 ASP cc_start: 0.8699 (m-30) cc_final: 0.8371 (t0) REVERT: C 59 ASP cc_start: 0.8780 (t0) cc_final: 0.8428 (t0) REVERT: C 246 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7944 (mm-30) REVERT: C 440 MET cc_start: 0.8649 (ttt) cc_final: 0.8367 (ttt) REVERT: C 797 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7718 (ppt-90) REVERT: C 996 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7786 (mtm110) REVERT: D 143 MET cc_start: 0.7918 (mmp) cc_final: 0.7177 (mtm) REVERT: D 154 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8031 (mp0) REVERT: D 357 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8654 (tt) REVERT: D 506 ARG cc_start: 0.9448 (OUTLIER) cc_final: 0.8395 (ptt-90) REVERT: D 741 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.6591 (ppp80) REVERT: D 978 CYS cc_start: 0.9297 (OUTLIER) cc_final: 0.8983 (m) REVERT: D 1012 MET cc_start: 0.7199 (mpp) cc_final: 0.6982 (mpp) REVERT: D 1080 ILE cc_start: 0.7549 (OUTLIER) cc_final: 0.6736 (tp) REVERT: E 79 VAL cc_start: 0.9253 (OUTLIER) cc_final: 0.8923 (m) REVERT: F 246 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8189 (pm20) REVERT: J 7 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8314 (ptm-80) REVERT: J 99 LYS cc_start: 0.8839 (tppt) cc_final: 0.8414 (tptp) outliers start: 124 outliers final: 101 residues processed: 256 average time/residue: 0.1834 time to fit residues: 75.5598 Evaluate side-chains 251 residues out of total 2837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 138 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 686 GLN Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 797 ARG Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 928 ILE Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 991 CYS Chi-restraints excluded: chain C residue 996 ARG Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1135 VAL Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 154 GLU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 421 ARG Chi-restraints excluded: chain D residue 441 CYS Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 741 ARG Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 890 ASP Chi-restraints excluded: chain D residue 936 VAL Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 978 CYS Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1033 GLU Chi-restraints excluded: chain D residue 1061 PHE Chi-restraints excluded: chain D residue 1078 ASP Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1089 PHE Chi-restraints excluded: chain D residue 1098 VAL Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 282 MET Chi-restraints excluded: chain F residue 310 TYR Chi-restraints excluded: chain F residue 359 MET Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 418 ARG Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 461 GLN Chi-restraints excluded: chain F residue 463 VAL Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain J residue 7 ARG Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 76 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 87 optimal weight: 0.9980 chunk 291 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 chunk 141 optimal weight: 0.9980 chunk 289 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 224 optimal weight: 0.9990 chunk 333 optimal weight: 10.0000 chunk 92 optimal weight: 0.7980 chunk 316 optimal weight: 5.9990 chunk 182 optimal weight: 8.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 ASN D 369 ASN J 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.094784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.068643 restraints weight = 66510.578| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.76 r_work: 0.2973 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27841 Z= 0.121 Angle : 0.620 14.976 37967 Z= 0.314 Chirality : 0.042 0.188 4324 Planarity : 0.005 0.122 4797 Dihedral : 14.406 164.756 4506 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.91 % Favored : 93.97 % Rotamer: Outliers : 3.44 % Allowed : 17.95 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.16 % Twisted Proline : 1.16 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.15), residues: 3335 helix: 1.01 (0.15), residues: 1227 sheet: -0.97 (0.28), residues: 360 loop : -1.61 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 211 TYR 0.024 0.001 TYR E 56 PHE 0.010 0.001 PHE D1089 TRP 0.020 0.001 TRP C 63 HIS 0.006 0.001 HIS E 106 Details of bonding type rmsd covalent geometry : bond 0.00274 (27833) covalent geometry : angle 0.61901 (37955) hydrogen bonds : bond 0.03567 ( 1058) hydrogen bonds : angle 4.08993 ( 2927) metal coordination : bond 0.00403 ( 8) metal coordination : angle 2.26192 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 152 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.8546 (ttm) cc_final: 0.7996 (ttm) REVERT: B 141 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7942 (pm20) REVERT: B 206 ASP cc_start: 0.8825 (m-30) cc_final: 0.8443 (t0) REVERT: C 59 ASP cc_start: 0.8838 (t0) cc_final: 0.8541 (t0) REVERT: C 246 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7939 (mm-30) REVERT: C 429 GLU cc_start: 0.8903 (tm-30) cc_final: 0.8690 (mp0) REVERT: C 455 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9098 (mt) REVERT: C 465 ARG cc_start: 0.7854 (ttm-80) cc_final: 0.7452 (ttm-80) REVERT: C 467 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.7254 (ppt170) REVERT: C 559 VAL cc_start: 0.8682 (t) cc_final: 0.8301 (m) REVERT: C 797 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7927 (ppt-90) REVERT: D 143 MET cc_start: 0.7914 (mmp) cc_final: 0.7184 (mtt) REVERT: D 154 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8087 (mp0) REVERT: D 357 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8648 (tt) REVERT: D 506 ARG cc_start: 0.9446 (OUTLIER) cc_final: 0.8439 (ptt-90) REVERT: D 677 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8935 (mp) REVERT: D 741 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.6248 (ppp80) REVERT: D 978 CYS cc_start: 0.9310 (OUTLIER) cc_final: 0.9024 (m) REVERT: D 1012 MET cc_start: 0.7266 (mpp) cc_final: 0.7065 (mpp) REVERT: D 1080 ILE cc_start: 0.7577 (OUTLIER) cc_final: 0.6725 (tp) REVERT: E 66 ASP cc_start: 0.8651 (m-30) cc_final: 0.8426 (m-30) REVERT: F 204 TRP cc_start: 0.7862 (p-90) cc_final: 0.7606 (p-90) REVERT: F 246 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8328 (pm20) REVERT: F 282 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7695 (mmp) REVERT: J 7 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8396 (ptm-80) REVERT: J 58 ASN cc_start: 0.9203 (OUTLIER) cc_final: 0.8941 (t0) REVERT: J 99 LYS cc_start: 0.8839 (tppt) cc_final: 0.8340 (tptp) outliers start: 96 outliers final: 69 residues processed: 240 average time/residue: 0.1965 time to fit residues: 75.3602 Evaluate side-chains 231 residues out of total 2837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 147 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 467 ARG Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 686 GLN Chi-restraints excluded: chain C residue 797 ARG Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 928 ILE Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 991 CYS Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1135 VAL Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 154 GLU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 421 ARG Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 741 ARG Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 890 ASP Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 978 CYS Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1033 GLU Chi-restraints excluded: chain D residue 1061 PHE Chi-restraints excluded: chain D residue 1078 ASP Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain D residue 1089 PHE Chi-restraints excluded: chain D residue 1098 VAL Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 282 MET Chi-restraints excluded: chain F residue 310 TYR Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 461 GLN Chi-restraints excluded: chain J residue 7 ARG Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 76 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 208 optimal weight: 0.5980 chunk 55 optimal weight: 9.9990 chunk 156 optimal weight: 0.0170 chunk 302 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 248 optimal weight: 7.9990 chunk 141 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 264 optimal weight: 0.0770 chunk 33 optimal weight: 4.9990 chunk 283 optimal weight: 6.9990 overall best weight: 0.9378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 775 ASN J 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.095546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.069097 restraints weight = 66182.851| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.78 r_work: 0.2889 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27841 Z= 0.118 Angle : 0.611 15.614 37967 Z= 0.309 Chirality : 0.042 0.195 4324 Planarity : 0.005 0.122 4797 Dihedral : 14.314 164.110 4501 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.12 % Favored : 93.76 % Rotamer: Outliers : 3.12 % Allowed : 18.38 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.23 % Cis-general : 0.16 % Twisted Proline : 1.16 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.15), residues: 3335 helix: 1.13 (0.15), residues: 1229 sheet: -0.85 (0.27), residues: 360 loop : -1.49 (0.15), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 211 TYR 0.028 0.001 TYR E 56 PHE 0.010 0.001 PHE C 153 TRP 0.019 0.001 TRP C 63 HIS 0.007 0.001 HIS E 106 Details of bonding type rmsd covalent geometry : bond 0.00269 (27833) covalent geometry : angle 0.60973 (37955) hydrogen bonds : bond 0.03491 ( 1058) hydrogen bonds : angle 4.01852 ( 2927) metal coordination : bond 0.00421 ( 8) metal coordination : angle 2.30640 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6733.47 seconds wall clock time: 115 minutes 55.50 seconds (6955.50 seconds total)