Starting phenix.real_space_refine on Sat Mar 7 03:07:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pfq_71610/03_2026/9pfq_71610.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pfq_71610/03_2026/9pfq_71610.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pfq_71610/03_2026/9pfq_71610.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pfq_71610/03_2026/9pfq_71610.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pfq_71610/03_2026/9pfq_71610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pfq_71610/03_2026/9pfq_71610.map" } resolution = 4.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.033 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 121 5.49 5 Mg 1 5.21 5 S 124 5.16 5 C 22278 2.51 5 N 6464 2.21 5 O 7050 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36040 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1763 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 14, 'TRANS': 218} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2387 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 20, 'TRANS': 303} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'ASN:plan1': 5, 'ASP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "C" Number of atoms: 10273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1350, 10273 Classifications: {'peptide': 1350} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 64, 'TRANS': 1285} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 295 Unresolved non-hydrogen angles: 355 Unresolved non-hydrogen dihedrals: 240 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 12, 'ASP:plan': 11, 'GLU:plan': 17, 'PHE:plan': 1, 'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 194 Chain: "D" Number of atoms: 10123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1343, 10123 Classifications: {'peptide': 1343} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PCIS': 1, 'PTRANS': 62, 'TRANS': 1279} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 309 Unresolved non-hydrogen angles: 384 Unresolved non-hydrogen dihedrals: 248 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ARG:plan': 15, 'GLU:plan': 17, 'ASP:plan': 7, 'ASN:plan1': 3, 'TYR:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 188 Chain: "E" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 506 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 3584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3584 Classifications: {'peptide': 483} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 12, 'TRANS': 470} Chain breaks: 1 Unresolved non-hydrogen bonds: 303 Unresolved non-hydrogen angles: 379 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 16, 'GLU:plan': 14, 'TRP:plan': 1, 'TYR:plan': 4, 'PHE:plan': 3, 'ASP:plan': 5, 'GLN:plan1': 3, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 219 Chain: "H" Number of atoms: 1301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 1301 Classifications: {'DNA': 64} Link IDs: {'rna3p': 63} Chain: "I" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1050 Classifications: {'DNA': 51} Link IDs: {'rna3p': 50} Chain breaks: 1 Chain: "Q" Number of atoms: 2476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2476 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 311} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'ARG:plan': 2, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Classifications: {'DNA': 3} Link IDs: {'rna3p': 2} Chain: "Y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Classifications: {'DNA': 3} Link IDs: {'rna3p': 2} Chain: "R" Number of atoms: 2452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2452 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 306} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14888 SG CYS D 71 106.936 119.411 100.536 1.00101.31 S ATOM 14902 SG CYS D 73 104.868 122.886 102.593 1.00103.40 S ATOM 15001 SG CYS D 86 106.884 120.270 103.678 1.00 95.99 S ATOM 20614 SG CYS D 810 117.493 54.580 89.331 1.00 73.02 S ATOM 21144 SG CYS D 884 114.643 56.799 89.933 1.00 73.47 S ATOM 21192 SG CYS D 891 116.161 56.887 86.540 1.00 64.56 S ATOM 21207 SG CYS D 894 114.160 54.141 87.077 1.00 69.49 S Time building chain proxies: 7.98, per 1000 atoms: 0.22 Number of scatterers: 36040 At special positions: 0 Unit cell: (153.36, 205.2, 183.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 124 16.00 P 121 15.00 Mg 1 11.99 O 7050 8.00 N 6464 7.00 C 22278 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: 2.88 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 86 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 73 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 71 " pdb=" ZN D2003 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 891 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 884 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 894 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 810 " Number of angles added : 6 8854 Ramachandran restraints generated. 4427 Oldfield, 0 Emsley, 4427 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8196 Finding SS restraints... Secondary structure from input PDB file: 161 helices and 52 sheets defined 42.5% alpha, 10.6% beta 22 base pairs and 63 stacking pairs defined. Time for finding SS restraints: 4.18 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 removed outlier: 3.839A pdb=" N LEU A 9 " --> pdb=" O ASN A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 51 removed outlier: 4.214A pdb=" N THR A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 89 Processing helix chain 'A' and resid 211 through 227 Processing helix chain 'B' and resid 37 through 53 removed outlier: 3.848A pdb=" N THR B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER B 52 " --> pdb=" O ARG B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 91 Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 211 through 228 Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'B' and resid 233 through 244 Processing helix chain 'B' and resid 251 through 256 removed outlier: 3.742A pdb=" N LEU B 254 " --> pdb=" O ASN B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 275 Processing helix chain 'B' and resid 286 through 291 Processing helix chain 'B' and resid 297 through 301 removed outlier: 3.637A pdb=" N LEU B 301 " --> pdb=" O ARG B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 312 Processing helix chain 'C' and resid 5 through 10 removed outlier: 4.014A pdb=" N LYS C 9 " --> pdb=" O PHE C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 35 removed outlier: 4.075A pdb=" N SER C 34 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 61 removed outlier: 3.821A pdb=" N VAL C 56 " --> pdb=" O GLY C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 93 removed outlier: 4.413A pdb=" N ILE C 90 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLN C 91 " --> pdb=" O GLU C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 218 Processing helix chain 'C' and resid 224 through 229 removed outlier: 3.647A pdb=" N THR C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 224 through 229' Processing helix chain 'C' and resid 279 through 287 removed outlier: 3.501A pdb=" N PHE C 285 " --> pdb=" O GLN C 281 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 302 removed outlier: 3.958A pdb=" N GLY C 302 " --> pdb=" O ALA C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 334 removed outlier: 4.500A pdb=" N GLN C 331 " --> pdb=" O VAL C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 361 removed outlier: 3.910A pdb=" N THR C 358 " --> pdb=" O TYR C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 379 Processing helix chain 'C' and resid 385 through 398 Processing helix chain 'C' and resid 406 through 418 Processing helix chain 'C' and resid 429 through 445 removed outlier: 3.979A pdb=" N ASP C 445 " --> pdb=" O VAL C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 457 No H-bonds generated for 'chain 'C' and resid 455 through 457' Processing helix chain 'C' and resid 463 through 490 removed outlier: 3.714A pdb=" N LEU C 467 " --> pdb=" O SER C 463 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU C 485 " --> pdb=" O ARG C 481 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER C 488 " --> pdb=" O LYS C 484 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER C 489 " --> pdb=" O GLU C 485 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL C 490 " --> pdb=" O ARG C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 516 removed outlier: 3.913A pdb=" N VAL C 510 " --> pdb=" O ALA C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 535 Processing helix chain 'C' and resid 548 through 552 removed outlier: 3.739A pdb=" N ALA C 551 " --> pdb=" O ARG C 548 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLY C 552 " --> pdb=" O GLU C 549 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 548 through 552' Processing helix chain 'C' and resid 616 through 622 removed outlier: 3.544A pdb=" N GLU C 619 " --> pdb=" O ALA C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 667 removed outlier: 3.916A pdb=" N VAL C 667 " --> pdb=" O PRO C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 675 Processing helix chain 'C' and resid 682 through 693 removed outlier: 4.383A pdb=" N MET C 688 " --> pdb=" O ASN C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 719 removed outlier: 3.696A pdb=" N ALA C 716 " --> pdb=" O GLU C 712 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ARG C 717 " --> pdb=" O ALA C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 825 through 831 removed outlier: 3.930A pdb=" N VAL C 829 " --> pdb=" O SER C 825 " (cutoff:3.500A) Processing helix chain 'C' and resid 865 through 869 Processing helix chain 'C' and resid 902 through 913 Processing helix chain 'C' and resid 948 through 982 Processing helix chain 'C' and resid 1003 through 1009 removed outlier: 3.890A pdb=" N GLN C1009 " --> pdb=" O GLU C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1018 removed outlier: 3.828A pdb=" N ILE C1018 " --> pdb=" O TRP C1015 " (cutoff:3.500A) Processing helix chain 'C' and resid 1024 through 1055 removed outlier: 4.314A pdb=" N SER C1031 " --> pdb=" O GLY C1027 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C1032 " --> pdb=" O GLU C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1106 through 1110 removed outlier: 3.736A pdb=" N THR C1110 " --> pdb=" O ALA C1107 " (cutoff:3.500A) Processing helix chain 'C' and resid 1119 through 1124 removed outlier: 4.592A pdb=" N SER C1123 " --> pdb=" O LEU C1119 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG C1124 " --> pdb=" O GLY C1120 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1119 through 1124' Processing helix chain 'C' and resid 1127 through 1151 removed outlier: 3.579A pdb=" N PHE C1131 " --> pdb=" O VAL C1127 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU C1142 " --> pdb=" O ALA C1138 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY C1143 " --> pdb=" O CYS C1139 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS C1144 " --> pdb=" O ALA C1140 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU C1149 " --> pdb=" O GLN C1145 " (cutoff:3.500A) Processing helix chain 'C' and resid 1152 through 1154 No H-bonds generated for 'chain 'C' and resid 1152 through 1154' Processing helix chain 'C' and resid 1160 through 1170 Processing helix chain 'C' and resid 1179 through 1190 removed outlier: 4.078A pdb=" N GLU C1185 " --> pdb=" O GLU C1181 " (cutoff:3.500A) Processing helix chain 'C' and resid 1205 through 1216 Processing helix chain 'C' and resid 1275 through 1279 removed outlier: 3.616A pdb=" N GLN C1278 " --> pdb=" O GLY C1275 " (cutoff:3.500A) Processing helix chain 'C' and resid 1285 through 1295 removed outlier: 3.578A pdb=" N TYR C1295 " --> pdb=" O ALA C1291 " (cutoff:3.500A) Processing helix chain 'C' and resid 1298 through 1307 Processing helix chain 'C' and resid 1313 through 1325 removed outlier: 3.605A pdb=" N LYS C1317 " --> pdb=" O ALA C1313 " (cutoff:3.500A) Processing helix chain 'C' and resid 1334 through 1346 Processing helix chain 'D' and resid 27 through 34 Processing helix chain 'D' and resid 59 through 64 Processing helix chain 'D' and resid 71 through 75 removed outlier: 3.967A pdb=" N GLY D 74 " --> pdb=" O CYS D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 102 removed outlier: 3.633A pdb=" N GLU D 101 " --> pdb=" O ARG D 97 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 102' Processing helix chain 'D' and resid 115 through 120 Processing helix chain 'D' and resid 123 through 130 Processing helix chain 'D' and resid 132 through 141 Processing helix chain 'D' and resid 162 through 173 Processing helix chain 'D' and resid 182 through 192 removed outlier: 3.522A pdb=" N ALA D 186 " --> pdb=" O ILE D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 208 removed outlier: 3.665A pdb=" N GLU D 199 " --> pdb=" O ASP D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 233 removed outlier: 3.526A pdb=" N LYS D 221 " --> pdb=" O LYS D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 238 Processing helix chain 'D' and resid 248 through 252 Processing helix chain 'D' and resid 265 through 287 removed outlier: 4.200A pdb=" N ASP D 269 " --> pdb=" O SER D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 310 Processing helix chain 'D' and resid 330 through 335 removed outlier: 3.590A pdb=" N LYS D 334 " --> pdb=" O ALA D 330 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLY D 335 " --> pdb=" O ASP D 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 330 through 335' Processing helix chain 'D' and resid 372 through 379 Processing helix chain 'D' and resid 379 through 391 Processing helix chain 'D' and resid 395 through 406 Processing helix chain 'D' and resid 409 through 418 removed outlier: 3.784A pdb=" N ILE D 413 " --> pdb=" O GLN D 409 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE D 418 " --> pdb=" O LEU D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 460 removed outlier: 4.345A pdb=" N ALA D 458 " --> pdb=" O LEU D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 485 Processing helix chain 'D' and resid 487 through 491 Processing helix chain 'D' and resid 506 through 516 removed outlier: 3.649A pdb=" N LEU D 510 " --> pdb=" O GLN D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 541 Processing helix chain 'D' and resid 571 through 579 Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.571A pdb=" N ILE D 592 " --> pdb=" O HIS D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 613 through 635 removed outlier: 3.734A pdb=" N ALA D 635 " --> pdb=" O GLU D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 667 removed outlier: 3.622A pdb=" N ILE D 653 " --> pdb=" O ARG D 649 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN D 667 " --> pdb=" O GLU D 663 " (cutoff:3.500A) Processing helix chain 'D' and resid 673 through 703 removed outlier: 4.590A pdb=" N TRP D 686 " --> pdb=" O VAL D 682 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ALA D 687 " --> pdb=" O VAL D 683 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET D 703 " --> pdb=" O ALA D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 716 through 724 removed outlier: 3.701A pdb=" N SER D 724 " --> pdb=" O MET D 720 " (cutoff:3.500A) Processing helix chain 'D' and resid 729 through 738 Processing helix chain 'D' and resid 764 through 800 removed outlier: 4.008A pdb=" N HIS D 773 " --> pdb=" O PHE D 769 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY D 774 " --> pdb=" O ASN D 770 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N THR D 786 " --> pdb=" O THR D 782 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ALA D 787 " --> pdb=" O ALA D 783 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ASN D 788 " --> pdb=" O LEU D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 861 through 871 removed outlier: 3.534A pdb=" N ALA D 871 " --> pdb=" O ALA D 867 " (cutoff:3.500A) Processing helix chain 'D' and resid 893 through 895 No H-bonds generated for 'chain 'D' and resid 893 through 895' Processing helix chain 'D' and resid 911 through 921 Processing helix chain 'D' and resid 1128 through 1138 Processing helix chain 'D' and resid 1212 through 1220 removed outlier: 3.705A pdb=" N ARG D1218 " --> pdb=" O HIS D1214 " (cutoff:3.500A) Processing helix chain 'D' and resid 1221 through 1241 removed outlier: 4.012A pdb=" N VAL D1236 " --> pdb=" O GLU D1232 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TYR D1237 " --> pdb=" O ILE D1233 " (cutoff:3.500A) Processing helix chain 'D' and resid 1246 through 1257 removed outlier: 3.531A pdb=" N LEU D1257 " --> pdb=" O VAL D1253 " (cutoff:3.500A) Processing helix chain 'D' and resid 1278 through 1292 Processing helix chain 'D' and resid 1304 through 1309 Processing helix chain 'D' and resid 1314 through 1322 removed outlier: 4.193A pdb=" N ALA D1318 " --> pdb=" O SER D1314 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN D1322 " --> pdb=" O ALA D1318 " (cutoff:3.500A) Processing helix chain 'D' and resid 1326 through 1335 Processing helix chain 'D' and resid 1342 through 1350 removed outlier: 3.737A pdb=" N ASN D1346 " --> pdb=" O GLY D1342 " (cutoff:3.500A) Processing helix chain 'D' and resid 1356 through 1378 removed outlier: 4.446A pdb=" N GLN D1378 " --> pdb=" O GLN D1374 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 17 through 30 removed outlier: 3.652A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 53 removed outlier: 3.810A pdb=" N LEU E 50 " --> pdb=" O PRO E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 56 No H-bonds generated for 'chain 'E' and resid 54 through 56' Processing helix chain 'E' and resid 60 through 66 removed outlier: 4.161A pdb=" N LYS E 64 " --> pdb=" O HIS E 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 124 Processing helix chain 'F' and resid 131 through 151 removed outlier: 3.642A pdb=" N ALA F 135 " --> pdb=" O GLU F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 166 removed outlier: 3.898A pdb=" N VAL F 163 " --> pdb=" O GLU F 159 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N TRP F 164 " --> pdb=" O ALA F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 188 removed outlier: 3.505A pdb=" N THR F 184 " --> pdb=" O ASP F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 259 removed outlier: 3.774A pdb=" N SER F 255 " --> pdb=" O ASP F 251 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLU F 256 " --> pdb=" O ALA F 252 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA F 259 " --> pdb=" O SER F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 274 removed outlier: 3.585A pdb=" N ASP F 265 " --> pdb=" O ARG F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 298 removed outlier: 3.768A pdb=" N ARG F 282 " --> pdb=" O SER F 278 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA F 284 " --> pdb=" O ALA F 280 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY F 287 " --> pdb=" O LYS F 283 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN F 294 " --> pdb=" O ALA F 290 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR F 298 " --> pdb=" O GLN F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 335 removed outlier: 3.514A pdb=" N GLN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA F 315 " --> pdb=" O GLU F 311 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU F 330 " --> pdb=" O ARG F 326 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER F 333 " --> pdb=" O ARG F 329 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N TYR F 334 " --> pdb=" O LEU F 330 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY F 335 " --> pdb=" O ALA F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 348 removed outlier: 4.357A pdb=" N GLY F 347 " --> pdb=" O LYS F 343 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER F 348 " --> pdb=" O ALA F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 356 Processing helix chain 'F' and resid 357 through 362 Processing helix chain 'F' and resid 368 through 391 removed outlier: 3.942A pdb=" N GLN F 374 " --> pdb=" O GLU F 370 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SER F 375 " --> pdb=" O ASN F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 421 Processing helix chain 'F' and resid 422 through 429 removed outlier: 4.447A pdb=" N VAL F 426 " --> pdb=" O ASN F 422 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE F 427 " --> pdb=" O LEU F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 430 through 434 removed outlier: 3.730A pdb=" N TYR F 433 " --> pdb=" O ALA F 430 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR F 434 " --> pdb=" O LYS F 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 430 through 434' Processing helix chain 'F' and resid 439 through 456 removed outlier: 4.188A pdb=" N ASP F 456 " --> pdb=" O MET F 452 " (cutoff:3.500A) Processing helix chain 'F' and resid 466 through 485 removed outlier: 4.985A pdb=" N TRP F 472 " --> pdb=" O THR F 468 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TRP F 473 " --> pdb=" O TYR F 469 " (cutoff:3.500A) Processing helix chain 'F' and resid 492 through 511 removed outlier: 3.895A pdb=" N HIS F 511 " --> pdb=" O ARG F 507 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 527 removed outlier: 3.956A pdb=" N GLU F 524 " --> pdb=" O GLU F 520 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 537 removed outlier: 3.653A pdb=" N LEU F 537 " --> pdb=" O VAL F 533 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 562 removed outlier: 3.801A pdb=" N PHE F 561 " --> pdb=" O HIS F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 588 removed outlier: 3.510A pdb=" N ALA F 588 " --> pdb=" O THR F 584 " (cutoff:3.500A) Processing helix chain 'F' and resid 591 through 602 Processing helix chain 'F' and resid 611 through 620 removed outlier: 3.527A pdb=" N VAL F 615 " --> pdb=" O THR F 611 " (cutoff:3.500A) Processing helix chain 'F' and resid 625 through 638 Processing helix chain 'F' and resid 643 through 648 removed outlier: 3.810A pdb=" N SER F 648 " --> pdb=" O ARG F 644 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1 through 19 Processing helix chain 'Q' and resid 24 through 32 removed outlier: 3.792A pdb=" N MET Q 28 " --> pdb=" O THR Q 24 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA Q 30 " --> pdb=" O ASP Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 36 through 50 Processing helix chain 'Q' and resid 78 through 96 removed outlier: 3.666A pdb=" N ALA Q 84 " --> pdb=" O GLU Q 80 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU Q 85 " --> pdb=" O GLU Q 81 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG Q 86 " --> pdb=" O LEU Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 113 removed outlier: 3.863A pdb=" N GLU Q 108 " --> pdb=" O LEU Q 104 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ALA Q 109 " --> pdb=" O TYR Q 105 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS Q 110 " --> pdb=" O ALA Q 106 " (cutoff:3.500A) Processing helix chain 'Q' and resid 116 through 124 removed outlier: 3.992A pdb=" N ARG Q 121 " --> pdb=" O GLY Q 117 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ARG Q 122 " --> pdb=" O SER Q 118 " (cutoff:3.500A) Processing helix chain 'Q' and resid 126 through 133 Processing helix chain 'Q' and resid 147 through 159 Processing helix chain 'Q' and resid 228 through 234 Processing helix chain 'Q' and resid 255 through 261 removed outlier: 3.835A pdb=" N ARG Q 261 " --> pdb=" O GLU Q 257 " (cutoff:3.500A) Processing helix chain 'Q' and resid 286 through 298 removed outlier: 3.819A pdb=" N LEU Q 290 " --> pdb=" O GLY Q 286 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N TRP Q 292 " --> pdb=" O ARG Q 288 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N HIS Q 293 " --> pdb=" O GLU Q 289 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR Q 296 " --> pdb=" O TRP Q 292 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TRP Q 297 " --> pdb=" O HIS Q 293 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY Q 298 " --> pdb=" O LEU Q 294 " (cutoff:3.500A) Processing helix chain 'Q' and resid 306 through 325 removed outlier: 4.144A pdb=" N MET Q 313 " --> pdb=" O LEU Q 309 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N VAL Q 314 " --> pdb=" O LYS Q 310 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLN Q 315 " --> pdb=" O ASP Q 311 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU Q 316 " --> pdb=" O MET Q 312 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS Q 324 " --> pdb=" O ALA Q 320 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 18 removed outlier: 4.158A pdb=" N LEU R 9 " --> pdb=" O LYS R 5 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY R 18 " --> pdb=" O ARG R 14 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 33 removed outlier: 3.568A pdb=" N MET R 28 " --> pdb=" O THR R 24 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA R 29 " --> pdb=" O LEU R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 36 through 50 removed outlier: 4.299A pdb=" N GLU R 40 " --> pdb=" O ARG R 36 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG R 41 " --> pdb=" O ARG R 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 95 removed outlier: 3.969A pdb=" N LEU R 82 " --> pdb=" O THR R 78 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER R 95 " --> pdb=" O SER R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 115 Processing helix chain 'R' and resid 116 through 123 Processing helix chain 'R' and resid 123 through 132 removed outlier: 3.716A pdb=" N VAL R 127 " --> pdb=" O VAL R 123 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN R 132 " --> pdb=" O GLU R 128 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 161 removed outlier: 3.603A pdb=" N ALA R 153 " --> pdb=" O ALA R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 211 No H-bonds generated for 'chain 'R' and resid 209 through 211' Processing helix chain 'R' and resid 228 through 236 removed outlier: 3.926A pdb=" N SER R 236 " --> pdb=" O PHE R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 255 through 261 Processing helix chain 'R' and resid 286 through 296 removed outlier: 4.338A pdb=" N THR R 296 " --> pdb=" O TRP R 292 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 324 removed outlier: 3.558A pdb=" N LYS R 310 " --> pdb=" O PRO R 306 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET R 312 " --> pdb=" O VAL R 308 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N MET R 313 " --> pdb=" O LEU R 309 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL R 314 " --> pdb=" O LYS R 310 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLN R 315 " --> pdb=" O ASP R 311 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG R 318 " --> pdb=" O VAL R 314 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.664A pdb=" N GLU A 205 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ARG A 181 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.702A pdb=" N MET A 103 " --> pdb=" O PHE A 146 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ARG A 143 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ILE A 64 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLU A 145 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ILE A 62 " --> pdb=" O GLU A 145 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR A 147 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN A 149 " --> pdb=" O ALA A 58 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA A 58 " --> pdb=" O ASN A 149 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY A 151 " --> pdb=" O GLY A 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 112 through 114 removed outlier: 7.085A pdb=" N VAL A 113 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 17 through 20 removed outlier: 4.952A pdb=" N GLY B 20 " --> pdb=" O LYS B 26 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N LYS B 26 " --> pdb=" O GLY B 20 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ARG B 25 " --> pdb=" O THR B 206 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU B 200 " --> pdb=" O ALA B 31 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ASP B 198 " --> pdb=" O PRO B 33 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N TYR B 197 " --> pdb=" O THR B 189 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 101 through 106 removed outlier: 7.814A pdb=" N ARG B 143 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ILE B 64 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLU B 145 " --> pdb=" O ILE B 62 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE B 62 " --> pdb=" O GLU B 145 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N THR B 147 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE B 62 " --> pdb=" O ILE B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 111 through 114 removed outlier: 3.788A pdb=" N VAL B 113 " --> pdb=" O CYS B 134 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N CYS B 134 " --> pdb=" O VAL B 113 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.387A pdb=" N LYS C 13 " --> pdb=" O ALA C1197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 63 through 64 removed outlier: 5.330A pdb=" N TYR C 74 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ARG C 105 " --> pdb=" O TYR C 74 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 97 through 98 removed outlier: 3.739A pdb=" N ALA C 98 " --> pdb=" O ILE C 133 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE C 133 " --> pdb=" O ALA C 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 149 through 151 Processing sheet with id=AB2, first strand: chain 'C' and resid 459 through 462 removed outlier: 6.057A pdb=" N SER C 153 " --> pdb=" O SER C 539 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 160 through 164 removed outlier: 3.821A pdb=" N ASP C 191 " --> pdb=" O ARG C 203 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG C 203 " --> pdb=" O ASP C 191 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 233 through 236 Processing sheet with id=AB5, first strand: chain 'C' and resid 244 through 245 Processing sheet with id=AB6, first strand: chain 'C' and resid 261 through 262 Processing sheet with id=AB7, first strand: chain 'C' and resid 607 through 614 removed outlier: 5.464A pdb=" N GLU C 610 " --> pdb=" O ARG C 601 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 642 through 644 Processing sheet with id=AB9, first strand: chain 'C' and resid 754 through 758 removed outlier: 6.866A pdb=" N ARG C 738 " --> pdb=" O ILE C 734 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ILE C 734 " --> pdb=" O ARG C 738 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL C 740 " --> pdb=" O GLU C 732 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY C 729 " --> pdb=" O ILE C 783 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 763 through 764 removed outlier: 3.867A pdb=" N GLN C 763 " --> pdb=" O ILE C 771 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE C 771 " --> pdb=" O GLN C 763 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 1114 through 1116 removed outlier: 4.735A pdb=" N THR C1240 " --> pdb=" O PHE C 810 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 852 through 853 removed outlier: 3.934A pdb=" N THR C 849 " --> pdb=" O GLY C 852 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LYS C1066 " --> pdb=" O ALA C 846 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASP C 848 " --> pdb=" O VAL C1064 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL C1064 " --> pdb=" O ASP C 848 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP C 936 " --> pdb=" O PHE C1071 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ALA C1073 " --> pdb=" O ILE C 934 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ILE C 934 " --> pdb=" O ALA C1073 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 855 through 856 removed outlier: 3.606A pdb=" N GLU C 855 " --> pdb=" O VAL C 893 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 888 through 890 removed outlier: 3.923A pdb=" N VAL C 890 " --> pdb=" O LEU C 924 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1258 through 1259 Processing sheet with id=AC7, first strand: chain 'C' and resid 1282 through 1283 Processing sheet with id=AC8, first strand: chain 'C' and resid 1352 through 1354 removed outlier: 6.696A pdb=" N GLU C1352 " --> pdb=" O ILE D 21 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ILE D 21 " --> pdb=" O GLU C1352 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 104 through 113 removed outlier: 7.433A pdb=" N THR D 242 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N SER D 110 " --> pdb=" O VAL D 240 " (cutoff:3.500A) removed outlier: 10.533A pdb=" N VAL D 240 " --> pdb=" O SER D 110 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 160 through 161 Processing sheet with id=AD2, first strand: chain 'D' and resid 254 through 256 Processing sheet with id=AD3, first strand: chain 'D' and resid 368 through 371 removed outlier: 6.249A pdb=" N CYS D 368 " --> pdb=" O LYS D 442 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE D 444 " --> pdb=" O CYS D 368 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N LEU D 370 " --> pdb=" O ILE D 444 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'D' and resid 550 through 553 Processing sheet with id=AD5, first strand: chain 'D' and resid 556 through 557 removed outlier: 3.684A pdb=" N LEU D 564 " --> pdb=" O GLU D 556 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 805 through 807 Processing sheet with id=AD7, first strand: chain 'D' and resid 816 through 818 removed outlier: 4.683A pdb=" N PHE D 839 " --> pdb=" O ARG D 879 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 821 through 823 removed outlier: 7.793A pdb=" N VAL D 821 " --> pdb=" O LEU D 828 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU D 828 " --> pdb=" O VAL D 821 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 844 through 845 removed outlier: 3.658A pdb=" N VAL D 854 " --> pdb=" O VAL D 844 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 952 through 956 removed outlier: 4.174A pdb=" N GLU D 986 " --> pdb=" O VAL D 978 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 959 through 961 Processing sheet with id=AE3, first strand: chain 'D' and resid 995 through 996 removed outlier: 4.420A pdb=" N ARG D 995 " --> pdb=" O ASP D1012 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASP D1012 " --> pdb=" O ARG D 995 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'D' and resid 1017 through 1021 removed outlier: 4.042A pdb=" N ALA D1113 " --> pdb=" O ILE D1020 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1027 through 1031 removed outlier: 3.960A pdb=" N ALA D1069 " --> pdb=" O GLU D1031 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1039 through 1043 Processing sheet with id=AE7, first strand: chain 'D' and resid 1168 through 1169 Processing sheet with id=AE8, first strand: chain 'D' and resid 1275 through 1277 removed outlier: 6.869A pdb=" N VAL D1297 " --> pdb=" O LEU D1263 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Q' and resid 134 through 136 removed outlier: 6.909A pdb=" N THR Q 135 " --> pdb=" O PHE R 187 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU R 186 " --> pdb=" O TYR R 192 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TYR R 192 " --> pdb=" O LEU R 186 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU R 193 " --> pdb=" O TRP R 206 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP R 206 " --> pdb=" O LEU R 193 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Q' and resid 186 through 187 Processing sheet with id=AF2, first strand: chain 'Q' and resid 186 through 187 Processing sheet with id=AF3, first strand: chain 'Q' and resid 268 through 272 removed outlier: 7.758A pdb=" N VAL Q 248 " --> pdb=" O VAL Q 304 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N VAL Q 304 " --> pdb=" O VAL Q 248 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Q' and resid 262 through 263 removed outlier: 4.014A pdb=" N ARG Q 263 " --> pdb=" O GLY R 141 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY R 141 " --> pdb=" O ARG Q 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'R' and resid 54 through 56 Processing sheet with id=AF6, first strand: chain 'R' and resid 165 through 166 Processing sheet with id=AF7, first strand: chain 'R' and resid 271 through 272 removed outlier: 3.931A pdb=" N THR R 271 " --> pdb=" O LEU R 279 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU R 279 " --> pdb=" O THR R 271 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL R 278 " --> pdb=" O ILE R 251 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA R 305 " --> pdb=" O VAL R 248 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ARG R 250 " --> pdb=" O ILE R 303 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ILE R 303 " --> pdb=" O ARG R 250 " (cutoff:3.500A) 1371 hydrogen bonds defined for protein. 3876 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 59 hydrogen bonds 114 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 63 stacking parallelities Total time for adding SS restraints: 8.88 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11772 1.34 - 1.46: 6221 1.46 - 1.58: 18409 1.58 - 1.70: 238 1.70 - 1.82: 225 Bond restraints: 36865 Sorted by residual: bond pdb=" C ASP F 484 " pdb=" N GLN F 485 " ideal model delta sigma weight residual 1.334 1.443 -0.110 1.30e-02 5.92e+03 7.11e+01 bond pdb=" N PRO D 958 " pdb=" CD PRO D 958 " ideal model delta sigma weight residual 1.473 1.557 -0.084 1.40e-02 5.10e+03 3.56e+01 bond pdb=" C GLN F 485 " pdb=" N ALA F 486 " ideal model delta sigma weight residual 1.332 1.256 0.076 1.31e-02 5.83e+03 3.32e+01 bond pdb=" C VAL F 586 " pdb=" N LEU F 587 " ideal model delta sigma weight residual 1.335 1.271 0.064 1.38e-02 5.25e+03 2.13e+01 bond pdb=" N ILE F 336 " pdb=" CA ILE F 336 " ideal model delta sigma weight residual 1.458 1.502 -0.043 1.20e-02 6.94e+03 1.31e+01 ... (remaining 36860 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.51: 50442 8.51 - 17.02: 6 17.02 - 25.53: 0 25.53 - 34.04: 0 34.04 - 42.55: 1 Bond angle restraints: 50449 Sorted by residual: angle pdb=" C GLY D 957 " pdb=" N PRO D 958 " pdb=" CD PRO D 958 " ideal model delta sigma weight residual 125.00 82.45 42.55 4.10e+00 5.95e-02 1.08e+02 angle pdb=" CA PRO D 236 " pdb=" N PRO D 236 " pdb=" CD PRO D 236 " ideal model delta sigma weight residual 112.00 104.48 7.52 1.40e+00 5.10e-01 2.88e+01 angle pdb=" N GLY F 339 " pdb=" CA GLY F 339 " pdb=" C GLY F 339 " ideal model delta sigma weight residual 113.27 106.18 7.09 1.33e+00 5.65e-01 2.84e+01 angle pdb=" C ARG B 159 " pdb=" CA ARG B 159 " pdb=" CB ARG B 159 " ideal model delta sigma weight residual 111.40 118.05 -6.65 1.29e+00 6.01e-01 2.66e+01 angle pdb=" N TYR F 397 " pdb=" CA TYR F 397 " pdb=" CB TYR F 397 " ideal model delta sigma weight residual 109.91 116.99 -7.08 1.46e+00 4.69e-01 2.35e+01 ... (remaining 50444 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.69: 21300 35.69 - 71.38: 766 71.38 - 107.07: 41 107.07 - 142.76: 3 142.76 - 178.45: 3 Dihedral angle restraints: 22113 sinusoidal: 9399 harmonic: 12714 Sorted by residual: dihedral pdb=" CD ARG B 159 " pdb=" NE ARG B 159 " pdb=" CZ ARG B 159 " pdb=" NH1 ARG B 159 " ideal model delta sinusoidal sigma weight residual 0.00 -53.86 53.86 1 1.00e+01 1.00e-02 3.94e+01 dihedral pdb=" CA LYS C 504 " pdb=" C LYS C 504 " pdb=" N PRO C 505 " pdb=" CA PRO C 505 " ideal model delta harmonic sigma weight residual 180.00 151.03 28.97 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CD ARG F 398 " pdb=" NE ARG F 398 " pdb=" CZ ARG F 398 " pdb=" NH1 ARG F 398 " ideal model delta sinusoidal sigma weight residual 0.00 48.86 -48.86 1 1.00e+01 1.00e-02 3.28e+01 ... (remaining 22110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 4992 0.062 - 0.125: 770 0.125 - 0.187: 47 0.187 - 0.249: 4 0.249 - 0.311: 1 Chirality restraints: 5814 Sorted by residual: chirality pdb=" CB ILE E 68 " pdb=" CA ILE E 68 " pdb=" CG1 ILE E 68 " pdb=" CG2 ILE E 68 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CA THR D 959 " pdb=" N THR D 959 " pdb=" C THR D 959 " pdb=" CB THR D 959 " both_signs ideal model delta sigma weight residual False 2.53 2.76 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB THR R 76 " pdb=" CA THR R 76 " pdb=" OG1 THR R 76 " pdb=" CG2 THR R 76 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.20 2.00e-01 2.50e+01 9.67e-01 ... (remaining 5811 not shown) Planarity restraints: 6201 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 159 " -0.888 9.50e-02 1.11e+02 3.98e-01 9.61e+01 pdb=" NE ARG B 159 " 0.053 2.00e-02 2.50e+03 pdb=" CZ ARG B 159 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B 159 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 159 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY D 957 " -0.158 5.00e-02 4.00e+02 2.35e-01 8.84e+01 pdb=" N PRO D 958 " 0.403 5.00e-02 4.00e+02 pdb=" CA PRO D 958 " -0.166 5.00e-02 4.00e+02 pdb=" CD PRO D 958 " -0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 398 " -0.829 9.50e-02 1.11e+02 3.72e-01 8.40e+01 pdb=" NE ARG F 398 " 0.049 2.00e-02 2.50e+03 pdb=" CZ ARG F 398 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG F 398 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG F 398 " -0.024 2.00e-02 2.50e+03 ... (remaining 6198 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 277 2.57 - 3.16: 29527 3.16 - 3.74: 55340 3.74 - 4.32: 69792 4.32 - 4.90: 114664 Nonbonded interactions: 269600 Sorted by model distance: nonbonded pdb=" OD1 ASP D 464 " pdb="MG MG D2001 " model vdw 1.993 2.170 nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D2001 " model vdw 2.016 2.170 nonbonded pdb=" O LEU D 72 " pdb="ZN ZN D2002 " model vdw 2.030 2.230 nonbonded pdb=" NZ LYS B 89 " pdb=" OE2 GLU D 534 " model vdw 2.128 3.120 nonbonded pdb=" O LEU D 308 " pdb=" OG SER D 328 " model vdw 2.145 3.040 ... (remaining 269595 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 'L' selection = chain 'Y' } ncs_group { reference = (chain 'Q' and (resid 4 through 92 or (resid 93 through 94 and (name N or name C \ A or name C or name O or name CB )) or resid 95 through 161 or (resid 162 throug \ h 163 and (name N or name CA or name C or name O or name CB )) or resid 164 thro \ ugh 217 or (resid 218 through 219 and (name N or name CA or name C or name O or \ name CB )) or resid 220 through 226 or (resid 227 and (name N or name CA or name \ C or name O or name CB )) or resid 228 through 245 or (resid 246 and (name N or \ name CA or name C or name O or name CB )) or resid 247 through 311 or (resid 31 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 313 through \ 318 or (resid 319 through 320 and (name N or name CA or name C or name O or name \ CB )) or resid 321 through 327)) selection = (chain 'R' and (resid 4 through 74 or (resid 75 and (name N or name CA or name C \ or name O or name CB )) or resid 76 through 103 or (resid 104 and (name N or na \ me CA or name C or name O or name CB )) or resid 105 through 115 or (resid 116 a \ nd (name N or name CA or name C or name O or name CB )) or resid 117 through 124 \ or (resid 125 and (name N or name CA or name C or name O or name CB )) or resid \ 126 through 138 or (resid 139 through 140 and (name N or name CA or name C or n \ ame O or name CB )) or resid 141 through 158 or (resid 159 and (name N or name C \ A or name C or name O or name CB )) or resid 160 through 175 or (resid 176 and ( \ name N or name CA or name C or name O or name CB )) or resid 177 through 198 or \ (resid 199 and (name N or name CA or name C or name O or name CB )) or resid 200 \ through 223 or (resid 224 and (name N or name CA or name C or name O or name CB \ )) or resid 225 through 310 or (resid 311 through 312 and (name N or name CA or \ name C or name O or name CB )) or resid 313 through 315 or (resid 316 and (name \ N or name CA or name C or name O or name CB )) or resid 317 through 327)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.490 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: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 39.440 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.080 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 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 : 0.004 0.110 36872 Z= 0.182 Angle : 0.703 42.548 50455 Z= 0.367 Chirality : 0.043 0.311 5814 Planarity : 0.011 0.398 6201 Dihedral : 17.015 178.446 13917 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.79 % Favored : 92.16 % Rotamer: Outliers : 0.21 % Allowed : 0.50 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.12), residues: 4427 helix: 0.40 (0.13), residues: 1647 sheet: -0.49 (0.24), residues: 464 loop : -1.93 (0.12), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG D 433 TYR 0.031 0.001 TYR A 176 PHE 0.024 0.001 PHE D 219 TRP 0.042 0.002 TRP D 34 HIS 0.005 0.001 HIS D 432 Details of bonding type rmsd covalent geometry : bond 0.00362 (36865) covalent geometry : angle 0.69742 (50449) hydrogen bonds : bond 0.16482 ( 1428) hydrogen bonds : angle 6.19238 ( 3990) metal coordination : bond 0.00997 ( 7) metal coordination : angle 8.18117 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8854 Ramachandran restraints generated. 4427 Oldfield, 0 Emsley, 4427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8854 Ramachandran restraints generated. 4427 Oldfield, 0 Emsley, 4427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 3683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 795 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7331 (tp30) cc_final: 0.7102 (tp30) REVERT: B 16 GLN cc_start: 0.8303 (pp30) cc_final: 0.7954 (pp30) REVERT: B 60 THR cc_start: 0.7674 (p) cc_final: 0.7467 (p) REVERT: B 149 ASN cc_start: 0.6755 (m-40) cc_final: 0.6017 (m-40) REVERT: B 314 HIS cc_start: 0.2133 (OUTLIER) cc_final: 0.1527 (t70) REVERT: C 166 ASP cc_start: 0.7112 (t70) cc_final: 0.6766 (t0) REVERT: C 205 ASP cc_start: 0.7817 (t0) cc_final: 0.7525 (t0) REVERT: C 206 ARG cc_start: 0.7303 (mmm-85) cc_final: 0.6974 (mtp180) REVERT: C 480 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7232 (tm-30) REVERT: C 596 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7937 (mt-10) REVERT: C 824 ILE cc_start: 0.9091 (tp) cc_final: 0.8864 (tp) REVERT: C 847 ARG cc_start: 0.7366 (mtm110) cc_final: 0.6930 (mtm180) REVERT: C 914 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7487 (tm-30) REVERT: C 958 GLU cc_start: 0.7158 (tp30) cc_final: 0.6939 (tp30) REVERT: C 962 LEU cc_start: 0.8743 (mt) cc_final: 0.8458 (mt) REVERT: C 1097 ILE cc_start: 0.8124 (mm) cc_final: 0.7701 (mt) REVERT: C 1125 MET cc_start: 0.7659 (mpp) cc_final: 0.6572 (mpp) REVERT: C 1352 GLU cc_start: 0.8185 (pm20) cc_final: 0.7881 (pm20) REVERT: D 214 MET cc_start: 0.7576 (mmp) cc_final: 0.7308 (mmt) REVERT: D 271 TYR cc_start: 0.8285 (m-10) cc_final: 0.7088 (m-80) REVERT: D 433 ARG cc_start: 0.6155 (ptm-80) cc_final: 0.3216 (ptm-80) REVERT: D 528 ILE cc_start: 0.8172 (mp) cc_final: 0.7926 (mp) REVERT: D 600 GLU cc_start: 0.8339 (tt0) cc_final: 0.8115 (mt-10) REVERT: D 703 MET cc_start: 0.7696 (ppp) cc_final: 0.7378 (ptt) REVERT: D 732 GLN cc_start: 0.8297 (mm110) cc_final: 0.7793 (mm-40) REVERT: D 756 VAL cc_start: 0.8535 (m) cc_final: 0.8255 (t) REVERT: D 770 ASN cc_start: 0.7881 (m110) cc_final: 0.7444 (m-40) REVERT: D 879 ARG cc_start: 0.7650 (ptt180) cc_final: 0.7136 (ptt180) REVERT: D 1234 GLN cc_start: 0.7829 (tp-100) cc_final: 0.7440 (tp40) REVERT: D 1237 TYR cc_start: 0.8527 (m-80) cc_final: 0.7917 (m-80) REVERT: D 1270 LEU cc_start: 0.8253 (tp) cc_final: 0.7995 (tp) REVERT: F 147 MET cc_start: 0.7172 (mpp) cc_final: 0.6940 (mpp) REVERT: F 162 MET cc_start: -0.0012 (tpt) cc_final: -0.0643 (tpt) REVERT: Q 27 GLU cc_start: 0.6329 (mt-10) cc_final: 0.6091 (mt-10) REVERT: Q 81 GLU cc_start: 0.8110 (tt0) cc_final: 0.7805 (tt0) REVERT: Q 234 ASP cc_start: 0.6562 (p0) cc_final: 0.6251 (p0) REVERT: R 313 MET cc_start: 0.0782 (ptp) cc_final: 0.0150 (mtm) outliers start: 7 outliers final: 4 residues processed: 799 average time/residue: 0.2286 time to fit residues: 294.3449 Evaluate side-chains 705 residues out of total 3683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 700 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 4.9990 chunk 424 optimal weight: 0.0060 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN B 224 GLN C 471 GLN D 268 ASN D 276 ASN ** D 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 730 GLN D 735 GLN ** D1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.215788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.174332 restraints weight = 47221.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.171739 restraints weight = 73746.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.170185 restraints weight = 62055.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.165456 restraints weight = 41619.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.166507 restraints weight = 37870.759| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.0790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 36872 Z= 0.138 Angle : 0.588 11.575 50455 Z= 0.307 Chirality : 0.041 0.217 5814 Planarity : 0.005 0.088 6201 Dihedral : 16.215 178.456 6108 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.54 % Favored : 92.43 % Rotamer: Outliers : 0.03 % Allowed : 4.89 % Favored : 95.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.13), residues: 4427 helix: 0.64 (0.13), residues: 1698 sheet: -0.63 (0.25), residues: 448 loop : -1.90 (0.12), residues: 2281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 61 TYR 0.016 0.001 TYR D1199 PHE 0.021 0.001 PHE D 219 TRP 0.030 0.001 TRP D 34 HIS 0.005 0.001 HIS D 158 Details of bonding type rmsd covalent geometry : bond 0.00305 (36865) covalent geometry : angle 0.58323 (50449) hydrogen bonds : bond 0.04198 ( 1428) hydrogen bonds : angle 4.76339 ( 3990) metal coordination : bond 0.00792 ( 7) metal coordination : angle 7.06530 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8854 Ramachandran restraints generated. 4427 Oldfield, 0 Emsley, 4427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8854 Ramachandran restraints generated. 4427 Oldfield, 0 Emsley, 4427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 3683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 801 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ASP cc_start: 0.7211 (p0) cc_final: 0.6986 (p0) REVERT: A 145 GLU cc_start: 0.5656 (mt-10) cc_final: 0.5316 (mt-10) REVERT: A 149 ASN cc_start: 0.8250 (m110) cc_final: 0.7971 (m110) REVERT: A 160 ASN cc_start: 0.7556 (p0) cc_final: 0.7271 (p0) REVERT: B 16 GLN cc_start: 0.8511 (pp30) cc_final: 0.8234 (pp30) REVERT: B 60 THR cc_start: 0.7446 (p) cc_final: 0.7118 (p) REVERT: B 87 ASN cc_start: 0.8315 (m-40) cc_final: 0.8041 (m-40) REVERT: B 149 ASN cc_start: 0.6425 (m-40) cc_final: 0.5845 (m-40) REVERT: C 166 ASP cc_start: 0.7164 (t70) cc_final: 0.6958 (t0) REVERT: C 468 LEU cc_start: 0.9154 (tp) cc_final: 0.8943 (tp) REVERT: C 619 GLU cc_start: 0.7323 (mt-10) cc_final: 0.7101 (mt-10) REVERT: C 665 ARG cc_start: 0.8478 (ptt180) cc_final: 0.8078 (ptt180) REVERT: C 688 MET cc_start: 0.7386 (ptp) cc_final: 0.6853 (ptp) REVERT: C 824 ILE cc_start: 0.9146 (tp) cc_final: 0.8917 (tp) REVERT: C 847 ARG cc_start: 0.7407 (mtm110) cc_final: 0.7071 (mtm180) REVERT: C 958 GLU cc_start: 0.6763 (tp30) cc_final: 0.6320 (tp30) REVERT: C 1097 ILE cc_start: 0.8155 (mm) cc_final: 0.7702 (mt) REVERT: C 1117 ASN cc_start: 0.8711 (t0) cc_final: 0.8324 (t0) REVERT: D 271 TYR cc_start: 0.8422 (m-10) cc_final: 0.7310 (m-80) REVERT: D 433 ARG cc_start: 0.6012 (ptm-80) cc_final: 0.3403 (ptm-80) REVERT: D 651 THR cc_start: 0.8545 (p) cc_final: 0.8252 (t) REVERT: D 703 MET cc_start: 0.7598 (ppp) cc_final: 0.6981 (ptt) REVERT: D 756 VAL cc_start: 0.8418 (m) cc_final: 0.8182 (t) REVERT: D 770 ASN cc_start: 0.7579 (m110) cc_final: 0.7299 (m110) REVERT: D 879 ARG cc_start: 0.7550 (ptt180) cc_final: 0.6911 (ptt180) REVERT: D 1234 GLN cc_start: 0.8022 (tp-100) cc_final: 0.7466 (tp40) REVERT: D 1237 TYR cc_start: 0.8440 (m-80) cc_final: 0.7878 (m-80) REVERT: F 162 MET cc_start: -0.0336 (tpt) cc_final: -0.1217 (tpt) REVERT: F 485 GLN cc_start: 0.5505 (tp40) cc_final: 0.4402 (tp40) REVERT: F 623 ARG cc_start: 0.3673 (ptt90) cc_final: 0.3417 (ppt170) REVERT: Q 132 GLN cc_start: 0.7094 (tm-30) cc_final: 0.6870 (tm-30) REVERT: R 66 ILE cc_start: 0.8431 (mm) cc_final: 0.8162 (mm) REVERT: R 313 MET cc_start: 0.0943 (ptp) cc_final: 0.0214 (mtm) outliers start: 1 outliers final: 0 residues processed: 801 average time/residue: 0.2312 time to fit residues: 296.3136 Evaluate side-chains 700 residues out of total 3683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 700 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 289 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 240 optimal weight: 0.0770 chunk 438 optimal weight: 6.9990 chunk 236 optimal weight: 0.5980 chunk 360 optimal weight: 3.9990 chunk 120 optimal weight: 0.6980 chunk 361 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 354 optimal weight: 0.8980 chunk 310 optimal weight: 0.6980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN B 224 GLN C 471 GLN C 586 HIS C 622 HIS C 773 GLN C1111 HIS ** D 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 730 GLN ** D1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1258 GLN ** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.216694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.176202 restraints weight = 47253.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.173799 restraints weight = 67858.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.172568 restraints weight = 58556.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.170658 restraints weight = 47563.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.171956 restraints weight = 41884.622| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 36872 Z= 0.128 Angle : 0.574 11.386 50455 Z= 0.298 Chirality : 0.041 0.206 5814 Planarity : 0.005 0.087 6201 Dihedral : 16.182 178.748 6108 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.39 % Favored : 92.59 % Rotamer: Outliers : 0.03 % Allowed : 4.03 % Favored : 95.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.13), residues: 4427 helix: 0.75 (0.13), residues: 1700 sheet: -0.70 (0.24), residues: 456 loop : -1.87 (0.13), residues: 2271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 221 TYR 0.012 0.001 TYR C 613 PHE 0.020 0.001 PHE D 219 TRP 0.051 0.001 TRP D 34 HIS 0.005 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00287 (36865) covalent geometry : angle 0.56810 (50449) hydrogen bonds : bond 0.03747 ( 1428) hydrogen bonds : angle 4.53250 ( 3990) metal coordination : bond 0.01501 ( 7) metal coordination : angle 7.44786 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8854 Ramachandran restraints generated. 4427 Oldfield, 0 Emsley, 4427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8854 Ramachandran restraints generated. 4427 Oldfield, 0 Emsley, 4427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 3683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 822 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ASP cc_start: 0.7241 (p0) cc_final: 0.6946 (p0) REVERT: A 145 GLU cc_start: 0.5209 (mt-10) cc_final: 0.4798 (mt-10) REVERT: A 149 ASN cc_start: 0.8330 (m110) cc_final: 0.8098 (m110) REVERT: B 16 GLN cc_start: 0.8522 (pp30) cc_final: 0.8311 (pp30) REVERT: B 60 THR cc_start: 0.7146 (p) cc_final: 0.6861 (p) REVERT: B 87 ASN cc_start: 0.8207 (m-40) cc_final: 0.7994 (m-40) REVERT: B 148 VAL cc_start: 0.7281 (t) cc_final: 0.7078 (t) REVERT: B 149 ASN cc_start: 0.6241 (m-40) cc_final: 0.5731 (m-40) REVERT: C 619 GLU cc_start: 0.7316 (mt-10) cc_final: 0.7072 (mt-10) REVERT: C 665 ARG cc_start: 0.8286 (ptt180) cc_final: 0.7948 (ptt180) REVERT: C 682 ASP cc_start: 0.7556 (t0) cc_final: 0.7342 (t0) REVERT: C 688 MET cc_start: 0.7800 (ptp) cc_final: 0.7378 (ptp) REVERT: C 824 ILE cc_start: 0.9100 (tp) cc_final: 0.8874 (tp) REVERT: C 847 ARG cc_start: 0.7442 (mtm110) cc_final: 0.7079 (mtm180) REVERT: C 914 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8186 (tm-30) REVERT: C 958 GLU cc_start: 0.6312 (tp30) cc_final: 0.5894 (tp30) REVERT: C 1097 ILE cc_start: 0.8153 (mm) cc_final: 0.7782 (mt) REVERT: C 1117 ASN cc_start: 0.8753 (t0) cc_final: 0.8332 (t0) REVERT: C 1154 GLN cc_start: 0.7554 (mp-120) cc_final: 0.7119 (mp10) REVERT: C 1241 VAL cc_start: 0.8619 (m) cc_final: 0.7912 (t) REVERT: D 167 MET cc_start: 0.5996 (mpp) cc_final: 0.5280 (ppp) REVERT: D 271 TYR cc_start: 0.8422 (m-10) cc_final: 0.7324 (m-80) REVERT: D 374 MET cc_start: 0.7424 (mtm) cc_final: 0.7201 (mtm) REVERT: D 377 GLU cc_start: 0.7864 (tp30) cc_final: 0.7251 (tp30) REVERT: D 433 ARG cc_start: 0.6062 (ptm-80) cc_final: 0.3689 (ptm-80) REVERT: D 625 MET cc_start: 0.7998 (ttp) cc_final: 0.7545 (tmm) REVERT: D 651 THR cc_start: 0.8400 (p) cc_final: 0.8135 (t) REVERT: D 703 MET cc_start: 0.7497 (ppp) cc_final: 0.6796 (ptt) REVERT: D 879 ARG cc_start: 0.7355 (ptt180) cc_final: 0.6579 (ptt180) REVERT: D 1070 MET cc_start: 0.0662 (mmp) cc_final: -0.0438 (mmp) REVERT: D 1234 GLN cc_start: 0.7877 (tp-100) cc_final: 0.7405 (tp40) REVERT: D 1237 TYR cc_start: 0.8359 (m-80) cc_final: 0.7804 (m-80) REVERT: D 1252 ILE cc_start: 0.8842 (mm) cc_final: 0.8623 (mm) REVERT: F 120 ARG cc_start: 0.7782 (ppt170) cc_final: 0.7578 (ppt170) REVERT: F 162 MET cc_start: -0.0517 (tpt) cc_final: -0.1502 (tpt) REVERT: F 516 GLU cc_start: 0.5154 (pm20) cc_final: 0.4152 (tp30) REVERT: Q 10 LEU cc_start: 0.7938 (pp) cc_final: 0.7693 (mt) REVERT: Q 21 GLU cc_start: 0.6776 (pp20) cc_final: 0.5796 (pt0) REVERT: Q 132 GLN cc_start: 0.7362 (tm-30) cc_final: 0.7044 (tm-30) REVERT: Q 312 MET cc_start: 0.6665 (tpt) cc_final: 0.3906 (mmp) REVERT: R 313 MET cc_start: 0.0808 (ptp) cc_final: 0.0295 (mtm) outliers start: 1 outliers final: 0 residues processed: 822 average time/residue: 0.2388 time to fit residues: 313.8990 Evaluate side-chains 713 residues out of total 3683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 713 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 352 optimal weight: 4.9990 chunk 167 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 chunk 309 optimal weight: 1.9990 chunk 138 optimal weight: 0.3980 chunk 324 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 170 optimal weight: 0.6980 chunk 105 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 160 ASN B 224 GLN C 471 GLN C 586 HIS C 805 ASN C1154 GLN ** D 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 547 HIS D 589 HIS D 730 GLN ** D1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1346 ASN F 422 ASN F 639 HIS ** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.214886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.173039 restraints weight = 47251.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.170628 restraints weight = 70651.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.171078 restraints weight = 61768.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.169600 restraints weight = 43258.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.170355 restraints weight = 43440.077| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 36872 Z= 0.141 Angle : 0.590 13.262 50455 Z= 0.304 Chirality : 0.041 0.207 5814 Planarity : 0.005 0.088 6201 Dihedral : 16.186 178.794 6108 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.09 % Favored : 91.89 % Rotamer: Outliers : 0.03 % Allowed : 4.15 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.13), residues: 4427 helix: 0.79 (0.13), residues: 1703 sheet: -0.73 (0.25), residues: 452 loop : -1.89 (0.13), residues: 2272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 32 TYR 0.028 0.001 TYR Q 168 PHE 0.023 0.001 PHE R 64 TRP 0.034 0.001 TRP D 34 HIS 0.004 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00321 (36865) covalent geometry : angle 0.58212 (50449) hydrogen bonds : bond 0.03642 ( 1428) hydrogen bonds : angle 4.40588 ( 3990) metal coordination : bond 0.01289 ( 7) metal coordination : angle 8.56004 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8854 Ramachandran restraints generated. 4427 Oldfield, 0 Emsley, 4427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8854 Ramachandran restraints generated. 4427 Oldfield, 0 Emsley, 4427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 3683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 824 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8991 (ptpt) cc_final: 0.8708 (ptmt) REVERT: A 138 ASP cc_start: 0.7362 (p0) cc_final: 0.6970 (p0) REVERT: A 145 GLU cc_start: 0.5252 (mt-10) cc_final: 0.4790 (mt-10) REVERT: A 149 ASN cc_start: 0.8303 (m110) cc_final: 0.8039 (m110) REVERT: B 60 THR cc_start: 0.7048 (p) cc_final: 0.6756 (p) REVERT: B 87 ASN cc_start: 0.8390 (m-40) cc_final: 0.7993 (m-40) REVERT: B 148 VAL cc_start: 0.7322 (t) cc_final: 0.7097 (t) REVERT: B 149 ASN cc_start: 0.6297 (m-40) cc_final: 0.5809 (m-40) REVERT: B 199 LYS cc_start: 0.7353 (ptpt) cc_final: 0.7124 (ptmt) REVERT: C 473 ARG cc_start: 0.8092 (ttt90) cc_final: 0.7641 (ttt90) REVERT: C 619 GLU cc_start: 0.7323 (mt-10) cc_final: 0.7058 (mt-10) REVERT: C 665 ARG cc_start: 0.8365 (ptt180) cc_final: 0.7975 (ptt180) REVERT: C 688 MET cc_start: 0.7712 (ptp) cc_final: 0.7244 (ptp) REVERT: C 824 ILE cc_start: 0.8977 (tp) cc_final: 0.8740 (tp) REVERT: C 847 ARG cc_start: 0.7645 (mtm110) cc_final: 0.7152 (mtm180) REVERT: C 1111 HIS cc_start: 0.8093 (p90) cc_final: 0.7801 (p-80) REVERT: C 1117 ASN cc_start: 0.8753 (t0) cc_final: 0.8371 (t0) REVERT: C 1154 GLN cc_start: 0.7443 (mp10) cc_final: 0.6965 (mp10) REVERT: D 167 MET cc_start: 0.6241 (mpp) cc_final: 0.5277 (ppp) REVERT: D 271 TYR cc_start: 0.8529 (m-10) cc_final: 0.7533 (m-80) REVERT: D 374 MET cc_start: 0.7568 (mtm) cc_final: 0.7274 (mtm) REVERT: D 377 GLU cc_start: 0.7907 (tp30) cc_final: 0.7286 (tp30) REVERT: D 398 GLN cc_start: 0.8247 (mt0) cc_final: 0.7908 (mp10) REVERT: D 433 ARG cc_start: 0.6115 (ptm-80) cc_final: 0.3697 (ptm-80) REVERT: D 703 MET cc_start: 0.7512 (ppp) cc_final: 0.6815 (ptt) REVERT: D 770 ASN cc_start: 0.7558 (m110) cc_final: 0.7343 (m110) REVERT: D 879 ARG cc_start: 0.7485 (ptt180) cc_final: 0.6676 (ptt180) REVERT: D 1070 MET cc_start: 0.0761 (mmp) cc_final: -0.0523 (mmp) REVERT: D 1234 GLN cc_start: 0.8067 (tp-100) cc_final: 0.7489 (tp40) REVERT: D 1252 ILE cc_start: 0.8895 (mm) cc_final: 0.8653 (mm) REVERT: F 162 MET cc_start: -0.0498 (tpt) cc_final: -0.1490 (tpt) REVERT: F 485 GLN cc_start: 0.6177 (tm-30) cc_final: 0.5661 (tm-30) REVERT: F 516 GLU cc_start: 0.5319 (pm20) cc_final: 0.4227 (tp30) REVERT: F 575 ILE cc_start: 0.8373 (tt) cc_final: 0.8154 (tt) REVERT: Q 21 GLU cc_start: 0.6759 (pp20) cc_final: 0.5896 (pt0) REVERT: Q 81 GLU cc_start: 0.8140 (tt0) cc_final: 0.7919 (tm-30) REVERT: Q 132 GLN cc_start: 0.7498 (tm-30) cc_final: 0.7134 (tm-30) REVERT: Q 312 MET cc_start: 0.6190 (tpt) cc_final: 0.3530 (mmp) REVERT: R 92 LEU cc_start: 0.8779 (mm) cc_final: 0.8567 (mt) outliers start: 1 outliers final: 1 residues processed: 824 average time/residue: 0.2345 time to fit residues: 309.8932 Evaluate side-chains 707 residues out of total 3683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 706 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 216 optimal weight: 0.7980 chunk 416 optimal weight: 0.0270 chunk 26 optimal weight: 0.2980 chunk 183 optimal weight: 0.9980 chunk 362 optimal weight: 0.7980 chunk 283 optimal weight: 10.0000 chunk 190 optimal weight: 2.9990 chunk 233 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 218 optimal weight: 2.9990 chunk 250 optimal weight: 0.7980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 160 ASN B 224 GLN C 471 GLN C 628 ASN C 805 ASN ** C1223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 730 GLN ** D 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 ASN F 639 HIS ** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.216515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.175626 restraints weight = 47130.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.173275 restraints weight = 73799.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.169090 restraints weight = 61907.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.163262 restraints weight = 39638.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.163401 restraints weight = 35792.179| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36872 Z= 0.125 Angle : 0.581 13.326 50455 Z= 0.300 Chirality : 0.041 0.203 5814 Planarity : 0.005 0.090 6201 Dihedral : 16.183 179.501 6108 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.34 % Favored : 92.64 % Rotamer: Outliers : 0.03 % Allowed : 2.68 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.13), residues: 4427 helix: 0.88 (0.13), residues: 1692 sheet: -0.75 (0.25), residues: 456 loop : -1.84 (0.13), residues: 2279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 869 TYR 0.017 0.001 TYR C 35 PHE 0.022 0.001 PHE R 64 TRP 0.049 0.001 TRP D 34 HIS 0.005 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00283 (36865) covalent geometry : angle 0.57526 (50449) hydrogen bonds : bond 0.03400 ( 1428) hydrogen bonds : angle 4.30423 ( 3990) metal coordination : bond 0.00835 ( 7) metal coordination : angle 7.64390 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8854 Ramachandran restraints generated. 4427 Oldfield, 0 Emsley, 4427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8854 Ramachandran restraints generated. 4427 Oldfield, 0 Emsley, 4427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 3683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 829 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8966 (ptpt) cc_final: 0.8679 (ptmt) REVERT: A 138 ASP cc_start: 0.7583 (p0) cc_final: 0.7240 (p0) REVERT: A 145 GLU cc_start: 0.5488 (mt-10) cc_final: 0.4994 (mt-10) REVERT: A 149 ASN cc_start: 0.8302 (m110) cc_final: 0.8029 (m110) REVERT: B 16 GLN cc_start: 0.8595 (pp30) cc_final: 0.8109 (pp30) REVERT: B 60 THR cc_start: 0.7428 (p) cc_final: 0.7146 (p) REVERT: B 87 ASN cc_start: 0.8562 (m-40) cc_final: 0.8232 (m-40) REVERT: B 148 VAL cc_start: 0.6798 (t) cc_final: 0.6519 (t) REVERT: B 149 ASN cc_start: 0.6826 (m-40) cc_final: 0.6258 (m-40) REVERT: C 33 SER cc_start: 0.8805 (t) cc_final: 0.8591 (t) REVERT: C 136 MET cc_start: 0.9069 (mmm) cc_final: 0.8399 (mmm) REVERT: C 473 ARG cc_start: 0.8202 (ttt90) cc_final: 0.7602 (ttt90) REVERT: C 619 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7073 (mt-10) REVERT: C 665 ARG cc_start: 0.8505 (ptt180) cc_final: 0.8022 (ptt180) REVERT: C 682 ASP cc_start: 0.7580 (t0) cc_final: 0.7295 (t0) REVERT: C 688 MET cc_start: 0.7562 (ptp) cc_final: 0.7102 (ptp) REVERT: C 763 GLN cc_start: 0.8629 (mp-120) cc_final: 0.8417 (mp10) REVERT: C 847 ARG cc_start: 0.7502 (mtm110) cc_final: 0.7012 (mtm180) REVERT: C 1067 MET cc_start: 0.7283 (mmm) cc_final: 0.6473 (mmm) REVERT: C 1111 HIS cc_start: 0.8114 (p90) cc_final: 0.7847 (p-80) REVERT: C 1117 ASN cc_start: 0.8770 (t0) cc_final: 0.8351 (t0) REVERT: C 1206 MET cc_start: 0.7978 (mmm) cc_final: 0.7445 (mmm) REVERT: C 1304 MET cc_start: 0.8328 (tpp) cc_final: 0.7111 (tpp) REVERT: C 1350 ASN cc_start: 0.8191 (t0) cc_final: 0.7947 (t0) REVERT: D 167 MET cc_start: 0.5654 (mpp) cc_final: 0.5104 (ppp) REVERT: D 398 GLN cc_start: 0.8288 (mt0) cc_final: 0.7752 (mp10) REVERT: D 433 ARG cc_start: 0.6406 (ptm-80) cc_final: 0.3778 (ptm-80) REVERT: D 625 MET cc_start: 0.8096 (ttp) cc_final: 0.7783 (tmm) REVERT: D 703 MET cc_start: 0.7588 (ppp) cc_final: 0.6952 (ptt) REVERT: D 755 ILE cc_start: 0.8045 (mp) cc_final: 0.7665 (mt) REVERT: D 770 ASN cc_start: 0.7772 (m110) cc_final: 0.7424 (m110) REVERT: D 879 ARG cc_start: 0.7686 (ptt180) cc_final: 0.6768 (ptt180) REVERT: D 917 GLN cc_start: 0.8159 (tt0) cc_final: 0.7784 (tt0) REVERT: D 1070 MET cc_start: 0.2033 (mmp) cc_final: 0.0666 (mmp) REVERT: D 1155 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7515 (mp0) REVERT: F 117 MET cc_start: 0.6763 (mpp) cc_final: 0.5787 (mpp) REVERT: F 147 MET cc_start: 0.6947 (mpp) cc_final: 0.6685 (mpp) REVERT: F 162 MET cc_start: -0.0130 (tpt) cc_final: -0.0914 (tpt) REVERT: F 485 GLN cc_start: 0.6123 (tm-30) cc_final: 0.5872 (tm-30) REVERT: F 528 MET cc_start: 0.7342 (mtp) cc_final: 0.7110 (mtp) REVERT: Q 21 GLU cc_start: 0.6209 (pp20) cc_final: 0.5756 (pt0) REVERT: Q 312 MET cc_start: 0.5252 (tpt) cc_final: 0.2680 (mmp) REVERT: Q 313 MET cc_start: 0.4868 (mpp) cc_final: 0.4640 (mpp) REVERT: R 62 LYS cc_start: 0.8360 (ptpt) cc_final: 0.8142 (ptpt) REVERT: R 66 ILE cc_start: 0.8440 (mm) cc_final: 0.8166 (mm) REVERT: R 92 LEU cc_start: 0.8646 (mm) cc_final: 0.8412 (mt) REVERT: R 111 LEU cc_start: 0.8447 (tp) cc_final: 0.8245 (tp) outliers start: 1 outliers final: 1 residues processed: 829 average time/residue: 0.2388 time to fit residues: 317.2941 Evaluate side-chains 712 residues out of total 3683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 711 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 183 optimal weight: 0.3980 chunk 56 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 314 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 227 optimal weight: 0.4980 chunk 196 optimal weight: 2.9990 chunk 313 optimal weight: 0.9990 chunk 310 optimal weight: 0.5980 chunk 348 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN B 224 GLN C 471 GLN C 586 HIS C 622 HIS C 805 ASN ** C1223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 611 HIS ** D 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 ASN ** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.214954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.173661 restraints weight = 47168.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.170614 restraints weight = 73823.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.169775 restraints weight = 64844.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.166038 restraints weight = 53652.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.167806 restraints weight = 43399.795| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 36872 Z= 0.140 Angle : 0.595 11.105 50455 Z= 0.307 Chirality : 0.041 0.217 5814 Planarity : 0.005 0.094 6201 Dihedral : 16.183 179.280 6108 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.00 % Favored : 91.98 % Rotamer: Outliers : 0.03 % Allowed : 2.24 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.13), residues: 4427 helix: 0.86 (0.13), residues: 1694 sheet: -0.79 (0.24), residues: 458 loop : -1.84 (0.13), residues: 2275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Q 283 TYR 0.018 0.001 TYR D1199 PHE 0.023 0.001 PHE R 64 TRP 0.063 0.001 TRP D 34 HIS 0.005 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00318 (36865) covalent geometry : angle 0.58893 (50449) hydrogen bonds : bond 0.03460 ( 1428) hydrogen bonds : angle 4.30303 ( 3990) metal coordination : bond 0.01105 ( 7) metal coordination : angle 7.84164 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8854 Ramachandran restraints generated. 4427 Oldfield, 0 Emsley, 4427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8854 Ramachandran restraints generated. 4427 Oldfield, 0 Emsley, 4427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 3683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 795 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8897 (ptpt) cc_final: 0.8623 (ptmt) REVERT: A 138 ASP cc_start: 0.7492 (p0) cc_final: 0.7202 (p0) REVERT: A 145 GLU cc_start: 0.5247 (mt-10) cc_final: 0.4764 (mt-10) REVERT: A 149 ASN cc_start: 0.8324 (m110) cc_final: 0.8060 (m110) REVERT: B 16 GLN cc_start: 0.8536 (pp30) cc_final: 0.8139 (pp30) REVERT: B 60 THR cc_start: 0.7118 (p) cc_final: 0.6858 (p) REVERT: B 87 ASN cc_start: 0.8392 (m-40) cc_final: 0.8109 (m-40) REVERT: B 143 ARG cc_start: 0.6918 (ttm-80) cc_final: 0.5090 (ttm-80) REVERT: B 148 VAL cc_start: 0.7355 (t) cc_final: 0.7119 (t) REVERT: B 149 ASN cc_start: 0.6442 (m-40) cc_final: 0.6033 (m-40) REVERT: C 24 MET cc_start: 0.7361 (mtp) cc_final: 0.6226 (mtp) REVERT: C 136 MET cc_start: 0.8727 (mmm) cc_final: 0.8249 (mmm) REVERT: C 392 MET cc_start: 0.7801 (tmm) cc_final: 0.6921 (ttt) REVERT: C 473 ARG cc_start: 0.8132 (ttt90) cc_final: 0.7635 (ttt90) REVERT: C 596 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7852 (mt-10) REVERT: C 665 ARG cc_start: 0.8364 (ptt180) cc_final: 0.8013 (ptt180) REVERT: C 688 MET cc_start: 0.7839 (ptp) cc_final: 0.7356 (ptp) REVERT: C 847 ARG cc_start: 0.7579 (mtm110) cc_final: 0.7148 (mtm180) REVERT: C 1097 ILE cc_start: 0.8138 (mm) cc_final: 0.7778 (mt) REVERT: C 1117 ASN cc_start: 0.8756 (t0) cc_final: 0.8302 (t0) REVERT: C 1154 GLN cc_start: 0.7163 (mp10) cc_final: 0.6613 (mp10) REVERT: D 167 MET cc_start: 0.6184 (mpp) cc_final: 0.5355 (ppp) REVERT: D 271 TYR cc_start: 0.8639 (m-10) cc_final: 0.7612 (m-80) REVERT: D 398 GLN cc_start: 0.8236 (mt0) cc_final: 0.7846 (mp10) REVERT: D 433 ARG cc_start: 0.6346 (ptm-80) cc_final: 0.3675 (ptm-80) REVERT: D 487 MET cc_start: 0.8706 (mmm) cc_final: 0.8404 (mtm) REVERT: D 625 MET cc_start: 0.8161 (ttp) cc_final: 0.7759 (tmm) REVERT: D 703 MET cc_start: 0.7505 (ppp) cc_final: 0.6834 (ptt) REVERT: D 879 ARG cc_start: 0.7544 (ptt180) cc_final: 0.6626 (ptt180) REVERT: D 917 GLN cc_start: 0.8275 (tt0) cc_final: 0.7835 (tt0) REVERT: D 1070 MET cc_start: 0.0844 (mmp) cc_final: -0.0536 (mmp) REVERT: F 162 MET cc_start: -0.0440 (tpt) cc_final: -0.1398 (tpt) REVERT: F 485 GLN cc_start: 0.6480 (tm-30) cc_final: 0.6021 (tm-30) REVERT: Q 21 GLU cc_start: 0.6759 (pp20) cc_final: 0.6024 (pt0) REVERT: Q 108 GLU cc_start: 0.6864 (pm20) cc_final: 0.6598 (pm20) REVERT: Q 132 GLN cc_start: 0.7575 (tm-30) cc_final: 0.7261 (tm-30) REVERT: Q 265 HIS cc_start: 0.6139 (t-90) cc_final: 0.5427 (t-90) REVERT: Q 312 MET cc_start: 0.5857 (tpt) cc_final: 0.3117 (mmp) REVERT: R 43 ARG cc_start: 0.8789 (ttp80) cc_final: 0.8185 (ttp80) REVERT: R 86 ARG cc_start: 0.6236 (tpm170) cc_final: 0.5235 (mmm160) REVERT: R 111 LEU cc_start: 0.8350 (tp) cc_final: 0.8148 (tp) outliers start: 1 outliers final: 1 residues processed: 795 average time/residue: 0.2331 time to fit residues: 296.7800 Evaluate side-chains 716 residues out of total 3683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 715 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 63 optimal weight: 0.9980 chunk 72 optimal weight: 0.0070 chunk 108 optimal weight: 0.9980 chunk 217 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 237 optimal weight: 0.9980 chunk 429 optimal weight: 3.9990 chunk 404 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 310 optimal weight: 2.9990 chunk 201 optimal weight: 0.9980 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN B 224 GLN C 471 GLN C 622 HIS C 805 ASN C1111 HIS ** C1223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1251 HIS ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1285 GLN F 422 ASN F 639 HIS ** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.214235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.172804 restraints weight = 47195.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.169765 restraints weight = 74495.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.170840 restraints weight = 66030.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.170254 restraints weight = 41061.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.171405 restraints weight = 35686.752| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 36872 Z= 0.145 Angle : 0.609 12.225 50455 Z= 0.313 Chirality : 0.041 0.175 5814 Planarity : 0.005 0.097 6201 Dihedral : 16.189 178.879 6108 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.93 % Favored : 92.05 % Rotamer: Outliers : 0.06 % Allowed : 2.21 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.13), residues: 4427 helix: 0.85 (0.13), residues: 1698 sheet: -0.75 (0.24), residues: 468 loop : -1.87 (0.13), residues: 2261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Q 283 TYR 0.018 0.001 TYR C 35 PHE 0.022 0.001 PHE R 64 TRP 0.040 0.002 TRP D 34 HIS 0.007 0.001 HIS C1111 Details of bonding type rmsd covalent geometry : bond 0.00334 (36865) covalent geometry : angle 0.60260 (50449) hydrogen bonds : bond 0.03526 ( 1428) hydrogen bonds : angle 4.30074 ( 3990) metal coordination : bond 0.01107 ( 7) metal coordination : angle 8.28256 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8854 Ramachandran restraints generated. 4427 Oldfield, 0 Emsley, 4427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8854 Ramachandran restraints generated. 4427 Oldfield, 0 Emsley, 4427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 803 residues out of total 3683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 801 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8878 (ptpt) cc_final: 0.8563 (ptmt) REVERT: A 138 ASP cc_start: 0.7464 (p0) cc_final: 0.7194 (p0) REVERT: A 145 GLU cc_start: 0.5254 (mt-10) cc_final: 0.4717 (mt-10) REVERT: A 149 ASN cc_start: 0.8416 (m110) cc_final: 0.8113 (m110) REVERT: B 16 GLN cc_start: 0.8504 (pp30) cc_final: 0.8091 (pp30) REVERT: B 60 THR cc_start: 0.7073 (p) cc_final: 0.6783 (p) REVERT: B 87 ASN cc_start: 0.8348 (m-40) cc_final: 0.8078 (m-40) REVERT: B 149 ASN cc_start: 0.6369 (m-40) cc_final: 0.5951 (m-40) REVERT: C 136 MET cc_start: 0.8582 (mmm) cc_final: 0.8283 (mmm) REVERT: C 190 LEU cc_start: 0.7996 (mt) cc_final: 0.7750 (mt) REVERT: C 206 ARG cc_start: 0.8009 (mmm-85) cc_final: 0.7585 (mtp85) REVERT: C 378 MET cc_start: 0.6812 (mmm) cc_final: 0.6223 (tpp) REVERT: C 392 MET cc_start: 0.7745 (tmm) cc_final: 0.6911 (ttt) REVERT: C 473 ARG cc_start: 0.8096 (ttt90) cc_final: 0.7614 (ttt90) REVERT: C 596 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7784 (mt-10) REVERT: C 665 ARG cc_start: 0.8440 (ptt180) cc_final: 0.7993 (ptt180) REVERT: C 688 MET cc_start: 0.7809 (ptp) cc_final: 0.7392 (ptp) REVERT: C 759 MET cc_start: 0.8437 (mmm) cc_final: 0.8135 (mmm) REVERT: C 763 GLN cc_start: 0.8565 (mp-120) cc_final: 0.8204 (mp10) REVERT: C 847 ARG cc_start: 0.7566 (mtm110) cc_final: 0.6943 (mtm180) REVERT: C 1097 ILE cc_start: 0.8252 (mm) cc_final: 0.7940 (mt) REVERT: C 1101 GLU cc_start: 0.8091 (pm20) cc_final: 0.7888 (pm20) REVERT: C 1117 ASN cc_start: 0.8710 (t0) cc_final: 0.8285 (t0) REVERT: D 167 MET cc_start: 0.6294 (mpp) cc_final: 0.5339 (ppp) REVERT: D 271 TYR cc_start: 0.8600 (m-10) cc_final: 0.7510 (m-80) REVERT: D 398 GLN cc_start: 0.8169 (mt0) cc_final: 0.7803 (mp10) REVERT: D 433 ARG cc_start: 0.6421 (ptm-80) cc_final: 0.3849 (ptm-80) REVERT: D 703 MET cc_start: 0.7497 (ppp) cc_final: 0.6848 (ptt) REVERT: D 755 ILE cc_start: 0.8026 (mp) cc_final: 0.7691 (mt) REVERT: D 802 ASP cc_start: 0.8439 (p0) cc_final: 0.8221 (p0) REVERT: D 879 ARG cc_start: 0.7569 (ptt180) cc_final: 0.6609 (ptt180) REVERT: D 917 GLN cc_start: 0.8240 (tt0) cc_final: 0.7991 (tt0) REVERT: D 1070 MET cc_start: 0.0699 (mmp) cc_final: -0.0789 (mmp) REVERT: F 147 MET cc_start: 0.6263 (mpp) cc_final: 0.5949 (mpp) REVERT: F 162 MET cc_start: -0.0412 (tpt) cc_final: -0.1440 (tpt) REVERT: Q 21 GLU cc_start: 0.6733 (pp20) cc_final: 0.6184 (pt0) REVERT: Q 108 GLU cc_start: 0.6897 (pm20) cc_final: 0.6582 (pm20) REVERT: Q 132 GLN cc_start: 0.7637 (tm-30) cc_final: 0.7316 (tm-30) REVERT: Q 265 HIS cc_start: 0.6057 (t-90) cc_final: 0.5504 (t-90) REVERT: Q 312 MET cc_start: 0.5863 (tpt) cc_final: 0.3337 (mmp) REVERT: R 26 ASP cc_start: 0.7336 (m-30) cc_final: 0.6986 (m-30) REVERT: R 43 ARG cc_start: 0.8804 (ttp80) cc_final: 0.8277 (ttp80) REVERT: R 66 ILE cc_start: 0.8422 (mm) cc_final: 0.8151 (mm) REVERT: R 86 ARG cc_start: 0.6251 (tpm170) cc_final: 0.5277 (mmm160) REVERT: R 111 LEU cc_start: 0.8358 (tp) cc_final: 0.8141 (tp) outliers start: 2 outliers final: 1 residues processed: 802 average time/residue: 0.2278 time to fit residues: 291.5997 Evaluate side-chains 700 residues out of total 3683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 699 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 19 optimal weight: 5.9990 chunk 233 optimal weight: 0.9980 chunk 392 optimal weight: 4.9990 chunk 322 optimal weight: 0.8980 chunk 411 optimal weight: 6.9990 chunk 414 optimal weight: 3.9990 chunk 420 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 269 optimal weight: 1.9990 chunk 3 optimal weight: 0.1980 chunk 152 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 ASN C 156 HIS C 471 GLN C 805 ASN C1111 HIS ** C1223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 ASN ** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.216022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.175360 restraints weight = 46537.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.172889 restraints weight = 67802.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.173548 restraints weight = 59846.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.172527 restraints weight = 39087.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.172994 restraints weight = 39730.455| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 36872 Z= 0.200 Angle : 0.682 18.036 50455 Z= 0.348 Chirality : 0.043 0.171 5814 Planarity : 0.005 0.100 6201 Dihedral : 16.274 176.617 6108 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.04 % Favored : 90.94 % Rotamer: Outliers : 0.03 % Allowed : 1.59 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.13), residues: 4427 helix: 0.64 (0.13), residues: 1699 sheet: -1.00 (0.25), residues: 446 loop : -1.95 (0.13), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C1042 TYR 0.020 0.002 TYR D1199 PHE 0.025 0.002 PHE D 229 TRP 0.032 0.002 TRP D 34 HIS 0.009 0.001 HIS C1111 Details of bonding type rmsd covalent geometry : bond 0.00460 (36865) covalent geometry : angle 0.66832 (50449) hydrogen bonds : bond 0.04042 ( 1428) hydrogen bonds : angle 4.49305 ( 3990) metal coordination : bond 0.01802 ( 7) metal coordination : angle 12.33090 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8854 Ramachandran restraints generated. 4427 Oldfield, 0 Emsley, 4427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8854 Ramachandran restraints generated. 4427 Oldfield, 0 Emsley, 4427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 3683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 794 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8850 (ptpt) cc_final: 0.8541 (ptmt) REVERT: A 138 ASP cc_start: 0.7530 (p0) cc_final: 0.7278 (p0) REVERT: A 145 GLU cc_start: 0.5286 (mt-10) cc_final: 0.4850 (mt-10) REVERT: B 60 THR cc_start: 0.7126 (p) cc_final: 0.6836 (p) REVERT: B 87 ASN cc_start: 0.8486 (m-40) cc_final: 0.8094 (m-40) REVERT: B 148 VAL cc_start: 0.7547 (t) cc_final: 0.7243 (t) REVERT: B 149 ASN cc_start: 0.6488 (m-40) cc_final: 0.6129 (m-40) REVERT: C 136 MET cc_start: 0.8883 (mmm) cc_final: 0.8351 (mmm) REVERT: C 468 LEU cc_start: 0.9122 (tp) cc_final: 0.8868 (tp) REVERT: C 665 ARG cc_start: 0.8488 (ptt180) cc_final: 0.8260 (ptt180) REVERT: C 682 ASP cc_start: 0.7728 (t0) cc_final: 0.7524 (t0) REVERT: C 688 MET cc_start: 0.7817 (ptp) cc_final: 0.7335 (ptp) REVERT: C 845 MET cc_start: 0.7804 (ptt) cc_final: 0.7352 (ptp) REVERT: C 847 ARG cc_start: 0.7749 (mtm110) cc_final: 0.7324 (mtm180) REVERT: C 1117 ASN cc_start: 0.8775 (t0) cc_final: 0.8336 (t0) REVERT: C 1154 GLN cc_start: 0.7480 (mp10) cc_final: 0.6822 (mp10) REVERT: D 271 TYR cc_start: 0.8651 (m-80) cc_final: 0.7697 (m-80) REVERT: D 390 LYS cc_start: 0.8414 (ttpt) cc_final: 0.7866 (ttpt) REVERT: D 398 GLN cc_start: 0.8131 (mt0) cc_final: 0.7818 (mp10) REVERT: D 433 ARG cc_start: 0.6629 (ptm-80) cc_final: 0.3951 (ptm-80) REVERT: D 703 MET cc_start: 0.7489 (ppp) cc_final: 0.6926 (ptt) REVERT: D 802 ASP cc_start: 0.8469 (p0) cc_final: 0.8230 (p0) REVERT: D 879 ARG cc_start: 0.7669 (ptt180) cc_final: 0.6701 (ptt180) REVERT: D 917 GLN cc_start: 0.8256 (tt0) cc_final: 0.8032 (tt0) REVERT: E 28 ARG cc_start: 0.7539 (mpt180) cc_final: 0.7262 (mpt180) REVERT: F 120 ARG cc_start: 0.7801 (ppt170) cc_final: 0.7484 (ppt170) REVERT: F 147 MET cc_start: 0.5860 (mpp) cc_final: 0.5533 (mpp) REVERT: F 162 MET cc_start: -0.0554 (tpt) cc_final: -0.1569 (tpt) REVERT: F 456 ASP cc_start: 0.7999 (m-30) cc_final: 0.7729 (m-30) REVERT: Q 21 GLU cc_start: 0.6882 (pp20) cc_final: 0.6348 (pt0) REVERT: Q 128 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7352 (mm-30) REVERT: Q 132 GLN cc_start: 0.7753 (tm-30) cc_final: 0.7433 (tm-30) REVERT: Q 312 MET cc_start: 0.5861 (tpt) cc_final: 0.3388 (mmp) REVERT: R 26 ASP cc_start: 0.7254 (m-30) cc_final: 0.6941 (m-30) REVERT: R 66 ILE cc_start: 0.8441 (mm) cc_final: 0.8165 (mm) REVERT: R 86 ARG cc_start: 0.6250 (tpm170) cc_final: 0.5049 (mmm160) REVERT: R 111 LEU cc_start: 0.8343 (tp) cc_final: 0.8118 (tp) REVERT: R 112 LEU cc_start: 0.7995 (mt) cc_final: 0.7785 (mt) outliers start: 1 outliers final: 1 residues processed: 794 average time/residue: 0.2314 time to fit residues: 294.1293 Evaluate side-chains 700 residues out of total 3683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 699 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 226 optimal weight: 0.2980 chunk 233 optimal weight: 0.3980 chunk 79 optimal weight: 7.9990 chunk 347 optimal weight: 5.9990 chunk 107 optimal weight: 0.5980 chunk 403 optimal weight: 2.9990 chunk 389 optimal weight: 2.9990 chunk 402 optimal weight: 0.5980 chunk 131 optimal weight: 0.9980 chunk 203 optimal weight: 2.9990 chunk 401 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN B 224 GLN C 471 GLN C 586 HIS C 805 ASN C1111 HIS ** C1223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 ASN F 639 HIS Q 265 HIS ** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.213815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.173106 restraints weight = 46919.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.170229 restraints weight = 71446.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.170672 restraints weight = 62576.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.169368 restraints weight = 42101.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.169880 restraints weight = 41715.856| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 36872 Z= 0.134 Angle : 0.628 12.742 50455 Z= 0.322 Chirality : 0.042 0.191 5814 Planarity : 0.005 0.101 6201 Dihedral : 16.239 179.302 6108 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.68 % Favored : 92.30 % Rotamer: Outliers : 0.03 % Allowed : 0.59 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.13), residues: 4427 helix: 0.72 (0.13), residues: 1705 sheet: -0.83 (0.24), residues: 458 loop : -1.96 (0.13), residues: 2264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1046 TYR 0.017 0.001 TYR C 35 PHE 0.034 0.001 PHE B 71 TRP 0.034 0.002 TRP D 34 HIS 0.008 0.001 HIS C1111 Details of bonding type rmsd covalent geometry : bond 0.00306 (36865) covalent geometry : angle 0.62103 (50449) hydrogen bonds : bond 0.03546 ( 1428) hydrogen bonds : angle 4.31512 ( 3990) metal coordination : bond 0.01147 ( 7) metal coordination : angle 8.68167 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8854 Ramachandran restraints generated. 4427 Oldfield, 0 Emsley, 4427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8854 Ramachandran restraints generated. 4427 Oldfield, 0 Emsley, 4427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 3683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 791 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8871 (ptpt) cc_final: 0.8562 (ptmt) REVERT: A 145 GLU cc_start: 0.5337 (mt-10) cc_final: 0.4795 (mt-10) REVERT: B 60 THR cc_start: 0.7159 (p) cc_final: 0.6878 (p) REVERT: B 87 ASN cc_start: 0.8338 (m-40) cc_final: 0.8116 (m-40) REVERT: B 149 ASN cc_start: 0.6357 (m-40) cc_final: 0.5940 (m-40) REVERT: C 63 ILE cc_start: 0.7434 (pt) cc_final: 0.5846 (mt) REVERT: C 136 MET cc_start: 0.8609 (mmm) cc_final: 0.8252 (mmm) REVERT: C 190 LEU cc_start: 0.8202 (mt) cc_final: 0.7807 (mt) REVERT: C 206 ARG cc_start: 0.8083 (mmm-85) cc_final: 0.7638 (mtp85) REVERT: C 378 MET cc_start: 0.6850 (mmm) cc_final: 0.6387 (tpp) REVERT: C 473 ARG cc_start: 0.8048 (ttt90) cc_final: 0.7824 (ttt90) REVERT: C 665 ARG cc_start: 0.8361 (ptt180) cc_final: 0.7953 (ptt180) REVERT: C 688 MET cc_start: 0.7822 (ptp) cc_final: 0.7388 (ptp) REVERT: C 695 GLN cc_start: 0.8153 (mt0) cc_final: 0.7907 (mt0) REVERT: C 763 GLN cc_start: 0.8557 (mp-120) cc_final: 0.8127 (mp10) REVERT: C 845 MET cc_start: 0.7802 (ptt) cc_final: 0.7392 (ptp) REVERT: C 847 ARG cc_start: 0.7525 (mtm110) cc_final: 0.7176 (mtm180) REVERT: C 1101 GLU cc_start: 0.8161 (pm20) cc_final: 0.7957 (pm20) REVERT: C 1117 ASN cc_start: 0.8719 (t0) cc_final: 0.8253 (t0) REVERT: D 433 ARG cc_start: 0.6459 (ptm-80) cc_final: 0.3740 (ptm-80) REVERT: D 625 MET cc_start: 0.8143 (ttp) cc_final: 0.7648 (tmm) REVERT: D 703 MET cc_start: 0.7441 (ppp) cc_final: 0.6835 (ptt) REVERT: D 755 ILE cc_start: 0.7967 (mp) cc_final: 0.7612 (mt) REVERT: D 879 ARG cc_start: 0.7677 (ptt180) cc_final: 0.6668 (ptt180) REVERT: D 917 GLN cc_start: 0.8288 (tt0) cc_final: 0.7932 (tt0) REVERT: D 1234 GLN cc_start: 0.8034 (tp-100) cc_final: 0.7358 (tp40) REVERT: D 1252 ILE cc_start: 0.8744 (mm) cc_final: 0.8543 (mm) REVERT: E 28 ARG cc_start: 0.7545 (mpt180) cc_final: 0.7285 (mpt180) REVERT: F 120 ARG cc_start: 0.7740 (ppt170) cc_final: 0.7504 (ppt170) REVERT: F 162 MET cc_start: -0.0429 (tpt) cc_final: -0.1439 (tpt) REVERT: F 528 MET cc_start: 0.6942 (mtp) cc_final: 0.6692 (mtp) REVERT: Q 21 GLU cc_start: 0.6770 (pp20) cc_final: 0.6204 (pt0) REVERT: Q 128 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7285 (mm-30) REVERT: Q 132 GLN cc_start: 0.7728 (tm-30) cc_final: 0.7385 (tm-30) REVERT: Q 312 MET cc_start: 0.5683 (tpt) cc_final: 0.3391 (mmp) REVERT: R 26 ASP cc_start: 0.7293 (m-30) cc_final: 0.6958 (m-30) REVERT: R 66 ILE cc_start: 0.8401 (mm) cc_final: 0.8140 (mm) REVERT: R 86 ARG cc_start: 0.6168 (tpm170) cc_final: 0.5294 (mmm160) REVERT: R 112 LEU cc_start: 0.7919 (mt) cc_final: 0.7715 (mt) REVERT: R 128 GLU cc_start: 0.7136 (tp30) cc_final: 0.6911 (tp30) outliers start: 1 outliers final: 1 residues processed: 791 average time/residue: 0.2214 time to fit residues: 281.8042 Evaluate side-chains 710 residues out of total 3683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 709 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 319 optimal weight: 0.4980 chunk 430 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 375 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 146 optimal weight: 3.9990 chunk 188 optimal weight: 0.5980 chunk 53 optimal weight: 0.0570 chunk 199 optimal weight: 0.7980 chunk 452 optimal weight: 0.9980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 131 HIS B 224 GLN C 471 GLN C 622 HIS C 805 ASN ** C1223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1282 GLN ** D 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 ASN F 639 HIS ** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.211261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.173325 restraints weight = 44381.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.171109 restraints weight = 67957.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.172706 restraints weight = 60698.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.171678 restraints weight = 42210.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.172176 restraints weight = 42353.616| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 36872 Z= 0.130 Angle : 0.628 11.972 50455 Z= 0.321 Chirality : 0.042 0.259 5814 Planarity : 0.005 0.103 6201 Dihedral : 16.202 179.070 6108 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.13 % Favored : 91.85 % Rotamer: Outliers : 0.03 % Allowed : 0.50 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.13), residues: 4427 helix: 0.77 (0.13), residues: 1700 sheet: -0.77 (0.24), residues: 459 loop : -1.92 (0.13), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C1046 TYR 0.023 0.001 TYR C 74 PHE 0.028 0.001 PHE D1281 TRP 0.034 0.002 TRP D 34 HIS 0.005 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00299 (36865) covalent geometry : angle 0.62140 (50449) hydrogen bonds : bond 0.03471 ( 1428) hydrogen bonds : angle 4.26766 ( 3990) metal coordination : bond 0.01022 ( 7) metal coordination : angle 8.07366 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8854 Ramachandran restraints generated. 4427 Oldfield, 0 Emsley, 4427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8854 Ramachandran restraints generated. 4427 Oldfield, 0 Emsley, 4427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 3683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 777 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 GLU cc_start: 0.5258 (mt-10) cc_final: 0.4728 (mt-10) REVERT: B 60 THR cc_start: 0.7135 (p) cc_final: 0.6842 (p) REVERT: B 87 ASN cc_start: 0.8340 (m-40) cc_final: 0.8076 (m-40) REVERT: B 149 ASN cc_start: 0.6358 (m-40) cc_final: 0.5962 (m-40) REVERT: C 63 ILE cc_start: 0.7497 (pt) cc_final: 0.5927 (mt) REVERT: C 136 MET cc_start: 0.8751 (mmm) cc_final: 0.8169 (mmm) REVERT: C 190 LEU cc_start: 0.8189 (mt) cc_final: 0.7814 (mt) REVERT: C 378 MET cc_start: 0.6773 (mmm) cc_final: 0.6264 (tpp) REVERT: C 473 ARG cc_start: 0.7985 (ttt90) cc_final: 0.7781 (ttt90) REVERT: C 665 ARG cc_start: 0.8453 (ptt180) cc_final: 0.7932 (ptt180) REVERT: C 688 MET cc_start: 0.7726 (ptp) cc_final: 0.7231 (ptp) REVERT: C 695 GLN cc_start: 0.8201 (mt0) cc_final: 0.7985 (mt0) REVERT: C 763 GLN cc_start: 0.8526 (mp-120) cc_final: 0.8090 (mp10) REVERT: C 845 MET cc_start: 0.7791 (ptt) cc_final: 0.7371 (ptp) REVERT: C 847 ARG cc_start: 0.7498 (mtm110) cc_final: 0.7148 (mtm180) REVERT: C 1101 GLU cc_start: 0.8175 (pm20) cc_final: 0.7923 (pm20) REVERT: C 1117 ASN cc_start: 0.8765 (t0) cc_final: 0.8332 (t0) REVERT: D 53 GLU cc_start: 0.7348 (tp30) cc_final: 0.6824 (tp30) REVERT: D 433 ARG cc_start: 0.6429 (ptm-80) cc_final: 0.3662 (ptm-80) REVERT: D 487 MET cc_start: 0.8655 (mmm) cc_final: 0.8325 (mtm) REVERT: D 625 MET cc_start: 0.8138 (ttp) cc_final: 0.7838 (tmm) REVERT: D 703 MET cc_start: 0.7433 (ppp) cc_final: 0.6752 (ptt) REVERT: D 755 ILE cc_start: 0.7975 (mp) cc_final: 0.7552 (mt) REVERT: D 879 ARG cc_start: 0.7736 (ptt180) cc_final: 0.6694 (ptt180) REVERT: D 917 GLN cc_start: 0.8210 (tt0) cc_final: 0.7932 (tt0) REVERT: D 1155 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7407 (mp0) REVERT: D 1234 GLN cc_start: 0.8046 (tp-100) cc_final: 0.7607 (tp40) REVERT: F 120 ARG cc_start: 0.7662 (ppt170) cc_final: 0.7357 (ppt170) REVERT: F 162 MET cc_start: -0.0422 (tpt) cc_final: -0.1488 (tpt) REVERT: F 547 GLU cc_start: 0.7938 (mp0) cc_final: 0.7169 (mt-10) REVERT: Q 21 GLU cc_start: 0.6706 (pp20) cc_final: 0.6201 (pt0) REVERT: Q 108 GLU cc_start: 0.6884 (pm20) cc_final: 0.6552 (pm20) REVERT: Q 132 GLN cc_start: 0.7736 (tm-30) cc_final: 0.7476 (tm-30) REVERT: Q 312 MET cc_start: 0.5762 (tpt) cc_final: 0.3468 (mmp) REVERT: R 26 ASP cc_start: 0.7148 (m-30) cc_final: 0.6795 (m-30) REVERT: R 66 ILE cc_start: 0.8405 (mm) cc_final: 0.8143 (mm) REVERT: R 86 ARG cc_start: 0.6190 (tpm170) cc_final: 0.5323 (mmm160) REVERT: R 128 GLU cc_start: 0.7143 (tp30) cc_final: 0.6930 (tp30) outliers start: 1 outliers final: 1 residues processed: 777 average time/residue: 0.2161 time to fit residues: 269.4857 Evaluate side-chains 694 residues out of total 3683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 693 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 324 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 chunk 236 optimal weight: 0.5980 chunk 215 optimal weight: 1.9990 chunk 343 optimal weight: 10.0000 chunk 249 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 377 optimal weight: 0.8980 chunk 432 optimal weight: 7.9990 chunk 35 optimal weight: 0.0050 chunk 417 optimal weight: 8.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN B 224 GLN C 471 GLN C 766 ASN C 805 ASN ** D 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 735 GLN ** D1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 ASN F 639 HIS ** R 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.211231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.173128 restraints weight = 43981.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.170852 restraints weight = 69744.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.171414 restraints weight = 58670.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.170416 restraints weight = 40394.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.171208 restraints weight = 35071.326| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 36872 Z= 0.134 Angle : 0.632 12.336 50455 Z= 0.323 Chirality : 0.042 0.172 5814 Planarity : 0.005 0.104 6201 Dihedral : 16.175 179.253 6108 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.95 % Favored : 92.03 % Rotamer: Outliers : 0.03 % Allowed : 0.41 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.13), residues: 4427 helix: 0.76 (0.13), residues: 1704 sheet: -0.71 (0.25), residues: 454 loop : -1.95 (0.13), residues: 2269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C1046 TYR 0.025 0.001 TYR C 74 PHE 0.022 0.001 PHE D 219 TRP 0.069 0.002 TRP D 34 HIS 0.005 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00307 (36865) covalent geometry : angle 0.62570 (50449) hydrogen bonds : bond 0.03473 ( 1428) hydrogen bonds : angle 4.28459 ( 3990) metal coordination : bond 0.01052 ( 7) metal coordination : angle 8.18960 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6601.00 seconds wall clock time: 114 minutes 20.26 seconds (6860.26 seconds total)