Starting phenix.real_space_refine on Fri Mar 6 03:14:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6yxu_10996/03_2026/6yxu_10996.cif Found real_map, /net/cci-nas-00/data/ceres_data/6yxu_10996/03_2026/6yxu_10996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6yxu_10996/03_2026/6yxu_10996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6yxu_10996/03_2026/6yxu_10996.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6yxu_10996/03_2026/6yxu_10996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6yxu_10996/03_2026/6yxu_10996.map" } resolution = 3.08 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= 0.003 sd= 0.026 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 Mg 1 5.21 5 S 97 5.16 5 C 17396 2.51 5 N 4943 2.21 5 O 5352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 142 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: 27791 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1716 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 211} Chain: "B" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1771 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 218} Chain: "C" Number of atoms: 8424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8424 Classifications: {'peptide': 1088} Link IDs: {'PCIS': 1, 'PTRANS': 57, 'TRANS': 1029} Chain breaks: 1 Chain: "D" Number of atoms: 9916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1269, 9916 Classifications: {'peptide': 1269} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 55, 'TRANS': 1211} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 597 Classifications: {'peptide': 76} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 69} Chain breaks: 1 Chain: "H" Number of atoms: 5364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 691, 5364 Classifications: {'peptide': 691} Link IDs: {'PTRANS': 37, 'TRANS': 653} Chain breaks: 1 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 18930 SG CYS D 890 33.456 60.993 73.228 1.00 32.00 S ATOM 19492 SG CYS D 967 36.092 63.495 74.347 1.00 28.17 S ATOM 19534 SG CYS D 974 34.356 61.442 76.692 1.00 27.00 S ATOM 19553 SG CYS D 977 36.549 59.645 74.829 1.00 27.54 S ATOM 12370 SG CYS D 60 30.262 122.681 90.178 1.00 86.44 S ATOM 12388 SG CYS D 62 30.566 126.995 89.395 1.00 90.65 S ATOM 12497 SG CYS D 75 27.720 124.667 87.668 1.00 85.19 S ATOM 12523 SG CYS D 78 31.209 123.643 86.501 1.00 86.40 S Time building chain proxies: 6.08, per 1000 atoms: 0.22 Number of scatterers: 27791 At special positions: 0 Unit cell: (137.963, 149.598, 168.713, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 97 16.00 Mg 1 11.99 O 5352 8.00 N 4943 7.00 C 17396 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: 2.00 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 974 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 977 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 890 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 967 " pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 62 " Number of angles added : 12 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6606 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 42 sheets defined 37.8% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 30 through 45 Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 203 through 225 removed outlier: 3.510A pdb=" N ALA A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 45 removed outlier: 3.930A pdb=" N LEU B 34 " --> pdb=" O PHE B 30 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 removed outlier: 3.617A pdb=" N ILE B 76 " --> pdb=" O ASP B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 203 through 224 Processing helix chain 'C' and resid 45 through 55 removed outlier: 3.697A pdb=" N THR C 49 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER C 51 " --> pdb=" O VAL C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 67 Processing helix chain 'C' and resid 76 through 85 removed outlier: 3.759A pdb=" N VAL C 80 " --> pdb=" O GLY C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 117 Processing helix chain 'C' and resid 224 through 232 removed outlier: 3.973A pdb=" N LEU C 228 " --> pdb=" O PRO C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 243 Processing helix chain 'C' and resid 246 through 255 removed outlier: 3.507A pdb=" N MET C 250 " --> pdb=" O SER C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 273 Processing helix chain 'C' and resid 279 through 292 removed outlier: 4.171A pdb=" N PHE C 291 " --> pdb=" O LEU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 310 Processing helix chain 'C' and resid 311 through 313 No H-bonds generated for 'chain 'C' and resid 311 through 313' Processing helix chain 'C' and resid 325 through 341 removed outlier: 3.616A pdb=" N VAL C 329 " --> pdb=" O THR C 325 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE C 333 " --> pdb=" O VAL C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 394 Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.671A pdb=" N LEU C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 422 Processing helix chain 'C' and resid 435 through 444 Processing helix chain 'C' and resid 523 through 529 removed outlier: 3.772A pdb=" N ARG C 529 " --> pdb=" O ASP C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 604 Processing helix chain 'C' and resid 621 through 630 removed outlier: 3.566A pdb=" N ALA C 625 " --> pdb=" O MET C 621 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY C 630 " --> pdb=" O ALA C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 735 Processing helix chain 'C' and resid 891 through 895 removed outlier: 3.595A pdb=" N MET C 895 " --> pdb=" O VAL C 892 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 933 Processing helix chain 'C' and resid 972 through 983 removed outlier: 3.665A pdb=" N LEU C 976 " --> pdb=" O GLN C 972 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY C 981 " --> pdb=" O ALA C 977 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER C 982 " --> pdb=" O GLY C 978 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR C 983 " --> pdb=" O LEU C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 1028 through 1032 removed outlier: 3.839A pdb=" N ILE C1032 " --> pdb=" O ASP C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1060 through 1070 Processing helix chain 'C' and resid 1073 through 1081 Processing helix chain 'C' and resid 1087 through 1100 Processing helix chain 'C' and resid 1115 through 1120 Processing helix chain 'D' and resid 16 through 23 removed outlier: 3.750A pdb=" N ILE D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 89 removed outlier: 3.627A pdb=" N VAL D 87 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG D 89 " --> pdb=" O LYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 107 Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 147 through 186 Processing helix chain 'D' and resid 190 through 227 removed outlier: 3.748A pdb=" N ARG D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 246 Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 270 through 284 Processing helix chain 'D' and resid 286 through 305 removed outlier: 3.683A pdb=" N LYS D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL D 299 " --> pdb=" O ARG D 295 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE D 302 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN D 304 " --> pdb=" O ALA D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.897A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 339 through 360 Processing helix chain 'D' and resid 363 through 384 removed outlier: 3.764A pdb=" N VAL D 367 " --> pdb=" O PRO D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 406 Processing helix chain 'D' and resid 444 through 452 removed outlier: 3.553A pdb=" N ALA D 448 " --> pdb=" O PRO D 444 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLU D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 464 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 486 through 491 removed outlier: 3.531A pdb=" N ILE D 491 " --> pdb=" O LEU D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 578 through 589 Processing helix chain 'D' and resid 614 through 623 removed outlier: 3.674A pdb=" N MET D 620 " --> pdb=" O ALA D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 643 through 650 Processing helix chain 'D' and resid 666 through 674 Processing helix chain 'D' and resid 688 through 703 Processing helix chain 'D' and resid 704 through 722 removed outlier: 4.003A pdb=" N VAL D 708 " --> pdb=" O PRO D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 740 through 762 removed outlier: 3.697A pdb=" N GLU D 751 " --> pdb=" O ARG D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 767 through 778 Processing helix chain 'D' and resid 778 through 792 removed outlier: 3.730A pdb=" N GLU D 782 " --> pdb=" O GLN D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 796 through 804 removed outlier: 3.999A pdb=" N VAL D 802 " --> pdb=" O ILE D 798 " (cutoff:3.500A) Processing helix chain 'D' and resid 809 through 818 removed outlier: 3.546A pdb=" N THR D 813 " --> pdb=" O ASN D 809 " (cutoff:3.500A) Processing helix chain 'D' and resid 844 through 851 Processing helix chain 'D' and resid 851 through 880 removed outlier: 3.968A pdb=" N ALA D 855 " --> pdb=" O ASN D 851 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ALA D 863 " --> pdb=" O LEU D 859 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU D 864 " --> pdb=" O ALA D 860 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR D 866 " --> pdb=" O THR D 862 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER D 880 " --> pdb=" O LEU D 876 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 916 removed outlier: 4.450A pdb=" N GLU D 916 " --> pdb=" O ALA D 913 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 913 through 916' Processing helix chain 'D' and resid 944 through 950 Processing helix chain 'D' and resid 963 through 967 Processing helix chain 'D' and resid 975 through 979 Processing helix chain 'D' and resid 993 through 1004 removed outlier: 3.968A pdb=" N VAL D 997 " --> pdb=" O ALA D 993 " (cutoff:3.500A) Processing helix chain 'D' and resid 1005 through 1009 Processing helix chain 'D' and resid 1028 through 1037 Processing helix chain 'D' and resid 1118 through 1126 Processing helix chain 'D' and resid 1127 through 1145 Processing helix chain 'D' and resid 1151 through 1163 removed outlier: 4.311A pdb=" N ILE D1155 " --> pdb=" O HIS D1151 " (cutoff:3.500A) Processing helix chain 'D' and resid 1184 through 1194 Processing helix chain 'D' and resid 1221 through 1228 Processing helix chain 'D' and resid 1229 through 1240 Processing helix chain 'D' and resid 1249 through 1256 Processing helix chain 'D' and resid 1265 through 1270 removed outlier: 3.611A pdb=" N ASN D1270 " --> pdb=" O SER D1266 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 34 Processing helix chain 'E' and resid 39 through 44 removed outlier: 3.505A pdb=" N ARG E 43 " --> pdb=" O GLU E 39 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA E 44 " --> pdb=" O LEU E 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 39 through 44' Processing helix chain 'E' and resid 46 through 67 removed outlier: 4.048A pdb=" N ARG E 57 " --> pdb=" O TYR E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 98 Processing helix chain 'H' and resid 4 through 41 Processing helix chain 'H' and resid 45 through 67 Processing helix chain 'H' and resid 156 through 163 Processing helix chain 'H' and resid 170 through 188 removed outlier: 3.738A pdb=" N ASP H 174 " --> pdb=" O GLU H 170 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE H 175 " --> pdb=" O GLY H 171 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N VAL H 176 " --> pdb=" O MET H 172 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ALA H 177 " --> pdb=" O ARG H 173 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR H 178 " --> pdb=" O ASP H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 220 Processing helix chain 'H' and resid 235 through 245 Processing helix chain 'H' and resid 274 through 280 Processing helix chain 'H' and resid 284 through 293 removed outlier: 3.719A pdb=" N VAL H 288 " --> pdb=" O LYS H 284 " (cutoff:3.500A) Processing helix chain 'H' and resid 316 through 329 Processing helix chain 'H' and resid 337 through 358 removed outlier: 4.055A pdb=" N ARG H 352 " --> pdb=" O VAL H 348 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA H 353 " --> pdb=" O VAL H 349 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA H 355 " --> pdb=" O GLU H 351 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ARG H 356 " --> pdb=" O ARG H 352 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 382 Processing helix chain 'H' and resid 386 through 395 Processing helix chain 'H' and resid 399 through 409 removed outlier: 3.779A pdb=" N LEU H 404 " --> pdb=" O PRO H 400 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ALA H 405 " --> pdb=" O GLU H 401 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR H 409 " --> pdb=" O ALA H 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 418 removed outlier: 3.782A pdb=" N GLY H 418 " --> pdb=" O ARG H 415 " (cutoff:3.500A) Processing helix chain 'H' and resid 436 through 447 removed outlier: 3.521A pdb=" N VAL H 443 " --> pdb=" O LEU H 439 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP H 444 " --> pdb=" O ASP H 440 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU H 445 " --> pdb=" O GLU H 441 " (cutoff:3.500A) Processing helix chain 'H' and resid 450 through 465 Processing helix chain 'H' and resid 509 through 516 Processing helix chain 'H' and resid 529 through 533 removed outlier: 3.567A pdb=" N GLU H 532 " --> pdb=" O GLU H 529 " (cutoff:3.500A) Processing helix chain 'H' and resid 534 through 545 Processing helix chain 'H' and resid 555 through 559 Processing helix chain 'H' and resid 568 through 573 Processing helix chain 'H' and resid 593 through 604 removed outlier: 4.013A pdb=" N VAL H 598 " --> pdb=" O GLU H 594 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA H 599 " --> pdb=" O ILE H 595 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA H 601 " --> pdb=" O ALA H 597 " (cutoff:3.500A) Processing helix chain 'H' and resid 633 through 645 removed outlier: 4.274A pdb=" N GLU H 639 " --> pdb=" O SER H 635 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE H 640 " --> pdb=" O ALA H 636 " (cutoff:3.500A) Processing helix chain 'H' and resid 680 through 687 removed outlier: 3.750A pdb=" N ILE H 684 " --> pdb=" O GLU H 680 " (cutoff:3.500A) Processing helix chain 'H' and resid 691 through 699 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 10 Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 111 removed outlier: 4.042A pdb=" N TYR A 96 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER A 53 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLU A 141 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N VAL A 51 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLY A 143 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ALA A 49 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AA4, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA5, first strand: chain 'B' and resid 8 through 13 removed outlier: 5.906A pdb=" N ARG B 18 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N THR B 198 " --> pdb=" O ARG B 18 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ARG B 20 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL B 196 " --> pdb=" O ARG B 20 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N VAL B 22 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ILE B 194 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N GLU B 24 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU B 192 " --> pdb=" O GLU B 24 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 93 through 98 removed outlier: 7.768A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 105 through 106 removed outlier: 3.788A pdb=" N ALA B 126 " --> pdb=" O VAL B 105 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AA9, first strand: chain 'C' and resid 30 through 31 removed outlier: 6.615A pdb=" N VAL C 30 " --> pdb=" O ALA C 964 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 87 through 88 removed outlier: 5.928A pdb=" N LEU C 96 " --> pdb=" O ILE C 131 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ILE C 131 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N PHE C 98 " --> pdb=" O GLU C 129 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLU C 129 " --> pdb=" O PHE C 98 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ASP C 100 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR C 127 " --> pdb=" O ASP C 100 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY C 146 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL C 126 " --> pdb=" O PHE C 144 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N PHE C 144 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ALA C 128 " --> pdb=" O THR C 142 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N THR C 142 " --> pdb=" O ALA C 128 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 157 through 159 Processing sheet with id=AB3, first strand: chain 'C' and resid 367 through 370 removed outlier: 3.603A pdb=" N SER C 168 " --> pdb=" O ARG C 445 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 175 through 176 removed outlier: 3.642A pdb=" N SER C 192 " --> pdb=" O ASP C 179 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 175 through 176 removed outlier: 3.687A pdb=" N HIS C 191 " --> pdb=" O VAL C 207 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE C 205 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU C 203 " --> pdb=" O VAL C 195 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 346 through 347 Processing sheet with id=AB7, first strand: chain 'C' and resid 496 through 497 removed outlier: 6.719A pdb=" N ILE C 503 " --> pdb=" O LEU C 522 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU C 522 " --> pdb=" O ILE C 503 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR C 505 " --> pdb=" O ASP C 520 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASP C 520 " --> pdb=" O THR C 505 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N TYR C 507 " --> pdb=" O GLN C 518 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLN C 518 " --> pdb=" O TYR C 507 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N LYS C 509 " --> pdb=" O THR C 516 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 496 through 497 Processing sheet with id=AB9, first strand: chain 'C' and resid 550 through 553 Processing sheet with id=AC1, first strand: chain 'C' and resid 633 through 634 removed outlier: 6.537A pdb=" N VAL C 633 " --> pdb=" O ILE C 693 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 658 through 662 removed outlier: 6.146A pdb=" N MET C 652 " --> pdb=" O ILE C 641 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ILE C 641 " --> pdb=" O MET C 652 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 998 through 999 removed outlier: 7.514A pdb=" N ILE C 726 " --> pdb=" O GLY C 887 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE C 889 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU C 728 " --> pdb=" O ILE C 889 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE C 727 " --> pdb=" O ILE C 907 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N ILE C 906 " --> pdb=" O ASN C 709 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU C 711 " --> pdb=" O ILE C 906 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N LEU C 908 " --> pdb=" O LEU C 711 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ALA C 713 " --> pdb=" O LEU C 908 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N THR C1015 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 740 through 751 removed outlier: 8.234A pdb=" N ASN C 857 " --> pdb=" O SER C 845 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N SER C 845 " --> pdb=" O ASN C 857 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU C 859 " --> pdb=" O VAL C 843 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL C 843 " --> pdb=" O LEU C 859 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ARG C 861 " --> pdb=" O ILE C 841 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE C 841 " --> pdb=" O ARG C 861 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TYR C 863 " --> pdb=" O ILE C 839 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLY C 836 " --> pdb=" O VAL C 787 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 792 through 794 removed outlier: 3.745A pdb=" N VAL C 794 " --> pdb=" O LEU C 828 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 935 through 936 Processing sheet with id=AC7, first strand: chain 'C' and resid 1033 through 1035 removed outlier: 6.222A pdb=" N CYS D 441 " --> pdb=" O GLN D 515 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1127 through 1129 Processing sheet with id=AC9, first strand: chain 'D' and resid 24 through 27 removed outlier: 4.514A pdb=" N SER D 24 " --> pdb=" O MET D 92 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N HIS D 94 " --> pdb=" O SER D 24 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLY D 26 " --> pdb=" O HIS D 94 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLY D 93 " --> pdb=" O VAL D 319 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 101 through 102 Processing sheet with id=AD2, first strand: chain 'D' and resid 234 through 235 removed outlier: 5.654A pdb=" N ILE D 136 " --> pdb=" O ALA D 255 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ALA D 255 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 327 through 329 Processing sheet with id=AD4, first strand: chain 'D' and resid 633 through 637 Processing sheet with id=AD5, first strand: chain 'D' and resid 885 through 887 removed outlier: 3.511A pdb=" N ARG D 886 " --> pdb=" O VAL D 973 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'D' and resid 896 through 899 Processing sheet with id=AD7, first strand: chain 'D' and resid 901 through 902 Processing sheet with id=AD8, first strand: chain 'D' and resid 922 through 923 removed outlier: 4.268A pdb=" N ARG D 922 " --> pdb=" O LEU D 943 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 1044 through 1045 Processing sheet with id=AE1, first strand: chain 'D' and resid 1076 through 1082 removed outlier: 4.153A pdb=" N LYS D1080 " --> pdb=" O PHE D1063 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE D1063 " --> pdb=" O LYS D1080 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1181 through 1183 removed outlier: 5.308A pdb=" N ILE D1168 " --> pdb=" O ARG D1205 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ARG D1205 " --> pdb=" O ILE D1168 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1272 through 1275 removed outlier: 3.524A pdb=" N THR E 104 " --> pdb=" O GLN D1272 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN D1274 " --> pdb=" O GLU E 102 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 90 through 92 removed outlier: 6.316A pdb=" N ILE H 90 " --> pdb=" O LEU H 100 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP H 92 " --> pdb=" O GLU H 98 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU H 98 " --> pdb=" O ASP H 92 " (cutoff:3.500A) removed outlier: 9.215A pdb=" N ARG H 82 " --> pdb=" O LEU H 100 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N LEU H 102 " --> pdb=" O ARG H 82 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TYR H 84 " --> pdb=" O LEU H 102 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY H 73 " --> pdb=" O ILE H 85 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N PHE H 72 " --> pdb=" O GLN H 128 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N GLN H 128 " --> pdb=" O PHE H 72 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ARG H 74 " --> pdb=" O ARG H 126 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ARG H 126 " --> pdb=" O ARG H 74 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASP H 76 " --> pdb=" O ARG H 124 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP H 138 " --> pdb=" O HIS H 130 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 254 through 257 removed outlier: 6.497A pdb=" N VAL H 229 " --> pdb=" O VAL H 255 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N MET H 257 " --> pdb=" O VAL H 229 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL H 231 " --> pdb=" O MET H 257 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU H 230 " --> pdb=" O VAL H 526 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N VAL H 525 " --> pdb=" O THR H 551 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL H 194 " --> pdb=" O VAL H 581 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 653 through 654 1083 hydrogen bonds defined for protein. 3033 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.71 Time building geometry restraints manager: 2.70 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: 9639 1.34 - 1.46: 5676 1.46 - 1.58: 12781 1.58 - 1.70: 0 1.70 - 1.82: 172 Bond restraints: 28268 Sorted by residual: bond pdb=" C HIS D 544 " pdb=" N LEU D 545 " ideal model delta sigma weight residual 1.332 1.294 0.038 1.44e-02 4.82e+03 7.06e+00 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.59e+00 bond pdb=" CB VAL D1131 " pdb=" CG2 VAL D1131 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.45e+00 bond pdb=" CG1 ILE C 158 " pdb=" CD1 ILE C 158 " ideal model delta sigma weight residual 1.513 1.457 0.056 3.90e-02 6.57e+02 2.09e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.90e-02 2.77e+03 2.04e+00 ... (remaining 28263 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 35834 1.24 - 2.49: 2108 2.49 - 3.73: 291 3.73 - 4.97: 76 4.97 - 6.21: 14 Bond angle restraints: 38323 Sorted by residual: angle pdb=" N VAL D1195 " pdb=" CA VAL D1195 " pdb=" C VAL D1195 " ideal model delta sigma weight residual 112.12 107.06 5.06 8.40e-01 1.42e+00 3.63e+01 angle pdb=" N ILE C1043 " pdb=" CA ILE C1043 " pdb=" C ILE C1043 " ideal model delta sigma weight residual 113.71 108.57 5.14 9.50e-01 1.11e+00 2.93e+01 angle pdb=" N ARG D 624 " pdb=" CA ARG D 624 " pdb=" C ARG D 624 " ideal model delta sigma weight residual 114.04 110.02 4.02 1.24e+00 6.50e-01 1.05e+01 angle pdb=" CA PHE C 422 " pdb=" C PHE C 422 " pdb=" N GLY C 423 " ideal model delta sigma weight residual 118.27 113.41 4.86 1.59e+00 3.96e-01 9.35e+00 angle pdb=" N ILE D1169 " pdb=" CA ILE D1169 " pdb=" C ILE D1169 " ideal model delta sigma weight residual 111.62 109.39 2.23 7.90e-01 1.60e+00 7.96e+00 ... (remaining 38318 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 15644 17.97 - 35.93: 1385 35.93 - 53.90: 202 53.90 - 71.87: 45 71.87 - 89.83: 26 Dihedral angle restraints: 17302 sinusoidal: 7039 harmonic: 10263 Sorted by residual: dihedral pdb=" CA ALA H 563 " pdb=" C ALA H 563 " pdb=" N GLY H 564 " pdb=" CA GLY H 564 " ideal model delta harmonic sigma weight residual 180.00 152.96 27.04 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA ASP H 174 " pdb=" C ASP H 174 " pdb=" N ILE H 175 " pdb=" CA ILE H 175 " ideal model delta harmonic sigma weight residual -180.00 -154.06 -25.94 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA GLN D 600 " pdb=" C GLN D 600 " pdb=" N ALA D 601 " pdb=" CA ALA D 601 " ideal model delta harmonic sigma weight residual 180.00 156.89 23.11 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 17299 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2524 0.032 - 0.064: 1255 0.064 - 0.095: 394 0.095 - 0.127: 167 0.127 - 0.159: 16 Chirality restraints: 4356 Sorted by residual: chirality pdb=" CA PRO H 333 " pdb=" N PRO H 333 " pdb=" C PRO H 333 " pdb=" CB PRO H 333 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.33e-01 chirality pdb=" CA ILE C 319 " pdb=" N ILE C 319 " pdb=" C ILE C 319 " pdb=" CB ILE C 319 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.66e-01 chirality pdb=" CA ILE B 193 " pdb=" N ILE B 193 " pdb=" C ILE B 193 " pdb=" CB ILE B 193 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.63e-01 ... (remaining 4353 not shown) Planarity restraints: 5073 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU H 246 " -0.046 5.00e-02 4.00e+02 6.91e-02 7.64e+00 pdb=" N PRO H 247 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO H 247 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO H 247 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET C 895 " -0.045 5.00e-02 4.00e+02 6.91e-02 7.63e+00 pdb=" N PRO C 896 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 896 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 896 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 223 " -0.042 5.00e-02 4.00e+02 6.41e-02 6.57e+00 pdb=" N PRO C 224 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 224 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 224 " -0.035 5.00e-02 4.00e+02 ... (remaining 5070 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 160 2.47 - 3.08: 20622 3.08 - 3.68: 39577 3.68 - 4.29: 61267 4.29 - 4.90: 103683 Nonbonded interactions: 225309 Sorted by model distance: nonbonded pdb=" OD1 ASP D 539 " pdb="MG MG D2003 " model vdw 1.862 2.170 nonbonded pdb=" OH TYR C1070 " pdb=" O ILE D 509 " model vdw 1.976 3.040 nonbonded pdb=" OH TYR A 176 " pdb=" O GLY C1007 " model vdw 2.031 3.040 nonbonded pdb=" OD2 ASP H 253 " pdb=" OG SER H 511 " model vdw 2.062 3.040 nonbonded pdb=" O SER C 173 " pdb=" OH TYR C 177 " model vdw 2.075 3.040 ... (remaining 225304 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 226) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 27.550 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.060 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:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 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 : 0.007 0.380 28276 Z= 0.260 Angle : 0.679 9.018 38335 Z= 0.373 Chirality : 0.043 0.159 4356 Planarity : 0.006 0.069 5073 Dihedral : 13.999 89.832 10696 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.43 % Favored : 90.54 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -4.95 (0.11), residues: 3563 helix: -3.11 (0.10), residues: 1334 sheet: -2.16 (0.22), residues: 400 loop : -3.78 (0.11), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 28 TYR 0.037 0.002 TYR E 53 PHE 0.025 0.002 PHE C 364 TRP 0.016 0.001 TRP C 61 HIS 0.007 0.001 HIS H 368 Details of bonding type rmsd covalent geometry : bond 0.00580 (28268) covalent geometry : angle 0.67259 (38323) hydrogen bonds : bond 0.15654 ( 1079) hydrogen bonds : angle 7.13372 ( 3033) metal coordination : bond 0.18360 ( 8) metal coordination : angle 5.33201 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 1.060 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 outliers start: 0 outliers final: 0 residues processed: 323 average time/residue: 0.2254 time to fit residues: 107.0302 Evaluate side-chains 180 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 6.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 289 ASN C 470 HIS C 576 GLN D 213 GLN D 233 GLN D 515 GLN D 760 GLN H 130 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.069861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.054486 restraints weight = 86069.389| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.92 r_work: 0.2941 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 28276 Z= 0.220 Angle : 0.686 10.865 38335 Z= 0.354 Chirality : 0.046 0.175 4356 Planarity : 0.006 0.062 5073 Dihedral : 5.062 25.821 3932 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.94 % Allowed : 7.89 % Favored : 91.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.72 (0.13), residues: 3563 helix: -1.07 (0.13), residues: 1330 sheet: -1.38 (0.24), residues: 411 loop : -2.52 (0.13), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 662 TYR 0.034 0.002 TYR E 53 PHE 0.020 0.002 PHE C 364 TRP 0.019 0.002 TRP H 361 HIS 0.008 0.001 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.00511 (28268) covalent geometry : angle 0.67953 (38323) hydrogen bonds : bond 0.04478 ( 1079) hydrogen bonds : angle 5.06387 ( 3033) metal coordination : bond 0.01674 ( 8) metal coordination : angle 5.25735 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 1.039 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: C 992 MET cc_start: 0.8566 (mmp) cc_final: 0.8077 (mmp) REVERT: D 90 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7940 (pm20) REVERT: H 123 MET cc_start: 0.8436 (mmt) cc_final: 0.8118 (mmt) REVERT: H 462 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8068 (mp0) REVERT: H 630 ASP cc_start: 0.8672 (t0) cc_final: 0.8354 (t0) outliers start: 28 outliers final: 11 residues processed: 212 average time/residue: 0.1815 time to fit residues: 60.2468 Evaluate side-chains 168 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 943 VAL Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 956 ILE Chi-restraints excluded: chain D residue 1241 CYS Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 462 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 219 optimal weight: 0.9980 chunk 334 optimal weight: 9.9990 chunk 179 optimal weight: 3.9990 chunk 283 optimal weight: 0.9990 chunk 282 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 1 optimal weight: 8.9990 chunk 340 optimal weight: 0.6980 chunk 287 optimal weight: 0.9990 chunk 167 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 22 ASN D 369 ASN D 766 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.071279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.055801 restraints weight = 85971.254| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.95 r_work: 0.2978 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28276 Z= 0.113 Angle : 0.554 13.558 38335 Z= 0.285 Chirality : 0.042 0.198 4356 Planarity : 0.005 0.062 5073 Dihedral : 4.487 22.998 3932 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.21 % Allowed : 9.67 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.62 (0.14), residues: 3563 helix: 0.04 (0.15), residues: 1326 sheet: -0.87 (0.25), residues: 407 loop : -2.02 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 113 TYR 0.018 0.001 TYR A 168 PHE 0.012 0.001 PHE H 387 TRP 0.014 0.001 TRP H 361 HIS 0.003 0.001 HIS C1026 Details of bonding type rmsd covalent geometry : bond 0.00252 (28268) covalent geometry : angle 0.54634 (38323) hydrogen bonds : bond 0.03695 ( 1079) hydrogen bonds : angle 4.52215 ( 3033) metal coordination : bond 0.01302 ( 8) metal coordination : angle 5.23345 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 179 time to evaluate : 0.902 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: C 420 GLU cc_start: 0.8823 (tt0) cc_final: 0.8550 (mt-10) REVERT: C 992 MET cc_start: 0.8544 (mmp) cc_final: 0.8057 (mmp) REVERT: H 386 GLN cc_start: 0.8370 (mm-40) cc_final: 0.7689 (tm-30) REVERT: H 630 ASP cc_start: 0.8691 (t0) cc_final: 0.8371 (t0) outliers start: 36 outliers final: 21 residues processed: 208 average time/residue: 0.1919 time to fit residues: 62.1796 Evaluate side-chains 177 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 764 ILE Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 470 LYS Chi-restraints excluded: chain D residue 1131 VAL Chi-restraints excluded: chain D residue 1163 LEU Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 81 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 260 optimal weight: 0.0980 chunk 217 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 329 optimal weight: 0.4980 chunk 333 optimal weight: 10.0000 chunk 306 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 286 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 289 ASN C 926 HIS D 307 ASN ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.068465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.052891 restraints weight = 86641.547| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.94 r_work: 0.2903 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 28276 Z= 0.187 Angle : 0.599 12.849 38335 Z= 0.305 Chirality : 0.044 0.178 4356 Planarity : 0.005 0.059 5073 Dihedral : 4.472 24.433 3932 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 1.95 % Allowed : 10.21 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.20 (0.14), residues: 3563 helix: 0.34 (0.15), residues: 1328 sheet: -0.63 (0.25), residues: 437 loop : -1.74 (0.14), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 389 TYR 0.017 0.001 TYR A 168 PHE 0.014 0.002 PHE D1187 TRP 0.018 0.001 TRP D 58 HIS 0.006 0.001 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.00439 (28268) covalent geometry : angle 0.59106 (38323) hydrogen bonds : bond 0.04090 ( 1079) hydrogen bonds : angle 4.46764 ( 3033) metal coordination : bond 0.01160 ( 8) metal coordination : angle 5.61518 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 171 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.8136 (pmm) REVERT: C 45 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8368 (pp) REVERT: C 420 GLU cc_start: 0.8837 (tt0) cc_final: 0.8561 (mt-10) REVERT: C 602 MET cc_start: 0.9057 (mtt) cc_final: 0.8848 (mtt) REVERT: C 992 MET cc_start: 0.8561 (mmp) cc_final: 0.8143 (mmp) REVERT: D 90 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7968 (pm20) REVERT: D 148 LEU cc_start: 0.4865 (OUTLIER) cc_final: 0.4627 (pp) REVERT: D 389 ARG cc_start: 0.7716 (mmm160) cc_final: 0.7500 (mmp80) REVERT: D 406 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8718 (pp) REVERT: H 386 GLN cc_start: 0.8428 (mm-40) cc_final: 0.7730 (tm-30) REVERT: H 630 ASP cc_start: 0.8705 (t0) cc_final: 0.8408 (t0) outliers start: 58 outliers final: 24 residues processed: 223 average time/residue: 0.1820 time to fit residues: 63.8762 Evaluate side-chains 184 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 692 VAL Chi-restraints excluded: chain C residue 764 ILE Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 943 VAL Chi-restraints excluded: chain C residue 1088 VAL Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 799 ILE Chi-restraints excluded: chain D residue 1131 VAL Chi-restraints excluded: chain D residue 1241 CYS Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain H residue 231 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 73 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 337 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 125 optimal weight: 9.9990 chunk 135 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 278 optimal weight: 5.9990 chunk 257 optimal weight: 7.9990 chunk 194 optimal weight: 7.9990 chunk 299 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.067069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.051537 restraints weight = 87306.431| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.93 r_work: 0.2864 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 28276 Z= 0.230 Angle : 0.620 11.130 38335 Z= 0.317 Chirality : 0.045 0.215 4356 Planarity : 0.005 0.059 5073 Dihedral : 4.574 24.760 3932 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 1.95 % Allowed : 11.96 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.14), residues: 3563 helix: 0.38 (0.15), residues: 1335 sheet: -0.55 (0.25), residues: 444 loop : -1.54 (0.14), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 223 TYR 0.018 0.002 TYR D 134 PHE 0.019 0.002 PHE D1187 TRP 0.016 0.002 TRP D 58 HIS 0.006 0.001 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.00541 (28268) covalent geometry : angle 0.61261 (38323) hydrogen bonds : bond 0.04277 ( 1079) hydrogen bonds : angle 4.52188 ( 3033) metal coordination : bond 0.01141 ( 8) metal coordination : angle 5.36627 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 157 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8458 (pp) REVERT: C 420 GLU cc_start: 0.8904 (tt0) cc_final: 0.8617 (mt-10) REVERT: C 717 TRP cc_start: 0.9290 (OUTLIER) cc_final: 0.8678 (t60) REVERT: C 992 MET cc_start: 0.8591 (mmp) cc_final: 0.8146 (mmp) REVERT: D 74 ILE cc_start: 0.8164 (mm) cc_final: 0.7473 (tp) REVERT: D 90 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7922 (pm20) REVERT: D 406 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.8682 (pp) REVERT: D 1011 MET cc_start: 0.9203 (OUTLIER) cc_final: 0.8619 (mtt) REVERT: H 380 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8406 (tm-30) REVERT: H 386 GLN cc_start: 0.8434 (mm-40) cc_final: 0.7757 (tm-30) REVERT: H 630 ASP cc_start: 0.8745 (t0) cc_final: 0.8386 (t0) outliers start: 58 outliers final: 27 residues processed: 204 average time/residue: 0.1810 time to fit residues: 59.0609 Evaluate side-chains 184 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 151 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 692 VAL Chi-restraints excluded: chain C residue 715 MET Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 764 ILE Chi-restraints excluded: chain C residue 943 VAL Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 799 ILE Chi-restraints excluded: chain D residue 961 VAL Chi-restraints excluded: chain D residue 1011 MET Chi-restraints excluded: chain D residue 1131 VAL Chi-restraints excluded: chain D residue 1241 CYS Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 273 THR Chi-restraints excluded: chain H residue 380 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 138 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 340 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 chunk 139 optimal weight: 3.9990 chunk 287 optimal weight: 0.7980 chunk 250 optimal weight: 6.9990 chunk 329 optimal weight: 3.9990 chunk 201 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 603 GLN ** C 882 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.068048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.052662 restraints weight = 86437.607| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.86 r_work: 0.2898 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28276 Z= 0.141 Angle : 0.562 10.777 38335 Z= 0.285 Chirality : 0.043 0.197 4356 Planarity : 0.004 0.059 5073 Dihedral : 4.351 24.469 3932 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 1.65 % Allowed : 13.27 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.69 (0.14), residues: 3563 helix: 0.68 (0.15), residues: 1337 sheet: -0.39 (0.26), residues: 416 loop : -1.36 (0.15), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 549 TYR 0.029 0.001 TYR D 134 PHE 0.012 0.001 PHE D1187 TRP 0.014 0.001 TRP D 58 HIS 0.003 0.001 HIS C 911 Details of bonding type rmsd covalent geometry : bond 0.00331 (28268) covalent geometry : angle 0.55522 (38323) hydrogen bonds : bond 0.03740 ( 1079) hydrogen bonds : angle 4.31669 ( 3033) metal coordination : bond 0.01060 ( 8) metal coordination : angle 5.04145 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 161 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8403 (pp) REVERT: C 420 GLU cc_start: 0.8810 (tt0) cc_final: 0.8536 (mt-10) REVERT: C 717 TRP cc_start: 0.9316 (OUTLIER) cc_final: 0.8785 (t60) REVERT: C 992 MET cc_start: 0.8533 (mmp) cc_final: 0.8098 (mmp) REVERT: D 74 ILE cc_start: 0.8120 (mm) cc_final: 0.7457 (tp) REVERT: D 90 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7945 (pm20) REVERT: D 256 MET cc_start: 0.5756 (ttt) cc_final: 0.4824 (ttt) REVERT: D 406 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8694 (pp) REVERT: D 1011 MET cc_start: 0.9190 (OUTLIER) cc_final: 0.8624 (mtt) REVERT: H 380 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8338 (tm-30) REVERT: H 386 GLN cc_start: 0.8435 (mm-40) cc_final: 0.7740 (tm-30) REVERT: H 630 ASP cc_start: 0.8717 (t0) cc_final: 0.8362 (t0) outliers start: 49 outliers final: 26 residues processed: 204 average time/residue: 0.1793 time to fit residues: 58.6614 Evaluate side-chains 184 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 692 VAL Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 943 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 799 ILE Chi-restraints excluded: chain D residue 956 ILE Chi-restraints excluded: chain D residue 961 VAL Chi-restraints excluded: chain D residue 1011 MET Chi-restraints excluded: chain D residue 1131 VAL Chi-restraints excluded: chain D residue 1241 CYS Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 273 THR Chi-restraints excluded: chain H residue 380 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 113 optimal weight: 0.8980 chunk 156 optimal weight: 0.2980 chunk 299 optimal weight: 1.9990 chunk 258 optimal weight: 0.0770 chunk 152 optimal weight: 0.8980 chunk 311 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 163 optimal weight: 0.6980 chunk 111 optimal weight: 10.0000 chunk 147 optimal weight: 4.9990 chunk 238 optimal weight: 2.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 882 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 HIS ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.069692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.054199 restraints weight = 86029.092| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.92 r_work: 0.2939 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 28276 Z= 0.099 Angle : 0.530 14.308 38335 Z= 0.267 Chirality : 0.042 0.247 4356 Planarity : 0.004 0.060 5073 Dihedral : 4.072 23.788 3932 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.31 % Allowed : 14.14 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.40 (0.14), residues: 3563 helix: 0.96 (0.15), residues: 1339 sheet: -0.25 (0.26), residues: 418 loop : -1.23 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 84 TYR 0.018 0.001 TYR D 134 PHE 0.009 0.001 PHE B 219 TRP 0.032 0.001 TRP D 58 HIS 0.003 0.001 HIS H 42 Details of bonding type rmsd covalent geometry : bond 0.00221 (28268) covalent geometry : angle 0.52159 (38323) hydrogen bonds : bond 0.03278 ( 1079) hydrogen bonds : angle 4.12293 ( 3033) metal coordination : bond 0.01037 ( 8) metal coordination : angle 5.38655 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 171 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8254 (pp) REVERT: C 420 GLU cc_start: 0.8731 (tt0) cc_final: 0.8476 (mt-10) REVERT: D 74 ILE cc_start: 0.8203 (mm) cc_final: 0.7594 (tp) REVERT: D 90 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7981 (pm20) REVERT: D 256 MET cc_start: 0.5421 (ttt) cc_final: 0.5053 (ttt) REVERT: D 406 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8653 (pp) REVERT: D 1011 MET cc_start: 0.9168 (OUTLIER) cc_final: 0.8594 (mtt) REVERT: H 313 MET cc_start: 0.3763 (ppp) cc_final: 0.3408 (ppp) REVERT: H 380 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8294 (tm-30) REVERT: H 386 GLN cc_start: 0.8388 (mm-40) cc_final: 0.7834 (tm-30) REVERT: H 631 ASP cc_start: 0.8232 (m-30) cc_final: 0.7832 (m-30) outliers start: 39 outliers final: 24 residues processed: 206 average time/residue: 0.1699 time to fit residues: 56.5791 Evaluate side-chains 187 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 692 VAL Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 961 VAL Chi-restraints excluded: chain D residue 1011 MET Chi-restraints excluded: chain D residue 1241 CYS Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 273 THR Chi-restraints excluded: chain H residue 380 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 282 optimal weight: 5.9990 chunk 245 optimal weight: 20.0000 chunk 170 optimal weight: 10.0000 chunk 348 optimal weight: 1.9990 chunk 351 optimal weight: 6.9990 chunk 220 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 165 optimal weight: 10.0000 chunk 144 optimal weight: 0.9990 chunk 314 optimal weight: 7.9990 chunk 172 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN ** C 882 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.067488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.052029 restraints weight = 87424.283| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.92 r_work: 0.2880 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 28276 Z= 0.186 Angle : 0.579 13.895 38335 Z= 0.294 Chirality : 0.044 0.264 4356 Planarity : 0.004 0.062 5073 Dihedral : 4.216 23.831 3932 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 1.58 % Allowed : 14.38 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.40 (0.14), residues: 3563 helix: 0.90 (0.15), residues: 1341 sheet: -0.29 (0.25), residues: 431 loop : -1.17 (0.15), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 67 TYR 0.015 0.001 TYR D 251 PHE 0.015 0.002 PHE D1187 TRP 0.022 0.001 TRP D 58 HIS 0.004 0.001 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.00440 (28268) covalent geometry : angle 0.57094 (38323) hydrogen bonds : bond 0.03876 ( 1079) hydrogen bonds : angle 4.27016 ( 3033) metal coordination : bond 0.01087 ( 8) metal coordination : angle 5.45860 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 164 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8410 (pp) REVERT: C 420 GLU cc_start: 0.8828 (tt0) cc_final: 0.8560 (mt-10) REVERT: C 992 MET cc_start: 0.8611 (mmp) cc_final: 0.8122 (mmp) REVERT: D 74 ILE cc_start: 0.8178 (mm) cc_final: 0.7620 (tp) REVERT: D 90 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7988 (pm20) REVERT: D 97 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6817 (pp) REVERT: D 406 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8749 (pp) REVERT: D 1011 MET cc_start: 0.9194 (OUTLIER) cc_final: 0.8529 (mtt) REVERT: H 380 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8314 (tm-30) REVERT: H 386 GLN cc_start: 0.8412 (mm-40) cc_final: 0.7650 (tm-30) outliers start: 47 outliers final: 30 residues processed: 205 average time/residue: 0.1789 time to fit residues: 58.5354 Evaluate side-chains 194 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 692 VAL Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 943 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 799 ILE Chi-restraints excluded: chain D residue 961 VAL Chi-restraints excluded: chain D residue 1011 MET Chi-restraints excluded: chain D residue 1241 CYS Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 273 THR Chi-restraints excluded: chain H residue 380 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 284 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 287 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 318 optimal weight: 10.0000 chunk 142 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 882 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.067690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.052121 restraints weight = 87867.163| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.93 r_work: 0.2884 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 28276 Z= 0.160 Angle : 0.565 13.283 38335 Z= 0.287 Chirality : 0.043 0.275 4356 Planarity : 0.004 0.064 5073 Dihedral : 4.205 23.705 3932 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 1.55 % Allowed : 14.61 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.34 (0.14), residues: 3563 helix: 0.92 (0.15), residues: 1344 sheet: -0.15 (0.26), residues: 417 loop : -1.14 (0.15), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 412 TYR 0.019 0.001 TYR D 134 PHE 0.013 0.001 PHE D1187 TRP 0.021 0.001 TRP D 58 HIS 0.004 0.001 HIS C 911 Details of bonding type rmsd covalent geometry : bond 0.00378 (28268) covalent geometry : angle 0.55763 (38323) hydrogen bonds : bond 0.03710 ( 1079) hydrogen bonds : angle 4.25337 ( 3033) metal coordination : bond 0.01059 ( 8) metal coordination : angle 5.20147 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 162 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 420 GLU cc_start: 0.8823 (tt0) cc_final: 0.8543 (mt-10) REVERT: C 992 MET cc_start: 0.8592 (mmp) cc_final: 0.8116 (mmp) REVERT: D 74 ILE cc_start: 0.8183 (mm) cc_final: 0.7648 (tp) REVERT: D 90 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7965 (pm20) REVERT: D 97 LEU cc_start: 0.7088 (OUTLIER) cc_final: 0.6868 (pp) REVERT: D 145 HIS cc_start: 0.8819 (t70) cc_final: 0.8275 (m170) REVERT: D 327 MET cc_start: 0.6372 (mtp) cc_final: 0.6140 (mtt) REVERT: D 406 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8740 (pp) REVERT: D 1011 MET cc_start: 0.9178 (OUTLIER) cc_final: 0.8588 (mtt) REVERT: H 313 MET cc_start: 0.4114 (ppp) cc_final: 0.3738 (ppp) REVERT: H 374 ARG cc_start: 0.8552 (ptp-170) cc_final: 0.8335 (ptp-170) REVERT: H 380 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8325 (tm-30) REVERT: H 386 GLN cc_start: 0.8414 (mm-40) cc_final: 0.7833 (tm-30) outliers start: 46 outliers final: 34 residues processed: 201 average time/residue: 0.1697 time to fit residues: 55.0426 Evaluate side-chains 197 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 158 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 943 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 799 ILE Chi-restraints excluded: chain D residue 961 VAL Chi-restraints excluded: chain D residue 1011 MET Chi-restraints excluded: chain D residue 1131 VAL Chi-restraints excluded: chain D residue 1241 CYS Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 273 THR Chi-restraints excluded: chain H residue 380 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 247 optimal weight: 6.9990 chunk 233 optimal weight: 7.9990 chunk 136 optimal weight: 0.0870 chunk 210 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 281 optimal weight: 6.9990 chunk 270 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 278 optimal weight: 4.9990 chunk 229 optimal weight: 5.9990 chunk 295 optimal weight: 0.3980 overall best weight: 1.6562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 HIS ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 882 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.068090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.052576 restraints weight = 87014.489| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.91 r_work: 0.2898 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28276 Z= 0.135 Angle : 0.552 13.180 38335 Z= 0.279 Chirality : 0.043 0.266 4356 Planarity : 0.004 0.066 5073 Dihedral : 4.137 23.601 3932 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 1.48 % Allowed : 14.61 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.24 (0.14), residues: 3563 helix: 1.01 (0.15), residues: 1342 sheet: -0.10 (0.26), residues: 417 loop : -1.09 (0.15), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 412 TYR 0.016 0.001 TYR D 134 PHE 0.010 0.001 PHE B 219 TRP 0.018 0.001 TRP D 58 HIS 0.005 0.001 HIS B 61 Details of bonding type rmsd covalent geometry : bond 0.00318 (28268) covalent geometry : angle 0.54419 (38323) hydrogen bonds : bond 0.03568 ( 1079) hydrogen bonds : angle 4.20264 ( 3033) metal coordination : bond 0.01064 ( 8) metal coordination : angle 5.17329 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 162 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 420 GLU cc_start: 0.8795 (tt0) cc_final: 0.8500 (mt-10) REVERT: C 992 MET cc_start: 0.8584 (mmp) cc_final: 0.8087 (mmp) REVERT: D 74 ILE cc_start: 0.8150 (mm) cc_final: 0.7634 (tp) REVERT: D 90 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7967 (pm20) REVERT: D 97 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6863 (pp) REVERT: D 145 HIS cc_start: 0.8805 (t70) cc_final: 0.8277 (m170) REVERT: D 282 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.8594 (ttp-170) REVERT: D 327 MET cc_start: 0.6403 (mtp) cc_final: 0.6177 (mtt) REVERT: D 389 ARG cc_start: 0.7738 (mmp80) cc_final: 0.7500 (mmp80) REVERT: D 406 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8728 (pp) REVERT: D 1011 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8582 (mtt) REVERT: H 313 MET cc_start: 0.3991 (ppp) cc_final: 0.3620 (ppp) REVERT: H 374 ARG cc_start: 0.8574 (ptp-170) cc_final: 0.8340 (ptp-170) REVERT: H 380 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8305 (tm-30) REVERT: H 386 GLN cc_start: 0.8380 (mm-40) cc_final: 0.7842 (tm-30) outliers start: 44 outliers final: 35 residues processed: 199 average time/residue: 0.1746 time to fit residues: 55.8145 Evaluate side-chains 200 residues out of total 2980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 159 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 943 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 282 ARG Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 799 ILE Chi-restraints excluded: chain D residue 961 VAL Chi-restraints excluded: chain D residue 1011 MET Chi-restraints excluded: chain D residue 1131 VAL Chi-restraints excluded: chain D residue 1241 CYS Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 273 THR Chi-restraints excluded: chain H residue 380 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 248 optimal weight: 9.9990 chunk 121 optimal weight: 10.0000 chunk 171 optimal weight: 0.0570 chunk 221 optimal weight: 7.9990 chunk 237 optimal weight: 0.9980 chunk 224 optimal weight: 5.9990 chunk 129 optimal weight: 0.6980 chunk 309 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 chunk 271 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 overall best weight: 1.5502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 HIS C 314 ASN ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 882 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.068212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.052733 restraints weight = 86833.006| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.91 r_work: 0.2903 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28276 Z= 0.130 Angle : 0.548 13.078 38335 Z= 0.278 Chirality : 0.043 0.251 4356 Planarity : 0.004 0.066 5073 Dihedral : 4.090 23.420 3932 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.55 % Allowed : 14.75 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.19 (0.15), residues: 3563 helix: 1.05 (0.15), residues: 1352 sheet: -0.05 (0.26), residues: 417 loop : -1.07 (0.15), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 412 TYR 0.018 0.001 TYR D 134 PHE 0.014 0.001 PHE D 672 TRP 0.017 0.001 TRP D 58 HIS 0.005 0.001 HIS B 61 Details of bonding type rmsd covalent geometry : bond 0.00306 (28268) covalent geometry : angle 0.54056 (38323) hydrogen bonds : bond 0.03504 ( 1079) hydrogen bonds : angle 4.17147 ( 3033) metal coordination : bond 0.01059 ( 8) metal coordination : angle 5.17424 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5467.85 seconds wall clock time: 94 minutes 35.17 seconds (5675.17 seconds total)