Starting phenix.real_space_refine on Fri Mar 6 03:35:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6yys_11004/03_2026/6yys_11004.cif Found real_map, /net/cci-nas-00/data/ceres_data/6yys_11004/03_2026/6yys_11004.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6yys_11004/03_2026/6yys_11004.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6yys_11004/03_2026/6yys_11004.map" model { file = "/net/cci-nas-00/data/ceres_data/6yys_11004/03_2026/6yys_11004.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6yys_11004/03_2026/6yys_11004.cif" } 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= 0.025 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 98 5.16 5 C 17482 2.51 5 N 4963 2.21 5 O 5384 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 133 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: 27930 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1700 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 209} 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: 8433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1089, 8433 Classifications: {'peptide': 1089} Link IDs: {'PCIS': 1, 'PTRANS': 57, 'TRANS': 1030} Chain breaks: 1 Chain: "D" Number of atoms: 9983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1278, 9983 Classifications: {'peptide': 1278} Link IDs: {'PCIS': 2, 'PTRANS': 55, 'TRANS': 1220} Chain: "E" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 646 Classifications: {'peptide': 83} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 76} Chain: "H" Number of atoms: 5394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5394 Classifications: {'peptide': 690} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 35, 'TRANS': 654} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 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 18936 SG CYS D 890 32.412 58.908 85.500 1.00 20.18 S ATOM 19498 SG CYS D 967 35.112 61.401 86.427 1.00 17.64 S ATOM 19540 SG CYS D 974 33.241 59.760 89.058 1.00 16.19 S ATOM 19559 SG CYS D 977 35.392 57.643 87.140 1.00 15.04 S ATOM 12363 SG CYS D 60 35.972 123.749 100.192 1.00 71.56 S ATOM 12381 SG CYS D 62 36.317 128.117 100.110 1.00 72.47 S ATOM 12490 SG CYS D 75 32.830 125.496 98.665 1.00 69.70 S ATOM 12516 SG CYS D 78 36.162 125.705 96.570 1.00 72.83 S Time building chain proxies: 6.52, per 1000 atoms: 0.23 Number of scatterers: 27930 At special positions: 0 Unit cell: (130.483, 142.118, 181.18, 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 98 16.00 Mg 1 11.99 O 5384 8.00 N 4963 7.00 C 17482 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: 2.68 Conformation dependent library (CDL) restraints added in 1.4 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 78 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 62 " Number of angles added : 12 7162 Ramachandran restraints generated. 3581 Oldfield, 0 Emsley, 3581 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6628 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 43 sheets defined 38.8% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 31 through 46 removed outlier: 3.999A pdb=" N ILE A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 106 through 110 removed outlier: 3.595A pdb=" N ILE A 110 " --> pdb=" O ALA A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 156 removed outlier: 3.805A pdb=" N SER A 155 " --> pdb=" O GLN A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 220 Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'B' and resid 34 through 45 Processing helix chain 'B' and resid 72 through 81 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 49 through 57 Processing helix chain 'C' and resid 58 through 68 Processing helix chain 'C' and resid 76 through 85 Processing helix chain 'C' and resid 109 through 117 Processing helix chain 'C' and resid 217 through 220 Processing helix chain 'C' and resid 225 through 232 Processing helix chain 'C' and resid 235 through 243 Processing helix chain 'C' and resid 247 through 254 Processing helix chain 'C' and resid 260 through 273 Processing helix chain 'C' and resid 279 through 289 Processing helix chain 'C' and resid 300 through 312 Processing helix chain 'C' and resid 327 through 341 removed outlier: 3.994A pdb=" N ILE C 333 " --> pdb=" O VAL C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 396 removed outlier: 3.503A pdb=" N THR C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 Processing helix chain 'C' and resid 411 through 422 removed outlier: 3.541A pdb=" N VAL C 415 " --> pdb=" O ILE C 411 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA C 416 " --> pdb=" O ARG C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 441 Processing helix chain 'C' and resid 467 through 471 removed outlier: 3.818A pdb=" N TYR C 471 " --> pdb=" O PRO C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 528 Processing helix chain 'C' and resid 579 through 583 Processing helix chain 'C' and resid 587 through 591 Processing helix chain 'C' and resid 592 through 605 removed outlier: 3.969A pdb=" N GLN C 605 " --> pdb=" O ASN C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 628 Processing helix chain 'C' and resid 730 through 735 Processing helix chain 'C' and resid 768 through 773 removed outlier: 3.792A pdb=" N ALA C 773 " --> pdb=" O GLU C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 891 through 895 Processing helix chain 'C' and resid 919 through 933 Processing helix chain 'C' and resid 944 through 948 Processing helix chain 'C' and resid 973 through 978 removed outlier: 3.563A pdb=" N GLY C 978 " --> pdb=" O GLY C 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 983 removed outlier: 3.829A pdb=" N SER C 982 " --> pdb=" O GLY C 978 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR C 983 " --> pdb=" O LEU C 979 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 978 through 983' Processing helix chain 'C' and resid 1027 through 1031 Processing helix chain 'C' and resid 1060 through 1070 removed outlier: 3.663A pdb=" N TYR C1070 " --> pdb=" O ALA C1066 " (cutoff:3.500A) Processing helix chain 'C' and resid 1073 through 1082 Processing helix chain 'C' and resid 1089 through 1100 Processing helix chain 'C' and resid 1112 through 1121 Processing helix chain 'D' and resid 16 through 24 removed outlier: 3.765A pdb=" N ILE D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 40 removed outlier: 4.429A pdb=" N LYS D 40 " --> pdb=" O ARG D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'D' and resid 112 through 118 removed outlier: 3.666A pdb=" N TYR D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 130 removed outlier: 3.811A pdb=" N TYR D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 146 Processing helix chain 'D' and resid 149 through 187 removed outlier: 3.954A pdb=" N GLU D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 228 removed outlier: 4.165A pdb=" N ARG D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 247 Processing helix chain 'D' and resid 257 through 267 removed outlier: 3.595A pdb=" N ILE D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 284 Processing helix chain 'D' and resid 288 through 301 removed outlier: 4.425A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 313 Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 340 through 361 removed outlier: 4.792A pdb=" N ASP D 359 " --> pdb=" O LYS D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 382 removed outlier: 4.009A pdb=" N SER D 377 " --> pdb=" O MET D 373 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL D 378 " --> pdb=" O LEU D 374 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA D 380 " --> pdb=" O GLU D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 405 Processing helix chain 'D' and resid 447 through 452 removed outlier: 4.092A pdb=" N LEU D 451 " --> pdb=" O MET D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 469 through 479 Processing helix chain 'D' and resid 485 through 490 removed outlier: 3.939A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL D 490 " --> pdb=" O VAL D 486 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 485 through 490' 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 548 through 558 Processing helix chain 'D' and resid 578 through 589 Processing helix chain 'D' and resid 601 through 605 removed outlier: 4.060A pdb=" N LYS D 604 " --> pdb=" O ALA D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 624 removed outlier: 3.545A pdb=" N ALA D 618 " --> pdb=" O SER D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 643 through 651 removed outlier: 4.202A pdb=" N GLN D 649 " --> pdb=" O ASP D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 674 removed outlier: 3.525A pdb=" N VAL D 670 " --> pdb=" O THR D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 703 Processing helix chain 'D' and resid 704 through 725 removed outlier: 3.892A pdb=" N VAL D 708 " --> pdb=" O PRO D 704 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR D 724 " --> pdb=" O PHE D 720 " (cutoff:3.500A) Processing helix chain 'D' and resid 740 through 762 removed outlier: 3.963A pdb=" N GLU D 751 " --> pdb=" O ARG D 747 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU D 756 " --> pdb=" O ALA D 752 " (cutoff:3.500A) Processing helix chain 'D' and resid 765 through 777 Processing helix chain 'D' and resid 780 through 792 Processing helix chain 'D' and resid 796 through 804 removed outlier: 4.142A pdb=" N VAL D 802 " --> pdb=" O ILE D 798 " (cutoff:3.500A) Processing helix chain 'D' and resid 809 through 818 removed outlier: 3.582A pdb=" N THR D 813 " --> pdb=" O ASN D 809 " (cutoff:3.500A) Processing helix chain 'D' and resid 844 through 857 removed outlier: 3.619A pdb=" N HIS D 853 " --> pdb=" O PHE D 849 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLY D 854 " --> pdb=" O ILE D 850 " (cutoff:3.500A) Processing helix chain 'D' and resid 857 through 880 removed outlier: 4.241A pdb=" N ASP D 861 " --> pdb=" O LYS D 857 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR D 862 " --> pdb=" O GLY D 858 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA D 863 " --> pdb=" O LEU D 859 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N THR D 866 " --> pdb=" O THR D 862 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 919 Processing helix chain 'D' and resid 944 through 954 Processing helix chain 'D' and resid 975 through 979 Processing helix chain 'D' and resid 994 through 1004 removed outlier: 3.550A pdb=" N ALA D 998 " --> pdb=" O VAL D 994 " (cutoff:3.500A) Processing helix chain 'D' and resid 1005 through 1009 removed outlier: 3.692A pdb=" N LEU D1009 " --> pdb=" O GLY D1006 " (cutoff:3.500A) Processing helix chain 'D' and resid 1020 through 1024 removed outlier: 3.533A pdb=" N ASP D1024 " --> pdb=" O GLY D1021 " (cutoff:3.500A) Processing helix chain 'D' and resid 1028 through 1038 Processing helix chain 'D' and resid 1118 through 1126 Processing helix chain 'D' and resid 1129 through 1146 removed outlier: 3.726A pdb=" N ILE D1133 " --> pdb=" O ARG D1129 " (cutoff:3.500A) Processing helix chain 'D' and resid 1151 through 1161 removed outlier: 4.301A pdb=" N ILE D1155 " --> pdb=" O HIS D1151 " (cutoff:3.500A) Processing helix chain 'D' and resid 1184 through 1193 Processing helix chain 'D' and resid 1210 through 1217 removed outlier: 3.510A pdb=" N LEU D1216 " --> pdb=" O THR D1212 " (cutoff:3.500A) Processing helix chain 'D' and resid 1221 through 1227 removed outlier: 3.870A pdb=" N ALA D1225 " --> pdb=" O TRP D1221 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE D1227 " --> pdb=" O SER D1223 " (cutoff:3.500A) Processing helix chain 'D' and resid 1229 through 1241 Processing helix chain 'D' and resid 1251 through 1256 Processing helix chain 'D' and resid 1265 through 1270 Processing helix chain 'D' and resid 1276 through 1281 Processing helix chain 'E' and resid 30 through 34 Processing helix chain 'E' and resid 39 through 43 removed outlier: 3.585A pdb=" N SER E 42 " --> pdb=" O GLU E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 67 removed outlier: 4.197A pdb=" N ARG E 57 " --> pdb=" O TYR E 53 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN E 67 " --> pdb=" O ASP E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 98 Processing helix chain 'H' and resid 3 through 41 Processing helix chain 'H' and resid 45 through 67 Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.659A pdb=" N ARG H 110 " --> pdb=" O PRO H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 175 through 188 removed outlier: 3.615A pdb=" N ILE H 179 " --> pdb=" O ILE H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 220 Processing helix chain 'H' and resid 235 through 239 removed outlier: 3.797A pdb=" N PHE H 238 " --> pdb=" O THR H 235 " (cutoff:3.500A) Processing helix chain 'H' and resid 241 through 246 Processing helix chain 'H' and resid 246 through 251 Processing helix chain 'H' and resid 275 through 281 removed outlier: 3.990A pdb=" N VAL H 279 " --> pdb=" O GLU H 275 " (cutoff:3.500A) Processing helix chain 'H' and resid 283 through 295 removed outlier: 4.241A pdb=" N ASP H 287 " --> pdb=" O LEU H 283 " (cutoff:3.500A) removed outlier: 4.240A 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 333 through 355 removed outlier: 4.898A pdb=" N ALA H 339 " --> pdb=" O ASN H 335 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLU H 340 " --> pdb=" O GLU H 336 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU H 351 " --> pdb=" O TYR H 347 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ARG H 352 " --> pdb=" O VAL H 348 " (cutoff:3.500A) Processing helix chain 'H' and resid 372 through 377 Processing helix chain 'H' and resid 384 through 392 Processing helix chain 'H' and resid 401 through 409 removed outlier: 3.772A pdb=" N LEU H 407 " --> pdb=" O VAL H 403 " (cutoff:3.500A) Processing helix chain 'H' and resid 411 through 417 removed outlier: 4.342A pdb=" N ARG H 415 " --> pdb=" O HIS H 411 " (cutoff:3.500A) Processing helix chain 'H' and resid 435 through 447 removed outlier: 3.766A pdb=" N VAL H 443 " --> pdb=" O LEU H 439 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP H 444 " --> pdb=" O ASP H 440 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY H 447 " --> pdb=" O VAL H 443 " (cutoff:3.500A) Processing helix chain 'H' and resid 454 through 474 removed outlier: 3.729A pdb=" N ARG H 458 " --> pdb=" O GLU H 454 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET H 474 " --> pdb=" O VAL H 470 " (cutoff:3.500A) Processing helix chain 'H' and resid 494 through 500 Processing helix chain 'H' and resid 509 through 516 removed outlier: 3.517A pdb=" N ALA H 516 " --> pdb=" O GLU H 512 " (cutoff:3.500A) Processing helix chain 'H' and resid 529 through 533 removed outlier: 3.643A pdb=" N GLU H 532 " --> pdb=" O GLU H 529 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU H 533 " --> pdb=" O ALA H 530 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 529 through 533' Processing helix chain 'H' and resid 534 through 545 Processing helix chain 'H' and resid 567 through 573 removed outlier: 3.813A pdb=" N MET H 571 " --> pdb=" O SER H 567 " (cutoff:3.500A) Processing helix chain 'H' and resid 592 through 603 Processing helix chain 'H' and resid 632 through 645 removed outlier: 3.946A pdb=" N ALA H 645 " --> pdb=" O VAL H 641 " (cutoff:3.500A) Processing helix chain 'H' and resid 680 through 688 removed outlier: 4.299A pdb=" N GLY H 688 " --> pdb=" O ILE H 684 " (cutoff:3.500A) Processing helix chain 'H' and resid 690 through 700 removed outlier: 3.563A pdb=" N GLU H 694 " --> pdb=" O ARG H 690 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA H 698 " --> pdb=" O GLU H 694 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR H 700 " --> pdb=" O TYR H 696 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 removed outlier: 6.203A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 94 Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 94 removed outlier: 7.725A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 85 through 87 Processing sheet with id=AA5, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 12 removed outlier: 6.784A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 98 removed outlier: 7.761A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 86 removed outlier: 3.728A pdb=" N THR B 117 " --> pdb=" O SER B 86 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 104 through 106 removed outlier: 3.504A pdb=" N ALA B 126 " --> pdb=" O VAL B 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB2, first strand: chain 'C' and resid 30 through 31 removed outlier: 6.554A pdb=" N VAL C 30 " --> pdb=" O ALA C 964 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 87 through 88 removed outlier: 6.595A pdb=" N PHE C 125 " --> pdb=" O PRO C 101 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE C 103 " --> pdb=" O PRO C 123 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU C 137 " --> pdb=" O ASN C 132 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 87 through 88 removed outlier: 6.595A pdb=" N PHE C 125 " --> pdb=" O PRO C 101 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE C 103 " --> pdb=" O PRO C 123 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ALA C 122 " --> pdb=" O ASP C 147 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASP C 147 " --> pdb=" O ALA C 122 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU C 124 " --> pdb=" O MET C 145 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 157 through 159 Processing sheet with id=AB6, first strand: chain 'C' and resid 367 through 370 removed outlier: 3.822A pdb=" N SER C 168 " --> pdb=" O ARG C 445 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 175 through 177 Processing sheet with id=AB8, first strand: chain 'C' and resid 175 through 177 removed outlier: 4.090A pdb=" N HIS C 191 " --> pdb=" O VAL C 207 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL C 207 " --> pdb=" O HIS C 191 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 345 through 347 Processing sheet with id=AC1, first strand: chain 'C' and resid 496 through 497 removed outlier: 5.364A pdb=" N GLN C 518 " --> pdb=" O LYS C 509 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 496 through 497 Processing sheet with id=AC3, first strand: chain 'C' and resid 549 through 552 Processing sheet with id=AC4, first strand: chain 'C' and resid 633 through 634 removed outlier: 6.466A pdb=" N VAL C 633 " --> pdb=" O ILE C 693 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 639 through 644 removed outlier: 5.335A pdb=" N ILE C 641 " --> pdb=" O MET C 652 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N MET C 652 " --> pdb=" O ILE C 641 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 998 through 999 removed outlier: 6.812A pdb=" N ILE C 726 " --> pdb=" O LYS C 888 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N LEU C 890 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU C 728 " --> pdb=" O LEU C 890 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N THR C1015 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 740 through 751 removed outlier: 3.692A pdb=" N GLU C 858 " --> pdb=" O ALA C 750 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ASN C 857 " --> pdb=" O SER C 845 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N SER C 845 " --> pdb=" O ASN C 857 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU C 859 " --> pdb=" O VAL C 843 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N VAL C 843 " --> pdb=" O LEU C 859 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARG C 861 " --> pdb=" O ILE C 841 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ILE C 841 " --> pdb=" O ARG C 861 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N TYR C 863 " --> pdb=" O ILE C 839 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LYS C 867 " --> pdb=" O SER C 835 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N SER C 835 " --> pdb=" O LYS C 867 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY C 836 " --> pdb=" O VAL C 787 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 759 through 760 Processing sheet with id=AC9, first strand: chain 'C' and resid 792 through 794 removed outlier: 6.965A pdb=" N LEU C 828 " --> pdb=" O LEU C 793 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 935 through 936 Processing sheet with id=AD2, first strand: chain 'C' and resid 1033 through 1035 removed outlier: 8.182A pdb=" N ALA D 521 " --> pdb=" O PRO D 444 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1124 through 1128 removed outlier: 3.510A pdb=" N GLU C1127 " --> pdb=" O ARG D 11 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ARG D 11 " --> pdb=" O GLU C1127 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 94 through 95 Processing sheet with id=AD5, first strand: chain 'D' and resid 234 through 235 removed outlier: 3.559A pdb=" N TYR D 134 " --> pdb=" O ILE D 235 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AD7, first strand: chain 'D' and resid 885 through 887 Processing sheet with id=AD8, first strand: chain 'D' and resid 896 through 898 Processing sheet with id=AD9, first strand: chain 'D' and resid 902 through 903 Processing sheet with id=AE1, first strand: chain 'D' and resid 928 through 929 removed outlier: 3.647A pdb=" N ILE D 937 " --> pdb=" O ALA D 928 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1076 through 1082 removed outlier: 4.523A pdb=" N LYS D1080 " --> pdb=" O PHE D1063 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N PHE D1063 " --> pdb=" O LYS D1080 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1181 through 1183 removed outlier: 4.736A pdb=" N ARG D1165 " --> pdb=" O VAL D1207 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE D1169 " --> pdb=" O ALA D1203 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ALA D1203 " --> pdb=" O ILE D1169 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1272 through 1275 Processing sheet with id=AE5, first strand: chain 'H' and resid 98 through 103 removed outlier: 16.519A pdb=" N GLU H 98 " --> pdb=" O GLY H 86 " (cutoff:3.500A) removed outlier: 13.025A pdb=" N LEU H 88 " --> pdb=" O GLU H 98 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEU H 100 " --> pdb=" O LEU H 88 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE H 90 " --> pdb=" O LEU H 100 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LEU H 102 " --> pdb=" O ILE H 90 " (cutoff:3.500A) removed outlier: 11.901A pdb=" N ASP H 92 " --> pdb=" O LEU H 102 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU H 83 " --> pdb=" O ARG H 74 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ARG H 74 " --> pdb=" O LEU H 83 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE H 85 " --> pdb=" O PHE H 72 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N PHE H 72 " --> pdb=" O PHE H 129 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ARG H 74 " --> pdb=" O ARG H 127 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ARG H 126 " --> pdb=" O ASP H 141 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ASP H 141 " --> pdb=" O ARG H 126 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLN H 128 " --> pdb=" O PHE H 139 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N PHE H 139 " --> pdb=" O GLN H 128 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N HIS H 130 " --> pdb=" O VAL H 137 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 256 through 257 removed outlier: 7.702A pdb=" N MET H 257 " --> pdb=" O VAL H 229 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N VAL H 231 " --> pdb=" O MET H 257 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU H 230 " --> pdb=" O VAL H 526 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'H' and resid 624 through 627 removed outlier: 3.916A pdb=" N TRP H 624 " --> pdb=" O LEU H 706 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL H 708 " --> pdb=" O TRP H 624 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ASP H 674 " --> pdb=" O ARG H 705 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N GLY H 707 " --> pdb=" O ASP H 674 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL H 676 " --> pdb=" O GLY H 707 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N LEU H 709 " --> pdb=" O VAL H 676 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL H 678 " --> pdb=" O LEU H 709 " (cutoff:3.500A) 1098 hydrogen bonds defined for protein. 3060 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: 6.24 Time building geometry restraints manager: 3.50 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: 9690 1.34 - 1.47: 5827 1.47 - 1.59: 12718 1.59 - 1.71: 0 1.71 - 1.83: 174 Bond restraints: 28409 Sorted by residual: bond pdb=" N MET H 1 " pdb=" CA MET H 1 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.38e+00 bond pdb=" N THR C 479 " pdb=" CA THR C 479 " ideal model delta sigma weight residual 1.457 1.433 0.024 1.41e-02 5.03e+03 2.99e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.85e+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 2.63e+00 bond pdb=" C GLU C 613 " pdb=" N ALA C 614 " ideal model delta sigma weight residual 1.329 1.288 0.040 3.03e-02 1.09e+03 1.76e+00 ... (remaining 28404 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 37562 1.79 - 3.58: 856 3.58 - 5.37: 85 5.37 - 7.16: 4 7.16 - 8.94: 1 Bond angle restraints: 38508 Sorted by residual: angle pdb=" N LYS C 295 " pdb=" CA LYS C 295 " pdb=" C LYS C 295 " ideal model delta sigma weight residual 114.75 110.04 4.71 1.26e+00 6.30e-01 1.40e+01 angle pdb=" N THR C 479 " pdb=" CA THR C 479 " pdb=" C THR C 479 " ideal model delta sigma weight residual 109.81 102.81 7.00 2.21e+00 2.05e-01 1.00e+01 angle pdb=" C ILE C 919 " pdb=" CA ILE C 919 " pdb=" CB ILE C 919 " ideal model delta sigma weight residual 111.29 106.47 4.82 1.64e+00 3.72e-01 8.63e+00 angle pdb=" N LEU D 579 " pdb=" CA LEU D 579 " pdb=" C LEU D 579 " ideal model delta sigma weight residual 111.02 114.24 -3.22 1.22e+00 6.72e-01 6.97e+00 angle pdb=" CA TYR E 53 " pdb=" CB TYR E 53 " pdb=" CG TYR E 53 " ideal model delta sigma weight residual 113.90 118.52 -4.62 1.80e+00 3.09e-01 6.57e+00 ... (remaining 38503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 15744 17.90 - 35.80: 1372 35.80 - 53.71: 209 53.71 - 71.61: 40 71.61 - 89.51: 23 Dihedral angle restraints: 17388 sinusoidal: 7087 harmonic: 10301 Sorted by residual: dihedral pdb=" CA ASP D 605 " pdb=" C ASP D 605 " pdb=" N ALA D 606 " pdb=" CA ALA D 606 " ideal model delta harmonic sigma weight residual 180.00 152.62 27.38 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA GLN C 433 " pdb=" C GLN C 433 " pdb=" N ASN C 434 " pdb=" CA ASN C 434 " ideal model delta harmonic sigma weight residual 180.00 154.48 25.52 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA SER C 573 " pdb=" C SER C 573 " pdb=" N PRO C 574 " pdb=" CA PRO C 574 " ideal model delta harmonic sigma weight residual 180.00 155.66 24.34 0 5.00e+00 4.00e-02 2.37e+01 ... (remaining 17385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2483 0.030 - 0.061: 1231 0.061 - 0.091: 416 0.091 - 0.122: 211 0.122 - 0.152: 31 Chirality restraints: 4372 Sorted by residual: chirality pdb=" CA PRO D 577 " pdb=" N PRO D 577 " pdb=" C PRO D 577 " pdb=" CB PRO D 577 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.79e-01 chirality pdb=" CA ILE D 51 " pdb=" N ILE D 51 " pdb=" C ILE D 51 " pdb=" CB ILE D 51 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA PRO H 107 " pdb=" N PRO H 107 " pdb=" C PRO H 107 " pdb=" CB PRO H 107 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.10e-01 ... (remaining 4369 not shown) Planarity restraints: 5099 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 607 " 0.039 5.00e-02 4.00e+02 5.97e-02 5.70e+00 pdb=" N PRO C 608 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 608 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 608 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 680 " -0.038 5.00e-02 4.00e+02 5.83e-02 5.43e+00 pdb=" N PRO D 681 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO D 681 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 681 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG H 110 " 0.038 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PRO H 111 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO H 111 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO H 111 " 0.032 5.00e-02 4.00e+02 ... (remaining 5096 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 202 2.52 - 3.12: 22373 3.12 - 3.71: 40094 3.71 - 4.31: 60119 4.31 - 4.90: 101363 Nonbonded interactions: 224151 Sorted by model distance: nonbonded pdb=" OH TYR D 599 " pdb=" OE1 GLU D 608 " model vdw 1.926 3.040 nonbonded pdb=" OG SER A 210 " pdb=" O SER B 229 " model vdw 2.000 3.040 nonbonded pdb=" OG1 THR H 77 " pdb=" OD1 ASP H 79 " model vdw 2.058 3.040 nonbonded pdb=" OH TYR C 335 " pdb=" O PRO C 355 " model vdw 2.084 3.040 nonbonded pdb=" OG SER C 173 " pdb=" O ASN C 366 " model vdw 2.092 3.040 ... (remaining 224146 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 224) } 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: 3.120 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: 0.030 Extract box with map and model: 0.420 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 30.690 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 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 : 0.006 0.468 28417 Z= 0.239 Angle : 0.661 10.719 38520 Z= 0.364 Chirality : 0.044 0.152 4372 Planarity : 0.006 0.060 5099 Dihedral : 13.863 89.510 10760 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.82 % Favored : 91.15 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % 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: -4.90 (0.11), residues: 3581 helix: -3.20 (0.11), residues: 1242 sheet: -1.90 (0.23), residues: 408 loop : -3.72 (0.11), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 87 TYR 0.037 0.002 TYR E 53 PHE 0.030 0.002 PHE D1063 TRP 0.011 0.001 TRP C 61 HIS 0.013 0.001 HIS C 470 Details of bonding type rmsd covalent geometry : bond 0.00501 (28409) covalent geometry : angle 0.65616 (38508) hydrogen bonds : bond 0.16150 ( 1082) hydrogen bonds : angle 7.23300 ( 3060) metal coordination : bond 0.20354 ( 8) metal coordination : angle 4.71384 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7162 Ramachandran restraints generated. 3581 Oldfield, 0 Emsley, 3581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7162 Ramachandran restraints generated. 3581 Oldfield, 0 Emsley, 3581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 344 time to evaluate : 1.047 Fit side-chains 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: 344 average time/residue: 0.2354 time to fit residues: 117.5274 Evaluate side-chains 168 residues out of total 2997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 197 optimal weight: 0.2980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 0.7980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN B 151 GLN B 152 ASN ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 HIS D 410 GLN D 765 ASN H 64 ASN H 627 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.078815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.059982 restraints weight = 87251.243| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.84 r_work: 0.3100 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28417 Z= 0.145 Angle : 0.651 11.467 38520 Z= 0.335 Chirality : 0.046 0.243 4372 Planarity : 0.006 0.054 5099 Dihedral : 4.966 24.113 3949 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.83 % Allowed : 7.11 % Favored : 92.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % 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: -2.78 (0.12), residues: 3581 helix: -1.03 (0.13), residues: 1285 sheet: -1.37 (0.24), residues: 425 loop : -2.61 (0.12), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 89 TYR 0.030 0.001 TYR E 53 PHE 0.023 0.002 PHE H 640 TRP 0.020 0.001 TRP H 624 HIS 0.014 0.001 HIS D 145 Details of bonding type rmsd covalent geometry : bond 0.00322 (28409) covalent geometry : angle 0.64788 (38508) hydrogen bonds : bond 0.04162 ( 1082) hydrogen bonds : angle 4.88876 ( 3060) metal coordination : bond 0.01964 ( 8) metal coordination : angle 3.91404 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7162 Ramachandran restraints generated. 3581 Oldfield, 0 Emsley, 3581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7162 Ramachandran restraints generated. 3581 Oldfield, 0 Emsley, 3581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 199 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 270 ARG cc_start: 0.8792 (ttp-110) cc_final: 0.8569 (mtm-85) REVERT: D 232 LYS cc_start: 0.8510 (mtmm) cc_final: 0.8235 (mtpp) REVERT: D 373 MET cc_start: 0.7172 (tpt) cc_final: 0.6483 (tpt) REVERT: D 732 MET cc_start: 0.8188 (mmm) cc_final: 0.7984 (mmm) REVERT: D 1163 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9024 (tt) REVERT: E 63 ASP cc_start: 0.8695 (m-30) cc_final: 0.8465 (m-30) REVERT: H 596 MET cc_start: 0.7141 (tpp) cc_final: 0.6281 (ttt) outliers start: 25 outliers final: 11 residues processed: 219 average time/residue: 0.2067 time to fit residues: 71.1072 Evaluate side-chains 178 residues out of total 2997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 166 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 794 VAL Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 1163 LEU Chi-restraints excluded: chain E residue 34 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 292 optimal weight: 3.9990 chunk 131 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 319 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 315 optimal weight: 0.0970 chunk 265 optimal weight: 7.9990 chunk 316 optimal weight: 6.9990 chunk 191 optimal weight: 40.0000 chunk 37 optimal weight: 5.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 HIS C 238 GLN C 498 ASN C 536 ASN D 145 HIS D 375 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.074175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.055615 restraints weight = 87998.507| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.77 r_work: 0.2968 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 28417 Z= 0.228 Angle : 0.657 9.671 38520 Z= 0.339 Chirality : 0.046 0.159 4372 Planarity : 0.005 0.065 5099 Dihedral : 4.862 22.566 3949 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 1.57 % Allowed : 9.68 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % 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: -1.93 (0.13), residues: 3581 helix: -0.33 (0.14), residues: 1316 sheet: -1.04 (0.25), residues: 399 loop : -2.07 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D1192 TYR 0.034 0.002 TYR E 53 PHE 0.026 0.002 PHE C 364 TRP 0.016 0.002 TRP H 361 HIS 0.009 0.001 HIS D 494 Details of bonding type rmsd covalent geometry : bond 0.00529 (28409) covalent geometry : angle 0.65395 (38508) hydrogen bonds : bond 0.04584 ( 1082) hydrogen bonds : angle 4.70353 ( 3060) metal coordination : bond 0.01805 ( 8) metal coordination : angle 3.41313 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7162 Ramachandran restraints generated. 3581 Oldfield, 0 Emsley, 3581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7162 Ramachandran restraints generated. 3581 Oldfield, 0 Emsley, 3581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 180 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 516 THR cc_start: 0.9174 (OUTLIER) cc_final: 0.8906 (p) REVERT: D 92 MET cc_start: 0.5200 (OUTLIER) cc_final: 0.4693 (ptm) REVERT: D 373 MET cc_start: 0.7217 (tpt) cc_final: 0.6469 (mmm) REVERT: D 1163 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9091 (tt) REVERT: E 63 ASP cc_start: 0.8723 (m-30) cc_final: 0.8491 (m-30) REVERT: H 647 ARG cc_start: 0.5383 (ptp90) cc_final: 0.5124 (ptt90) outliers start: 47 outliers final: 22 residues processed: 217 average time/residue: 0.2008 time to fit residues: 69.0954 Evaluate side-chains 184 residues out of total 2997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ILE 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 200 ASN Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 1114 VAL Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 1163 LEU Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain H residue 348 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 120 optimal weight: 9.9990 chunk 170 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 329 optimal weight: 4.9990 chunk 184 optimal weight: 20.0000 chunk 317 optimal weight: 0.9980 chunk 322 optimal weight: 4.9990 chunk 275 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 GLN C 603 GLN ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1247 ASN E 66 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.073793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.054407 restraints weight = 88660.699| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.82 r_work: 0.2966 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 28417 Z= 0.204 Angle : 0.610 9.744 38520 Z= 0.315 Chirality : 0.046 0.278 4372 Planarity : 0.005 0.063 5099 Dihedral : 4.735 22.478 3949 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.74 % Allowed : 10.88 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % 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: -1.48 (0.13), residues: 3581 helix: 0.02 (0.14), residues: 1324 sheet: -0.83 (0.25), residues: 394 loop : -1.80 (0.13), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D1192 TYR 0.024 0.001 TYR E 53 PHE 0.026 0.002 PHE H 640 TRP 0.013 0.001 TRP H 361 HIS 0.007 0.001 HIS C 470 Details of bonding type rmsd covalent geometry : bond 0.00475 (28409) covalent geometry : angle 0.60741 (38508) hydrogen bonds : bond 0.04171 ( 1082) hydrogen bonds : angle 4.50677 ( 3060) metal coordination : bond 0.01594 ( 8) metal coordination : angle 3.51708 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7162 Ramachandran restraints generated. 3581 Oldfield, 0 Emsley, 3581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7162 Ramachandran restraints generated. 3581 Oldfield, 0 Emsley, 3581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 172 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 221 ARG cc_start: 0.8268 (ttp-110) cc_final: 0.7831 (ttp80) REVERT: C 577 MET cc_start: 0.9218 (ptm) cc_final: 0.8953 (ptt) REVERT: D 92 MET cc_start: 0.5211 (OUTLIER) cc_final: 0.4610 (ptm) REVERT: D 327 MET cc_start: 0.4319 (ttp) cc_final: 0.3291 (mtm) REVERT: D 1163 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9099 (tt) REVERT: H 123 MET cc_start: 0.8875 (mmt) cc_final: 0.8298 (mmt) REVERT: H 647 ARG cc_start: 0.5817 (ptp90) cc_final: 0.5460 (ptt90) outliers start: 52 outliers final: 29 residues processed: 216 average time/residue: 0.2051 time to fit residues: 69.3195 Evaluate side-chains 181 residues out of total 2997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 1114 VAL Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 1026 VAL Chi-restraints excluded: chain D residue 1062 PHE Chi-restraints excluded: chain D residue 1163 LEU Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain H residue 348 VAL Chi-restraints excluded: chain H residue 354 VAL Chi-restraints excluded: chain H residue 678 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 206 optimal weight: 5.9990 chunk 205 optimal weight: 0.2980 chunk 36 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 338 optimal weight: 0.9990 chunk 329 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 GLN C 603 GLN ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 GLN H 334 HIS H 505 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.072779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.053213 restraints weight = 88707.961| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.85 r_work: 0.2921 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 28417 Z= 0.219 Angle : 0.610 9.187 38520 Z= 0.315 Chirality : 0.045 0.170 4372 Planarity : 0.005 0.065 5099 Dihedral : 4.729 22.353 3949 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 1.90 % Allowed : 11.55 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % 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: -1.28 (0.14), residues: 3581 helix: 0.20 (0.14), residues: 1315 sheet: -0.68 (0.25), residues: 410 loop : -1.69 (0.13), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 683 TYR 0.022 0.001 TYR E 53 PHE 0.018 0.002 PHE H 640 TRP 0.014 0.001 TRP H 361 HIS 0.006 0.001 HIS C 470 Details of bonding type rmsd covalent geometry : bond 0.00512 (28409) covalent geometry : angle 0.60669 (38508) hydrogen bonds : bond 0.04296 ( 1082) hydrogen bonds : angle 4.48109 ( 3060) metal coordination : bond 0.01535 ( 8) metal coordination : angle 3.58947 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7162 Ramachandran restraints generated. 3581 Oldfield, 0 Emsley, 3581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7162 Ramachandran restraints generated. 3581 Oldfield, 0 Emsley, 3581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 157 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 151 MET cc_start: 0.9271 (ttm) cc_final: 0.8853 (ttt) REVERT: C 516 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8822 (p) REVERT: C 577 MET cc_start: 0.9237 (ptm) cc_final: 0.8969 (ptt) REVERT: C 704 MET cc_start: 0.8699 (mmt) cc_final: 0.8396 (mmt) REVERT: D 92 MET cc_start: 0.5433 (OUTLIER) cc_final: 0.4908 (ptm) REVERT: D 373 MET cc_start: 0.6878 (tpp) cc_final: 0.6557 (mmm) REVERT: D 1163 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9151 (tt) REVERT: H 647 ARG cc_start: 0.5915 (ptp90) cc_final: 0.5544 (ptt90) outliers start: 57 outliers final: 36 residues processed: 207 average time/residue: 0.1975 time to fit residues: 65.3062 Evaluate side-chains 184 residues out of total 2997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 145 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 194 ILE 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 178 VAL Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain C residue 1114 VAL Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 1026 VAL Chi-restraints excluded: chain D residue 1062 PHE Chi-restraints excluded: chain D residue 1163 LEU Chi-restraints excluded: chain D residue 1197 GLU Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain H residue 348 VAL Chi-restraints excluded: chain H residue 354 VAL Chi-restraints excluded: chain H residue 678 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 141 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 222 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 350 optimal weight: 20.0000 chunk 256 optimal weight: 0.5980 chunk 246 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 GLN C 603 GLN ** C 659 GLN ** 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 = 0.3545 r_free = 0.3545 target = 0.072827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.053741 restraints weight = 87744.935| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.82 r_work: 0.2930 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 28417 Z= 0.177 Angle : 0.579 9.127 38520 Z= 0.297 Chirality : 0.044 0.212 4372 Planarity : 0.005 0.061 5099 Dihedral : 4.617 22.439 3949 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.87 % Allowed : 12.69 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % 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: -1.04 (0.14), residues: 3581 helix: 0.39 (0.14), residues: 1320 sheet: -0.66 (0.24), residues: 424 loop : -1.52 (0.14), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 221 TYR 0.019 0.001 TYR E 53 PHE 0.026 0.002 PHE H 640 TRP 0.015 0.001 TRP H 361 HIS 0.005 0.001 HIS H 42 Details of bonding type rmsd covalent geometry : bond 0.00413 (28409) covalent geometry : angle 0.57539 (38508) hydrogen bonds : bond 0.04007 ( 1082) hydrogen bonds : angle 4.34609 ( 3060) metal coordination : bond 0.01496 ( 8) metal coordination : angle 3.63439 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7162 Ramachandran restraints generated. 3581 Oldfield, 0 Emsley, 3581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7162 Ramachandran restraints generated. 3581 Oldfield, 0 Emsley, 3581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 160 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 151 MET cc_start: 0.9306 (ttm) cc_final: 0.8904 (ttt) REVERT: C 221 ARG cc_start: 0.8250 (ttp-110) cc_final: 0.7901 (ttp80) REVERT: C 516 THR cc_start: 0.9084 (OUTLIER) cc_final: 0.8756 (p) REVERT: C 704 MET cc_start: 0.8721 (mmt) cc_final: 0.8404 (mmt) REVERT: D 92 MET cc_start: 0.5464 (OUTLIER) cc_final: 0.4955 (ptm) REVERT: D 327 MET cc_start: 0.4161 (mtm) cc_final: 0.3290 (mtm) REVERT: D 373 MET cc_start: 0.6876 (tpp) cc_final: 0.6571 (mmm) REVERT: D 687 MET cc_start: 0.9077 (mmp) cc_final: 0.8717 (mmp) REVERT: D 1163 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9152 (tt) REVERT: H 596 MET cc_start: 0.7057 (tpp) cc_final: 0.6162 (tpp) REVERT: H 647 ARG cc_start: 0.6080 (ptp90) cc_final: 0.5792 (ptt90) outliers start: 56 outliers final: 39 residues processed: 208 average time/residue: 0.1823 time to fit residues: 61.9269 Evaluate side-chains 186 residues out of total 2997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 144 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain C residue 1114 VAL Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 799 ILE Chi-restraints excluded: chain D residue 823 VAL Chi-restraints excluded: chain D residue 1026 VAL Chi-restraints excluded: chain D residue 1062 PHE Chi-restraints excluded: chain D residue 1092 HIS Chi-restraints excluded: chain D residue 1163 LEU Chi-restraints excluded: chain D residue 1197 GLU Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain H residue 348 VAL Chi-restraints excluded: chain H residue 354 VAL Chi-restraints excluded: chain H residue 473 LEU Chi-restraints excluded: chain H residue 678 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 307 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 14 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 chunk 151 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 211 optimal weight: 3.9990 chunk 277 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 chunk 310 optimal weight: 7.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 GLN C 284 GLN C 603 GLN ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.072598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.053118 restraints weight = 88246.283| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.83 r_work: 0.2923 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 28417 Z= 0.188 Angle : 0.585 8.852 38520 Z= 0.299 Chirality : 0.045 0.193 4372 Planarity : 0.005 0.061 5099 Dihedral : 4.586 21.887 3949 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.10 % Allowed : 12.95 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % 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: -0.91 (0.14), residues: 3581 helix: 0.48 (0.15), residues: 1317 sheet: -0.60 (0.25), residues: 424 loop : -1.42 (0.14), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 221 TYR 0.019 0.001 TYR E 53 PHE 0.022 0.002 PHE H 640 TRP 0.012 0.001 TRP D 722 HIS 0.005 0.001 HIS H 42 Details of bonding type rmsd covalent geometry : bond 0.00439 (28409) covalent geometry : angle 0.58197 (38508) hydrogen bonds : bond 0.04080 ( 1082) hydrogen bonds : angle 4.32117 ( 3060) metal coordination : bond 0.01470 ( 8) metal coordination : angle 3.63718 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7162 Ramachandran restraints generated. 3581 Oldfield, 0 Emsley, 3581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7162 Ramachandran restraints generated. 3581 Oldfield, 0 Emsley, 3581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 158 time to evaluate : 0.731 Fit side-chains revert: symmetry clash REVERT: C 221 ARG cc_start: 0.8268 (ttp-110) cc_final: 0.7895 (ttp80) REVERT: C 516 THR cc_start: 0.9100 (OUTLIER) cc_final: 0.8788 (p) REVERT: D 92 MET cc_start: 0.5356 (OUTLIER) cc_final: 0.4856 (ptm) REVERT: D 373 MET cc_start: 0.6894 (tpp) cc_final: 0.6573 (mmm) REVERT: D 687 MET cc_start: 0.9030 (mmp) cc_final: 0.8722 (mmp) REVERT: D 1163 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9168 (tt) REVERT: H 596 MET cc_start: 0.7007 (tpp) cc_final: 0.6174 (tpp) REVERT: H 647 ARG cc_start: 0.6147 (ptp90) cc_final: 0.5862 (ptt90) outliers start: 63 outliers final: 42 residues processed: 214 average time/residue: 0.1733 time to fit residues: 60.6491 Evaluate side-chains 191 residues out of total 2997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 146 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 194 ILE 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 147 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 584 MET Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain C residue 1114 VAL Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 799 ILE Chi-restraints excluded: chain D residue 823 VAL Chi-restraints excluded: chain D residue 1026 VAL Chi-restraints excluded: chain D residue 1062 PHE Chi-restraints excluded: chain D residue 1092 HIS Chi-restraints excluded: chain D residue 1163 LEU Chi-restraints excluded: chain D residue 1197 GLU Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain H residue 348 VAL Chi-restraints excluded: chain H residue 354 VAL Chi-restraints excluded: chain H residue 473 LEU Chi-restraints excluded: chain H residue 678 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 55 optimal weight: 6.9990 chunk 213 optimal weight: 4.9990 chunk 306 optimal weight: 1.9990 chunk 182 optimal weight: 0.0030 chunk 76 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 332 optimal weight: 5.9990 chunk 297 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 180 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 overall best weight: 1.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 GLN C 603 GLN ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1102 ASN D1111 GLN D1252 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.073850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.054331 restraints weight = 88558.246| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.85 r_work: 0.2960 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 28417 Z= 0.125 Angle : 0.549 10.630 38520 Z= 0.278 Chirality : 0.043 0.191 4372 Planarity : 0.004 0.057 5099 Dihedral : 4.392 21.579 3949 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.54 % Allowed : 13.56 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % 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: -0.64 (0.14), residues: 3581 helix: 0.72 (0.15), residues: 1314 sheet: -0.46 (0.25), residues: 424 loop : -1.26 (0.14), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 221 TYR 0.018 0.001 TYR D 251 PHE 0.026 0.001 PHE H 640 TRP 0.022 0.001 TRP H 361 HIS 0.005 0.001 HIS H 42 Details of bonding type rmsd covalent geometry : bond 0.00289 (28409) covalent geometry : angle 0.54537 (38508) hydrogen bonds : bond 0.03586 ( 1082) hydrogen bonds : angle 4.13860 ( 3060) metal coordination : bond 0.01449 ( 8) metal coordination : angle 3.52617 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7162 Ramachandran restraints generated. 3581 Oldfield, 0 Emsley, 3581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7162 Ramachandran restraints generated. 3581 Oldfield, 0 Emsley, 3581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 161 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 221 ARG cc_start: 0.8266 (ttp-110) cc_final: 0.7893 (ttp80) REVERT: C 516 THR cc_start: 0.9068 (OUTLIER) cc_final: 0.8770 (p) REVERT: D 92 MET cc_start: 0.5261 (OUTLIER) cc_final: 0.4771 (ptm) REVERT: D 256 MET cc_start: 0.6614 (ttt) cc_final: 0.6390 (ttt) REVERT: D 271 ASP cc_start: 0.8525 (t70) cc_final: 0.7719 (m-30) REVERT: D 327 MET cc_start: 0.3535 (mtm) cc_final: 0.3023 (mtp) REVERT: D 373 MET cc_start: 0.6905 (tpp) cc_final: 0.6570 (mmm) REVERT: D 687 MET cc_start: 0.9043 (mmp) cc_final: 0.8654 (mmp) REVERT: D 1163 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9142 (tt) REVERT: H 596 MET cc_start: 0.7064 (tpp) cc_final: 0.6282 (tpp) REVERT: H 647 ARG cc_start: 0.6159 (ptp90) cc_final: 0.5906 (ptt90) outliers start: 46 outliers final: 33 residues processed: 199 average time/residue: 0.1856 time to fit residues: 59.9318 Evaluate side-chains 181 residues out of total 2997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 145 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 1114 VAL Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 799 ILE Chi-restraints excluded: chain D residue 823 VAL Chi-restraints excluded: chain D residue 1026 VAL Chi-restraints excluded: chain D residue 1062 PHE Chi-restraints excluded: chain D residue 1092 HIS Chi-restraints excluded: chain D residue 1163 LEU Chi-restraints excluded: chain H residue 354 VAL Chi-restraints excluded: chain H residue 473 LEU Chi-restraints excluded: chain H residue 678 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 47 optimal weight: 6.9990 chunk 274 optimal weight: 0.9980 chunk 268 optimal weight: 0.6980 chunk 168 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 158 optimal weight: 6.9990 chunk 156 optimal weight: 6.9990 chunk 117 optimal weight: 8.9990 chunk 343 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 228 optimal weight: 0.4980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 603 GLN ** C 659 GLN ** 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 = 0.3567 r_free = 0.3567 target = 0.073708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.054795 restraints weight = 87337.255| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.75 r_work: 0.2964 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28417 Z= 0.126 Angle : 0.551 10.457 38520 Z= 0.279 Chirality : 0.043 0.190 4372 Planarity : 0.004 0.058 5099 Dihedral : 4.291 21.063 3949 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.47 % Allowed : 13.79 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % 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: -0.49 (0.14), residues: 3581 helix: 0.79 (0.15), residues: 1324 sheet: -0.35 (0.25), residues: 424 loop : -1.15 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D1192 TYR 0.016 0.001 TYR E 53 PHE 0.025 0.001 PHE H 640 TRP 0.019 0.001 TRP C 202 HIS 0.005 0.001 HIS H 42 Details of bonding type rmsd covalent geometry : bond 0.00292 (28409) covalent geometry : angle 0.54764 (38508) hydrogen bonds : bond 0.03570 ( 1082) hydrogen bonds : angle 4.07967 ( 3060) metal coordination : bond 0.01429 ( 8) metal coordination : angle 3.37602 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7162 Ramachandran restraints generated. 3581 Oldfield, 0 Emsley, 3581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7162 Ramachandran restraints generated. 3581 Oldfield, 0 Emsley, 3581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 158 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 221 ARG cc_start: 0.8239 (ttp-110) cc_final: 0.7867 (ttp80) REVERT: C 516 THR cc_start: 0.9062 (OUTLIER) cc_final: 0.8775 (p) REVERT: D 232 LYS cc_start: 0.8734 (mtmm) cc_final: 0.8311 (mtpp) REVERT: D 271 ASP cc_start: 0.8569 (t70) cc_final: 0.7775 (m-30) REVERT: D 327 MET cc_start: 0.3390 (mtm) cc_final: 0.2976 (mtp) REVERT: D 373 MET cc_start: 0.6901 (tpp) cc_final: 0.6418 (tmm) REVERT: D 687 MET cc_start: 0.9030 (mmp) cc_final: 0.8704 (mmp) REVERT: D 1163 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9160 (tt) REVERT: D 1193 ARG cc_start: 0.5241 (ppt170) cc_final: 0.4329 (ttp80) REVERT: H 596 MET cc_start: 0.7079 (tpp) cc_final: 0.6303 (tpp) REVERT: H 647 ARG cc_start: 0.6238 (ptp90) cc_final: 0.5857 (ptt90) outliers start: 44 outliers final: 36 residues processed: 198 average time/residue: 0.1806 time to fit residues: 59.6130 Evaluate side-chains 189 residues out of total 2997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 151 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 1114 VAL Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 666 THR Chi-restraints excluded: chain D residue 799 ILE Chi-restraints excluded: chain D residue 823 VAL Chi-restraints excluded: chain D residue 1026 VAL Chi-restraints excluded: chain D residue 1062 PHE Chi-restraints excluded: chain D residue 1092 HIS Chi-restraints excluded: chain D residue 1163 LEU Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain H residue 354 VAL Chi-restraints excluded: chain H residue 473 LEU Chi-restraints excluded: chain H residue 678 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 184 optimal weight: 0.0270 chunk 158 optimal weight: 5.9990 chunk 209 optimal weight: 3.9990 chunk 272 optimal weight: 10.0000 chunk 356 optimal weight: 0.9980 chunk 250 optimal weight: 0.9990 chunk 245 optimal weight: 20.0000 chunk 191 optimal weight: 6.9990 chunk 192 optimal weight: 10.0000 chunk 286 optimal weight: 0.7980 chunk 20 optimal weight: 0.0070 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 GLN C 603 GLN ** C 659 GLN ** 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 = 0.3602 r_free = 0.3602 target = 0.075336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.056849 restraints weight = 87219.985| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.74 r_work: 0.3006 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 28417 Z= 0.098 Angle : 0.534 10.922 38520 Z= 0.269 Chirality : 0.042 0.189 4372 Planarity : 0.004 0.058 5099 Dihedral : 4.112 21.230 3949 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.14 % Allowed : 14.36 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % 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: -0.25 (0.14), residues: 3581 helix: 1.06 (0.15), residues: 1310 sheet: -0.22 (0.25), residues: 419 loop : -1.06 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D1192 TYR 0.013 0.001 TYR E 53 PHE 0.025 0.001 PHE H 640 TRP 0.014 0.001 TRP H 361 HIS 0.005 0.001 HIS H 42 Details of bonding type rmsd covalent geometry : bond 0.00221 (28409) covalent geometry : angle 0.53096 (38508) hydrogen bonds : bond 0.03209 ( 1082) hydrogen bonds : angle 3.93955 ( 3060) metal coordination : bond 0.01446 ( 8) metal coordination : angle 3.25688 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7162 Ramachandran restraints generated. 3581 Oldfield, 0 Emsley, 3581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7162 Ramachandran restraints generated. 3581 Oldfield, 0 Emsley, 3581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 221 ARG cc_start: 0.8211 (ttp-110) cc_final: 0.7887 (ttp80) REVERT: C 516 THR cc_start: 0.9082 (OUTLIER) cc_final: 0.8847 (p) REVERT: D 232 LYS cc_start: 0.8714 (mtmm) cc_final: 0.8315 (mtpp) REVERT: D 271 ASP cc_start: 0.8518 (t70) cc_final: 0.7811 (m-30) REVERT: D 327 MET cc_start: 0.3322 (mtm) cc_final: 0.2914 (mtp) REVERT: D 373 MET cc_start: 0.6887 (tpp) cc_final: 0.6401 (tmm) REVERT: D 687 MET cc_start: 0.8995 (mmp) cc_final: 0.8585 (mmp) REVERT: D 1016 GLN cc_start: 0.7995 (mm-40) cc_final: 0.7230 (mp10) REVERT: D 1163 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9134 (tt) REVERT: D 1193 ARG cc_start: 0.5079 (ppt170) cc_final: 0.4186 (ttp80) REVERT: H 596 MET cc_start: 0.7022 (tpp) cc_final: 0.6306 (tpp) REVERT: H 647 ARG cc_start: 0.6216 (ptp90) cc_final: 0.5807 (ptt90) outliers start: 34 outliers final: 27 residues processed: 190 average time/residue: 0.1796 time to fit residues: 56.6784 Evaluate side-chains 182 residues out of total 2997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 1114 VAL Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 799 ILE Chi-restraints excluded: chain D residue 823 VAL Chi-restraints excluded: chain D residue 1062 PHE Chi-restraints excluded: chain D residue 1092 HIS Chi-restraints excluded: chain D residue 1163 LEU Chi-restraints excluded: chain H residue 354 VAL Chi-restraints excluded: chain H residue 473 LEU Chi-restraints excluded: chain H residue 678 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 280 optimal weight: 4.9990 chunk 334 optimal weight: 0.7980 chunk 62 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 109 optimal weight: 0.0000 chunk 1 optimal weight: 8.9990 chunk 174 optimal weight: 9.9990 chunk 289 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 overall best weight: 2.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 659 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 = 0.3560 r_free = 0.3560 target = 0.073447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.054885 restraints weight = 87481.161| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.73 r_work: 0.2956 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.4370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 28417 Z= 0.167 Angle : 0.576 11.110 38520 Z= 0.292 Chirality : 0.044 0.189 4372 Planarity : 0.005 0.061 5099 Dihedral : 4.275 20.745 3949 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.20 % Allowed : 14.52 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % 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: 3581 helix: 0.94 (0.15), residues: 1314 sheet: -0.31 (0.25), residues: 425 loop : -1.06 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D1192 TYR 0.019 0.001 TYR D 251 PHE 0.024 0.001 PHE H 640 TRP 0.014 0.001 TRP H 361 HIS 0.005 0.001 HIS H 42 Details of bonding type rmsd covalent geometry : bond 0.00390 (28409) covalent geometry : angle 0.57328 (38508) hydrogen bonds : bond 0.03811 ( 1082) hydrogen bonds : angle 4.07649 ( 3060) metal coordination : bond 0.01405 ( 8) metal coordination : angle 3.39395 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6100.23 seconds wall clock time: 105 minutes 26.58 seconds (6326.58 seconds total)