Starting phenix.real_space_refine on Mon Jun 23 21:00:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xxp_38757/06_2025/8xxp_38757.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xxp_38757/06_2025/8xxp_38757.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xxp_38757/06_2025/8xxp_38757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xxp_38757/06_2025/8xxp_38757.map" model { file = "/net/cci-nas-00/data/ceres_data/8xxp_38757/06_2025/8xxp_38757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xxp_38757/06_2025/8xxp_38757.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.075 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 6 6.06 5 Mg 1 5.21 5 S 167 5.16 5 C 17604 2.51 5 N 4767 2.21 5 O 5105 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27650 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 11216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1409, 11216 Classifications: {'peptide': 1409} Link IDs: {'PCIS': 2, 'PTRANS': 64, 'TRANS': 1342} Chain breaks: 2 Chain: "B" Number of atoms: 8590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1086, 8590 Classifications: {'peptide': 1086} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1034} Chain breaks: 9 Chain: "C" Number of atoms: 2915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2915 Classifications: {'peptide': 359} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 339} Chain: "D" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1669 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 193} Chain: "E" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 839 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "F" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1045 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain breaks: 2 Chain: "G" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 816 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "H" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 553 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain breaks: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 450 SG CYS A 59 97.625 49.319 68.947 1.00 67.21 S ATOM 471 SG CYS A 62 95.870 48.283 65.831 1.00 56.96 S ATOM 531 SG CYS A 69 94.656 51.273 68.025 1.00 55.92 S ATOM 775 SG CYS A 99 80.886 29.512 107.815 1.00 84.97 S ATOM 797 SG CYS A 102 81.818 26.132 106.164 1.00 93.53 S ATOM 1049 SG CYS A 134 78.849 26.298 108.378 1.00104.99 S ATOM 1074 SG CYS A 137 82.303 26.886 109.916 1.00106.76 S ATOM 19325 SG CYS B1180 88.428 34.370 68.150 1.00 52.11 S ATOM 19350 SG CYS B1183 87.589 35.404 71.740 1.00 54.58 S ATOM 19466 SG CYS B1198 91.251 35.276 70.483 1.00 70.83 S ATOM 19488 SG CYS B1201 89.430 32.096 70.770 1.00 70.75 S ATOM 26305 SG CYS G 4 53.273 70.822 138.025 1.00111.64 S ATOM 26325 SG CYS G 7 56.480 71.406 135.885 1.00117.51 S ATOM 26459 SG CYS G 24 54.369 68.296 135.465 1.00123.37 S ATOM 26471 SG CYS G 26 56.731 68.939 138.399 1.00122.89 S ATOM 26841 SG CYS G 73 25.323 104.186 109.474 1.00 90.21 S ATOM 26862 SG CYS G 76 27.163 107.512 109.976 1.00 97.48 S ATOM 27019 SG CYS G 96 28.987 104.655 108.554 1.00 88.48 S ATOM 27036 SG CYS G 98 27.885 104.489 112.229 1.00 80.99 S ATOM 27141 SG CYS H 7 61.717 107.578 48.183 1.00 37.38 S ATOM 27165 SG CYS H 10 60.708 108.027 44.484 1.00 43.24 S ATOM 27506 SG CYS H 65 58.068 107.523 47.253 1.00 40.41 S ATOM 27512 SG CYS H 66 60.037 110.747 46.554 1.00 46.06 S Time building chain proxies: 16.14, per 1000 atoms: 0.58 Number of scatterers: 27650 At special positions: 0 Unit cell: (133.66, 141.86, 149.24, 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 6 29.99 S 167 16.00 Mg 1 11.99 O 5105 8.00 N 4767 7.00 C 17604 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: 6.72 Conformation dependent library (CDL) restraints added in 3.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" NE2 HIS A 72 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 59 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 69 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 62 " pdb=" ZN A1502 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 99 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 137 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 102 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 134 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1201 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1180 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1198 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1183 " pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 24 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 7 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 26 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 4 " pdb=" ZN G 202 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 73 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 76 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 98 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 96 " pdb=" ZN H 101 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 10 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 66 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 65 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 7 " Number of angles added : 33 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6548 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 42 sheets defined 42.6% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.78 Creating SS restraints... Processing helix chain 'A' and resid 17 through 25 Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 87 through 96 removed outlier: 3.518A pdb=" N ARG A 96 " --> pdb=" O ARG A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 127 removed outlier: 4.336A pdb=" N LEU A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ILE A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER A 127 " --> pdb=" O GLU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 176 Processing helix chain 'A' and resid 178 through 185 Processing helix chain 'A' and resid 188 through 195 Proline residue: A 193 - end of helix Processing helix chain 'A' and resid 226 through 240 removed outlier: 3.841A pdb=" N ILE A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 273 removed outlier: 3.706A pdb=" N ASN A 259 " --> pdb=" O ASN A 255 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP A 273 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 303 removed outlier: 3.601A pdb=" N LEU A 303 " --> pdb=" O MET A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 348 Processing helix chain 'A' and resid 358 through 369 Proline residue: A 364 - end of helix Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.877A pdb=" N LEU A 393 " --> pdb=" O ILE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 426 No H-bonds generated for 'chain 'A' and resid 424 through 426' Processing helix chain 'A' and resid 450 through 455 removed outlier: 4.170A pdb=" N TYR A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 480 Processing helix chain 'A' and resid 482 through 487 removed outlier: 3.649A pdb=" N PHE A 487 " --> pdb=" O ARG A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 512 Processing helix chain 'A' and resid 524 through 531 removed outlier: 4.004A pdb=" N PHE A 531 " --> pdb=" O ALA A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 561 removed outlier: 3.522A pdb=" N LEU A 559 " --> pdb=" O VAL A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 609 Processing helix chain 'A' and resid 615 through 625 Processing helix chain 'A' and resid 625 through 648 removed outlier: 3.859A pdb=" N ASN A 646 " --> pdb=" O ASN A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 657 Processing helix chain 'A' and resid 659 through 686 Processing helix chain 'A' and resid 696 through 709 Processing helix chain 'A' and resid 712 through 714 No H-bonds generated for 'chain 'A' and resid 712 through 714' Processing helix chain 'A' and resid 715 through 723 removed outlier: 3.887A pdb=" N ILE A 719 " --> pdb=" O ILE A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 736 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 781 through 785 Processing helix chain 'A' and resid 797 through 834 Processing helix chain 'A' and resid 861 through 865 removed outlier: 4.068A pdb=" N LEU A 865 " --> pdb=" O ALA A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 874 removed outlier: 3.911A pdb=" N MET A 874 " --> pdb=" O GLU A 871 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 871 through 874' Processing helix chain 'A' and resid 876 through 885 Processing helix chain 'A' and resid 891 through 918 removed outlier: 3.567A pdb=" N GLU A 895 " --> pdb=" O SER A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 945 Processing helix chain 'A' and resid 953 through 970 Processing helix chain 'A' and resid 971 through 976 Processing helix chain 'A' and resid 977 through 984 Processing helix chain 'A' and resid 988 through 995 removed outlier: 3.585A pdb=" N ALA A 995 " --> pdb=" O LEU A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1006 Processing helix chain 'A' and resid 1007 through 1011 Processing helix chain 'A' and resid 1015 through 1032 Processing helix chain 'A' and resid 1040 through 1059 removed outlier: 3.605A pdb=" N GLU A1051 " --> pdb=" O GLN A1047 " (cutoff:3.500A) Proline residue: A1052 - end of helix removed outlier: 3.628A pdb=" N GLN A1055 " --> pdb=" O GLU A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1082 Processing helix chain 'A' and resid 1102 through 1105 removed outlier: 3.846A pdb=" N THR A1105 " --> pdb=" O GLU A1102 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1102 through 1105' Processing helix chain 'A' and resid 1106 through 1118 Processing helix chain 'A' and resid 1146 through 1150 removed outlier: 4.162A pdb=" N SER A1150 " --> pdb=" O ASP A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1151 through 1162 removed outlier: 3.821A pdb=" N ASP A1157 " --> pdb=" O GLU A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1181 through 1188 Processing helix chain 'A' and resid 1191 through 1203 Processing helix chain 'A' and resid 1229 through 1233 Processing helix chain 'A' and resid 1234 through 1239 removed outlier: 4.478A pdb=" N ASN A1237 " --> pdb=" O ARG A1234 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1256 Processing helix chain 'A' and resid 1299 through 1306 Processing helix chain 'A' and resid 1310 through 1314 removed outlier: 4.204A pdb=" N ILE A1314 " --> pdb=" O PRO A1311 " (cutoff:3.500A) Processing helix chain 'A' and resid 1318 through 1327 Processing helix chain 'A' and resid 1327 through 1344 removed outlier: 3.570A pdb=" N GLY A1344 " --> pdb=" O ARG A1340 " (cutoff:3.500A) Processing helix chain 'A' and resid 1345 through 1347 No H-bonds generated for 'chain 'A' and resid 1345 through 1347' Processing helix chain 'A' and resid 1349 through 1361 removed outlier: 3.820A pdb=" N LEU A1353 " --> pdb=" O ASN A1349 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1378 Processing helix chain 'A' and resid 1381 through 1389 Processing helix chain 'A' and resid 1390 through 1402 Processing helix chain 'A' and resid 1410 through 1416 Processing helix chain 'A' and resid 1422 through 1426 Processing helix chain 'A' and resid 1432 through 1440 Processing helix chain 'B' and resid 12 through 16 removed outlier: 3.630A pdb=" N VAL B 16 " --> pdb=" O ILE B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 38 removed outlier: 3.613A pdb=" N SER B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 removed outlier: 4.040A pdb=" N ILE B 44 " --> pdb=" O ILE B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 63 Processing helix chain 'B' and resid 113 through 121 Processing helix chain 'B' and resid 175 through 183 removed outlier: 3.651A pdb=" N ILE B 182 " --> pdb=" O ALA B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 279 Processing helix chain 'B' and resid 283 through 293 removed outlier: 3.658A pdb=" N VAL B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 315 Processing helix chain 'B' and resid 328 through 340 Processing helix chain 'B' and resid 359 through 372 removed outlier: 3.528A pdb=" N ASP B 369 " --> pdb=" O LEU B 365 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS B 370 " --> pdb=" O THR B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 377 Processing helix chain 'B' and resid 379 through 381 No H-bonds generated for 'chain 'B' and resid 379 through 381' Processing helix chain 'B' and resid 382 through 402 Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 421 through 437 removed outlier: 3.760A pdb=" N ASN B 434 " --> pdb=" O LYS B 430 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR B 435 " --> pdb=" O ALA B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 488 Processing helix chain 'B' and resid 513 through 521 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.753A pdb=" N ARG B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 592 removed outlier: 3.594A pdb=" N LEU B 586 " --> pdb=" O GLU B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 610 Processing helix chain 'B' and resid 627 through 642 Processing helix chain 'B' and resid 679 through 697 Processing helix chain 'B' and resid 700 through 705 Processing helix chain 'B' and resid 715 through 724 Processing helix chain 'B' and resid 728 through 735 Processing helix chain 'B' and resid 742 through 747 Processing helix chain 'B' and resid 754 through 761 Processing helix chain 'B' and resid 774 through 779 Processing helix chain 'B' and resid 780 through 786 removed outlier: 4.145A pdb=" N SER B 786 " --> pdb=" O ALA B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 792 Processing helix chain 'B' and resid 793 through 804 Processing helix chain 'B' and resid 805 through 807 No H-bonds generated for 'chain 'B' and resid 805 through 807' Processing helix chain 'B' and resid 836 through 841 Processing helix chain 'B' and resid 869 through 874 Processing helix chain 'B' and resid 903 through 907 removed outlier: 3.676A pdb=" N ASN B 906 " --> pdb=" O ILE B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 1011 through 1015 Processing helix chain 'B' and resid 1030 through 1033 Processing helix chain 'B' and resid 1038 through 1055 removed outlier: 3.861A pdb=" N MET B1042 " --> pdb=" O THR B1038 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA B1050 " --> pdb=" O THR B1046 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1078 Processing helix chain 'B' and resid 1114 through 1119 Processing helix chain 'B' and resid 1148 through 1158 Processing helix chain 'B' and resid 1162 through 1169 Processing helix chain 'B' and resid 1201 through 1205 Processing helix chain 'B' and resid 1214 through 1226 Processing helix chain 'C' and resid 19 through 31 Processing helix chain 'C' and resid 51 through 65 Processing helix chain 'C' and resid 89 through 99 Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 230 through 259 Processing helix chain 'C' and resid 260 through 262 No H-bonds generated for 'chain 'C' and resid 260 through 262' Processing helix chain 'C' and resid 287 through 302 Processing helix chain 'C' and resid 328 through 359 removed outlier: 3.628A pdb=" N ALA C 359 " --> pdb=" O ASP C 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 17 removed outlier: 4.372A pdb=" N TYR D 11 " --> pdb=" O PHE D 7 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU D 12 " --> pdb=" O THR D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 39 Processing helix chain 'D' and resid 67 through 80 removed outlier: 3.589A pdb=" N MET D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 98 removed outlier: 3.679A pdb=" N LEU D 97 " --> pdb=" O ASP D 93 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 93 through 98' Processing helix chain 'D' and resid 99 through 113 Processing helix chain 'D' and resid 122 through 127 removed outlier: 3.530A pdb=" N LEU D 125 " --> pdb=" O PRO D 122 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N CYS D 127 " --> pdb=" O HIS D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 133 Processing helix chain 'D' and resid 143 through 155 Processing helix chain 'D' and resid 157 through 161 Processing helix chain 'D' and resid 168 through 175 Processing helix chain 'E' and resid 44 through 49 removed outlier: 3.744A pdb=" N GLY E 48 " --> pdb=" O SER E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 65 removed outlier: 3.834A pdb=" N ARG E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 90 Processing helix chain 'E' and resid 101 through 112 Processing helix chain 'F' and resid 15 through 20 Processing helix chain 'F' and resid 22 through 36 Processing helix chain 'G' and resid 33 through 36 Processing helix chain 'G' and resid 53 through 60 Processing helix chain 'G' and resid 61 through 63 No H-bonds generated for 'chain 'G' and resid 61 through 63' Processing helix chain 'H' and resid 13 through 16 Processing helix chain 'H' and resid 17 through 33 Processing helix chain 'H' and resid 51 through 58 removed outlier: 3.567A pdb=" N LEU H 58 " --> pdb=" O LEU H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 73 removed outlier: 3.558A pdb=" N THR H 73 " --> pdb=" O HIS H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 80 removed outlier: 3.507A pdb=" N TYR H 79 " --> pdb=" O ASP H 75 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 removed outlier: 6.121A pdb=" N GLY A 4 " --> pdb=" O MET B1209 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ASP B1211 " --> pdb=" O GLY A 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1404 through 1406 Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36 removed outlier: 3.885A pdb=" N LEU A 39 " --> pdb=" O GLU A 36 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 74 through 83 removed outlier: 6.036A pdb=" N LYS A 199 " --> pdb=" O MET A 78 " (cutoff:3.500A) removed outlier: 10.603A pdb=" N ALA A 80 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 10.060A pdb=" N VAL A 197 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 143 through 146 removed outlier: 4.307A pdb=" N PHE A 154 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 317 through 318 Processing sheet with id=AA7, first strand: chain 'B' and resid 1120 through 1121 removed outlier: 7.297A pdb=" N PHE A 444 " --> pdb=" O ARG A 324 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N THR A 326 " --> pdb=" O PHE A 444 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N MET A 446 " --> pdb=" O THR A 326 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N CYS A 328 " --> pdb=" O MET A 446 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 349 through 353 removed outlier: 3.873A pdb=" N ARG A 378 " --> pdb=" O TYR A 406 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ASP A 408 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N CYS A 376 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 514 through 515 Processing sheet with id=AB1, first strand: chain 'A' and resid 521 through 523 Processing sheet with id=AB2, first strand: chain 'A' and resid 567 through 569 removed outlier: 6.822A pdb=" N GLN A 592 " --> pdb=" O ILE A 599 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 753 through 754 Processing sheet with id=AB4, first strand: chain 'A' and resid 836 through 838 removed outlier: 6.383A pdb=" N VAL A 844 " --> pdb=" O VAL A 851 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 866 through 869 Processing sheet with id=AB6, first strand: chain 'A' and resid 1267 through 1278 removed outlier: 6.432A pdb=" N ASN A1267 " --> pdb=" O THR A1295 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR A1295 " --> pdb=" O ASN A1267 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ASN A1269 " --> pdb=" O ILE A1293 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE A1293 " --> pdb=" O ASN A1269 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL A1271 " --> pdb=" O TYR A1291 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N TYR A1291 " --> pdb=" O VAL A1271 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU A1273 " --> pdb=" O ASN A1289 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASN A1289 " --> pdb=" O LEU A1273 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AB8, first strand: chain 'A' and resid 1206 through 1210 removed outlier: 5.242A pdb=" N TRP A1174 " --> pdb=" O LEU A1227 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ASN A1173 " --> pdb=" O TYR A1133 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TYR A1133 " --> pdb=" O ASN A1173 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N CYS A1175 " --> pdb=" O LEU A1131 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU A1131 " --> pdb=" O CYS A1175 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ARG A1177 " --> pdb=" O TRP A1129 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N TRP A1129 " --> pdb=" O ARG A1177 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLU A1179 " --> pdb=" O LEU A1127 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TYR A1133 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU G 38 " --> pdb=" O TYR A1133 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1428 through 1431 removed outlier: 6.869A pdb=" N ILE E 132 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL E 125 " --> pdb=" O GLN E 130 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLN E 130 " --> pdb=" O VAL E 125 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N THR E 56 " --> pdb=" O LYS E 131 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL E 133 " --> pdb=" O THR E 56 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL E 58 " --> pdb=" O VAL E 133 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ILE E 135 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N PHE B1239 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N ILE E 59 " --> pdb=" O PHE B1239 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 95 through 96 removed outlier: 3.905A pdb=" N ASN B 95 " --> pdb=" O ASN B 129 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 100 through 101 Processing sheet with id=AC3, first strand: chain 'B' and resid 193 through 195 Processing sheet with id=AC4, first strand: chain 'B' and resid 416 through 419 removed outlier: 3.787A pdb=" N LEU B 204 " --> pdb=" O THR B 523 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 213 through 216 removed outlier: 3.825A pdb=" N ILE B 228 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR B 250 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLN B 245 " --> pdb=" O ASN B 261 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 576 through 577 Processing sheet with id=AC7, first strand: chain 'B' and resid 710 through 712 removed outlier: 3.648A pdb=" N LEU B 674 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 596 through 597 removed outlier: 4.618A pdb=" N VAL B 615 " --> pdb=" O ILE B 622 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N CYS B 624 " --> pdb=" O ALA B 613 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ALA B 613 " --> pdb=" O CYS B 624 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 823 through 826 removed outlier: 3.826A pdb=" N ARG B 823 " --> pdb=" O TYR B 882 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ARG B 983 " --> pdb=" O ASP B 966 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR B 925 " --> pdb=" O VAL B 965 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 834 through 835 Processing sheet with id=AD2, first strand: chain 'B' and resid 1085 through 1086 removed outlier: 6.117A pdb=" N VAL B 865 " --> pdb=" O ALA B1006 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU B1008 " --> pdb=" O VAL B 865 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N PHE B1102 " --> pdb=" O TYR B 853 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 932 through 933 removed outlier: 3.512A pdb=" N VAL B 955 " --> pdb=" O ILE B 933 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1017 through 1018 Processing sheet with id=AD5, first strand: chain 'B' and resid 1188 through 1190 Processing sheet with id=AD6, first strand: chain 'C' and resid 5 through 12 removed outlier: 4.578A pdb=" N ASN C 7 " --> pdb=" O ASP C 46 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL C 39 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA C 225 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ARG C 218 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE C 184 " --> pdb=" O ARG C 218 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLY C 220 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 68 through 73 removed outlier: 4.671A pdb=" N ILE C 159 " --> pdb=" O LYS C 79 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 68 through 73 removed outlier: 4.124A pdb=" N ASP C 162 " --> pdb=" O PHE C 111 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N PHE C 111 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 123 through 126 Processing sheet with id=AE1, first strand: chain 'C' and resid 267 through 271 Processing sheet with id=AE2, first strand: chain 'D' and resid 20 through 21 removed outlier: 6.354A pdb=" N ILE D 52 " --> pdb=" O GLU D 87 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ILE D 89 " --> pdb=" O ILE D 52 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N SER D 54 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ILE D 91 " --> pdb=" O SER D 54 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE D 56 " --> pdb=" O ILE D 91 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 138 through 142 removed outlier: 3.713A pdb=" N LYS D 138 " --> pdb=" O GLU D 185 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N PHE D 181 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N MET D 162 " --> pdb=" O PHE D 199 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N THR D 201 " --> pdb=" O MET D 162 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE D 164 " --> pdb=" O THR D 201 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 2 through 10 removed outlier: 6.208A pdb=" N SER F 75 " --> pdb=" O VAL F 51 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N VAL F 51 " --> pdb=" O SER F 75 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL F 77 " --> pdb=" O THR F 49 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N THR F 49 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N SER F 79 " --> pdb=" O ASN F 47 " (cutoff:3.500A) removed outlier: 9.520A pdb=" N ASN F 47 " --> pdb=" O SER F 79 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 86 through 91 removed outlier: 5.031A pdb=" N VAL F 110 " --> pdb=" O SER F 104 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY F 152 " --> pdb=" O VAL F 113 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL F 130 " --> pdb=" O ALA F 89 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ALA F 89 " --> pdb=" O VAL F 130 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 68 through 70 1209 hydrogen bonds defined for protein. 3318 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: 12.78 Time building geometry restraints manager: 8.01 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: 9073 1.34 - 1.46: 5416 1.46 - 1.58: 13420 1.58 - 1.70: 2 1.70 - 1.82: 275 Bond restraints: 28186 Sorted by residual: bond pdb=" CA ALA B1007 " pdb=" CB ALA B1007 " ideal model delta sigma weight residual 1.530 1.475 0.055 2.20e-02 2.07e+03 6.20e+00 bond pdb=" CB PRO A1168 " pdb=" CG PRO A1168 " ideal model delta sigma weight residual 1.492 1.610 -0.118 5.00e-02 4.00e+02 5.53e+00 bond pdb=" CB GLU A 476 " pdb=" CG GLU A 476 " ideal model delta sigma weight residual 1.520 1.457 0.063 3.00e-02 1.11e+03 4.34e+00 bond pdb=" CB PRO A1220 " pdb=" CG PRO A1220 " ideal model delta sigma weight residual 1.492 1.590 -0.098 5.00e-02 4.00e+02 3.84e+00 bond pdb=" CG PRO A1220 " pdb=" CD PRO A1220 " ideal model delta sigma weight residual 1.503 1.563 -0.060 3.40e-02 8.65e+02 3.08e+00 ... (remaining 28181 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 37684 2.36 - 4.73: 405 4.73 - 7.09: 36 7.09 - 9.46: 11 9.46 - 11.82: 5 Bond angle restraints: 38141 Sorted by residual: angle pdb=" C VAL E 125 " pdb=" N THR E 126 " pdb=" CA THR E 126 " ideal model delta sigma weight residual 120.49 132.31 -11.82 1.42e+00 4.96e-01 6.93e+01 angle pdb=" CA PRO A1168 " pdb=" N PRO A1168 " pdb=" CD PRO A1168 " ideal model delta sigma weight residual 112.00 103.35 8.65 1.40e+00 5.10e-01 3.82e+01 angle pdb=" CA GLU C 275 " pdb=" CB GLU C 275 " pdb=" CG GLU C 275 " ideal model delta sigma weight residual 114.10 125.23 -11.13 2.00e+00 2.50e-01 3.09e+01 angle pdb=" C MET D 192 " pdb=" N HIS D 193 " pdb=" CA HIS D 193 " ideal model delta sigma weight residual 121.54 131.68 -10.14 1.91e+00 2.74e-01 2.82e+01 angle pdb=" CA PRO A1220 " pdb=" N PRO A1220 " pdb=" CD PRO A1220 " ideal model delta sigma weight residual 112.00 104.94 7.06 1.40e+00 5.10e-01 2.54e+01 ... (remaining 38136 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.04: 15015 18.04 - 36.08: 1622 36.08 - 54.13: 412 54.13 - 72.17: 90 72.17 - 90.21: 39 Dihedral angle restraints: 17178 sinusoidal: 7046 harmonic: 10132 Sorted by residual: dihedral pdb=" CA ILE A1422 " pdb=" C ILE A1422 " pdb=" N GLY A1423 " pdb=" CA GLY A1423 " ideal model delta harmonic sigma weight residual -180.00 -141.50 -38.50 0 5.00e+00 4.00e-02 5.93e+01 dihedral pdb=" CA ILE B 227 " pdb=" C ILE B 227 " pdb=" N ILE B 228 " pdb=" CA ILE B 228 " ideal model delta harmonic sigma weight residual 180.00 146.55 33.45 0 5.00e+00 4.00e-02 4.48e+01 dihedral pdb=" CA ALA B1007 " pdb=" C ALA B1007 " pdb=" N LEU B1008 " pdb=" CA LEU B1008 " ideal model delta harmonic sigma weight residual 180.00 153.61 26.39 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 17175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3491 0.058 - 0.116: 757 0.116 - 0.174: 78 0.174 - 0.232: 3 0.232 - 0.290: 1 Chirality restraints: 4330 Sorted by residual: chirality pdb=" CB ILE A1074 " pdb=" CA ILE A1074 " pdb=" CG1 ILE A1074 " pdb=" CG2 ILE A1074 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CA TYR F 69 " pdb=" N TYR F 69 " pdb=" C TYR F 69 " pdb=" CB TYR F 69 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB ILE B 622 " pdb=" CA ILE B 622 " pdb=" CG1 ILE B 622 " pdb=" CG2 ILE B 622 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.41e-01 ... (remaining 4327 not shown) Planarity restraints: 4906 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A1219 " -0.065 5.00e-02 4.00e+02 9.38e-02 1.41e+01 pdb=" N PRO A1220 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO A1220 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A1220 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A1167 " 0.045 5.00e-02 4.00e+02 6.39e-02 6.53e+00 pdb=" N PRO A1168 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A1168 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A1168 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 11 " 0.038 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PRO B 12 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 12 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 12 " 0.032 5.00e-02 4.00e+02 ... (remaining 4903 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 175 2.50 - 3.10: 19882 3.10 - 3.70: 44231 3.70 - 4.30: 68063 4.30 - 4.90: 111294 Nonbonded interactions: 243645 Sorted by model distance: nonbonded pdb=" OD1 ASP A 459 " pdb="MG MG A1503 " model vdw 1.896 2.170 nonbonded pdb=" OD1 ASP A 457 " pdb="MG MG A1503 " model vdw 1.931 2.170 nonbonded pdb=" OG1 THR A1424 " pdb=" O ALA B1160 " model vdw 2.086 3.040 nonbonded pdb=" OD2 ASP A 332 " pdb=" OH TYR B 859 " model vdw 2.122 3.040 nonbonded pdb=" O HIS B1152 " pdb=" OG1 THR B1156 " model vdw 2.127 3.040 ... (remaining 243640 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 12.150 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: 0.020 Extract box with map and model: 1.030 Check model and map are aligned: 0.190 Set scattering table: 0.220 Process input model: 68.890 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.100 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:12.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 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 0.118 28210 Z= 0.241 Angle : 0.653 12.095 38174 Z= 0.338 Chirality : 0.047 0.290 4330 Planarity : 0.005 0.094 4906 Dihedral : 16.527 90.211 10630 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.94 % Favored : 95.77 % Rotamer: Outliers : 2.01 % Allowed : 18.13 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.14), residues: 3430 helix: 0.23 (0.14), residues: 1261 sheet: -0.28 (0.22), residues: 510 loop : -0.08 (0.16), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A1154 HIS 0.026 0.002 HIS D 193 PHE 0.028 0.002 PHE A 918 TYR 0.023 0.002 TYR F 69 ARG 0.007 0.001 ARG B1036 Details of bonding type rmsd hydrogen bonds : bond 0.19863 ( 1203) hydrogen bonds : angle 7.28111 ( 3318) metal coordination : bond 0.00947 ( 24) metal coordination : angle 4.53522 ( 33) covalent geometry : bond 0.00580 (28186) covalent geometry : angle 0.63941 (38141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 353 time to evaluate : 3.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 643 LYS cc_start: 0.7768 (pttt) cc_final: 0.7505 (ptpt) REVERT: C 330 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7184 (pp20) REVERT: D 86 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7205 (tt0) outliers start: 62 outliers final: 52 residues processed: 408 average time/residue: 1.3600 time to fit residues: 649.4096 Evaluate side-chains 398 residues out of total 3077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 344 time to evaluate : 2.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 67 LYS Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 1092 SER Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1188 LYS Chi-restraints excluded: chain A residue 1205 ASN Chi-restraints excluded: chain A residue 1252 ASP Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 609 ARG Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1080 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain B residue 1164 ILE Chi-restraints excluded: chain B residue 1198 CYS Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain D residue 33 GLN Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain G residue 52 LYS Chi-restraints excluded: chain G residue 103 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 288 optimal weight: 4.9990 chunk 259 optimal weight: 0.8980 chunk 143 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 138 optimal weight: 0.7980 chunk 268 optimal weight: 3.9990 chunk 103 optimal weight: 20.0000 chunk 162 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 chunk 310 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN A 420 GLN A 532 GLN A 721 ASN A 742 ASN A 744 ASN A 980 GLN A1062 HIS A1078 GLN A1090 GLN A1161 ASN B 101 HIS B 419 HIS ** B 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 761 HIS B 845 ASN ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN G 19 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.134101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.095182 restraints weight = 35518.474| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.89 r_work: 0.3064 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.0755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 28210 Z= 0.211 Angle : 0.629 13.825 38174 Z= 0.326 Chirality : 0.047 0.220 4330 Planarity : 0.005 0.050 4906 Dihedral : 7.168 76.523 3876 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.88 % Favored : 95.86 % Rotamer: Outliers : 4.22 % Allowed : 15.60 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.14), residues: 3430 helix: 0.60 (0.14), residues: 1289 sheet: -0.39 (0.22), residues: 495 loop : -0.06 (0.16), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 466 HIS 0.008 0.001 HIS D 193 PHE 0.029 0.002 PHE A 918 TYR 0.025 0.002 TYR F 69 ARG 0.005 0.000 ARG H 67 Details of bonding type rmsd hydrogen bonds : bond 0.05209 ( 1203) hydrogen bonds : angle 5.48613 ( 3318) metal coordination : bond 0.00914 ( 24) metal coordination : angle 4.62940 ( 33) covalent geometry : bond 0.00494 (28186) covalent geometry : angle 0.61477 (38141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 361 time to evaluate : 2.933 Fit side-chains revert: symmetry clash REVERT: A 383 ILE cc_start: 0.8007 (OUTLIER) cc_final: 0.7735 (pp) REVERT: A 1093 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7538 (mm-30) REVERT: A 1155 MET cc_start: 0.7861 (mtp) cc_final: 0.7627 (mtp) REVERT: A 1188 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.7924 (mtpp) REVERT: A 1223 ILE cc_start: 0.7966 (OUTLIER) cc_final: 0.7483 (mt) REVERT: B 567 MET cc_start: 0.7550 (OUTLIER) cc_final: 0.6752 (mmp) REVERT: B 643 LYS cc_start: 0.7850 (pttt) cc_final: 0.7486 (ptpt) REVERT: B 1234 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.7631 (mp) REVERT: C 330 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7245 (pp20) REVERT: D 20 VAL cc_start: 0.8353 (m) cc_final: 0.8149 (m) REVERT: D 46 GLU cc_start: 0.7707 (tt0) cc_final: 0.6921 (pt0) REVERT: D 80 ASN cc_start: 0.8325 (OUTLIER) cc_final: 0.7899 (p0) REVERT: D 86 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7332 (tt0) REVERT: D 108 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7912 (tp30) REVERT: F 133 GLN cc_start: 0.3329 (OUTLIER) cc_final: 0.2485 (mt0) REVERT: G 1 MET cc_start: 0.5244 (OUTLIER) cc_final: 0.4741 (tmm) REVERT: G 28 GLU cc_start: 0.7321 (tp30) cc_final: 0.7093 (tp30) REVERT: G 101 MET cc_start: 0.7507 (OUTLIER) cc_final: 0.7254 (tmm) REVERT: H 28 TYR cc_start: 0.8573 (t80) cc_final: 0.8370 (t80) outliers start: 130 outliers final: 56 residues processed: 443 average time/residue: 1.4256 time to fit residues: 743.7572 Evaluate side-chains 409 residues out of total 3077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 340 time to evaluate : 3.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1092 SER Chi-restraints excluded: chain A residue 1093 GLU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1188 LYS Chi-restraints excluded: chain A residue 1206 THR Chi-restraints excluded: chain A residue 1223 ILE Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1252 ASP Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1346 LYS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1088 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain B residue 1198 CYS Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain B residue 1234 LEU Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 270 PHE Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 69 TYR Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 133 GLN Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 101 MET Chi-restraints excluded: chain G residue 103 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 124 optimal weight: 4.9990 chunk 201 optimal weight: 0.5980 chunk 12 optimal weight: 8.9990 chunk 157 optimal weight: 0.9990 chunk 136 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 244 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 262 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 ASN A1078 GLN A1161 ASN B 321 GLN ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 GLN B 845 ASN B1134 GLN C 241 ASN ** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN G 19 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.137521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.100828 restraints weight = 36929.432| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.04 r_work: 0.3138 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28210 Z= 0.140 Angle : 0.565 14.691 38174 Z= 0.290 Chirality : 0.045 0.210 4330 Planarity : 0.004 0.053 4906 Dihedral : 6.249 73.953 3828 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.82 % Favored : 95.89 % Rotamer: Outliers : 3.64 % Allowed : 16.74 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.14), residues: 3430 helix: 0.85 (0.14), residues: 1290 sheet: -0.45 (0.22), residues: 510 loop : -0.00 (0.16), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 466 HIS 0.006 0.001 HIS D 193 PHE 0.027 0.001 PHE A 918 TYR 0.021 0.001 TYR F 69 ARG 0.004 0.000 ARG B1036 Details of bonding type rmsd hydrogen bonds : bond 0.04274 ( 1203) hydrogen bonds : angle 5.15155 ( 3318) metal coordination : bond 0.00614 ( 24) metal coordination : angle 4.05702 ( 33) covalent geometry : bond 0.00315 (28186) covalent geometry : angle 0.55279 (38141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 381 time to evaluate : 3.673 Fit side-chains REVERT: A 78 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.7601 (mmm) REVERT: A 383 ILE cc_start: 0.8016 (OUTLIER) cc_final: 0.7719 (pp) REVERT: A 716 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8391 (mm) REVERT: A 1155 MET cc_start: 0.7777 (mtp) cc_final: 0.7497 (mtp) REVERT: A 1188 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.7888 (mtpp) REVERT: A 1370 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8204 (mm-30) REVERT: B 19 GLU cc_start: 0.8207 (mp0) cc_final: 0.7857 (mm-30) REVERT: B 279 PHE cc_start: 0.6940 (m-80) cc_final: 0.6309 (t80) REVERT: B 567 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.6701 (mmp) REVERT: B 643 LYS cc_start: 0.7868 (pttt) cc_final: 0.7652 (ptpt) REVERT: B 969 MET cc_start: 0.6880 (OUTLIER) cc_final: 0.6378 (mpt) REVERT: B 1234 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.7582 (mp) REVERT: C 266 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7966 (pm20) REVERT: C 275 GLU cc_start: 0.7325 (tp30) cc_final: 0.7004 (tp30) REVERT: C 330 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7258 (pp20) REVERT: D 46 GLU cc_start: 0.7629 (tt0) cc_final: 0.6804 (pt0) REVERT: D 80 ASN cc_start: 0.8278 (OUTLIER) cc_final: 0.7839 (p0) REVERT: D 108 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7958 (tp30) REVERT: D 123 TYR cc_start: 0.8635 (m-10) cc_final: 0.8414 (m-10) REVERT: E 64 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8536 (mt-10) REVERT: G 1 MET cc_start: 0.5218 (OUTLIER) cc_final: 0.4790 (tmm) REVERT: G 21 ILE cc_start: 0.7469 (OUTLIER) cc_final: 0.7113 (mm) REVERT: G 28 GLU cc_start: 0.7353 (tp30) cc_final: 0.7079 (tp30) REVERT: G 101 MET cc_start: 0.7508 (OUTLIER) cc_final: 0.7305 (tmm) outliers start: 112 outliers final: 49 residues processed: 446 average time/residue: 1.8283 time to fit residues: 960.8659 Evaluate side-chains 411 residues out of total 3077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 346 time to evaluate : 4.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1188 LYS Chi-restraints excluded: chain A residue 1205 ASN Chi-restraints excluded: chain A residue 1252 ASP Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1346 LYS Chi-restraints excluded: chain A residue 1370 GLU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 969 MET Chi-restraints excluded: chain B residue 1088 MET Chi-restraints excluded: chain B residue 1164 ILE Chi-restraints excluded: chain B residue 1198 CYS Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain B residue 1234 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 270 PHE Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 69 TYR Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 97 ARG Chi-restraints excluded: chain G residue 101 MET Chi-restraints excluded: chain G residue 103 ASN Chi-restraints excluded: chain H residue 23 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 167 optimal weight: 9.9990 chunk 134 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 186 optimal weight: 8.9990 chunk 58 optimal weight: 0.5980 chunk 144 optimal weight: 9.9990 chunk 309 optimal weight: 3.9990 chunk 240 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 187 optimal weight: 0.9980 chunk 288 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1078 GLN A1161 ASN B 364 GLN B 845 ASN ** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN G 19 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.136678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.099102 restraints weight = 35917.242| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.75 r_work: 0.3123 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 28210 Z= 0.154 Angle : 0.570 14.486 38174 Z= 0.290 Chirality : 0.045 0.224 4330 Planarity : 0.004 0.051 4906 Dihedral : 5.629 74.685 3806 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.88 % Favored : 95.83 % Rotamer: Outliers : 4.06 % Allowed : 17.26 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.14), residues: 3430 helix: 0.92 (0.14), residues: 1289 sheet: -0.50 (0.22), residues: 514 loop : 0.03 (0.16), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 466 HIS 0.008 0.001 HIS D 193 PHE 0.027 0.002 PHE A 918 TYR 0.022 0.001 TYR F 69 ARG 0.005 0.000 ARG F 73 Details of bonding type rmsd hydrogen bonds : bond 0.04106 ( 1203) hydrogen bonds : angle 5.06106 ( 3318) metal coordination : bond 0.00672 ( 24) metal coordination : angle 4.25788 ( 33) covalent geometry : bond 0.00357 (28186) covalent geometry : angle 0.55599 (38141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 369 time to evaluate : 2.975 Fit side-chains REVERT: A 396 ASP cc_start: 0.5628 (OUTLIER) cc_final: 0.5085 (t0) REVERT: A 424 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8309 (mp0) REVERT: A 1155 MET cc_start: 0.7762 (mtp) cc_final: 0.7509 (mtp) REVERT: A 1188 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.7781 (mtpp) REVERT: A 1196 ILE cc_start: 0.8528 (mm) cc_final: 0.8303 (mm) REVERT: A 1223 ILE cc_start: 0.8061 (OUTLIER) cc_final: 0.7616 (mt) REVERT: A 1370 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8195 (mm-30) REVERT: B 479 ASN cc_start: 0.5326 (OUTLIER) cc_final: 0.4967 (t0) REVERT: B 567 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.6829 (mmp) REVERT: B 1113 LYS cc_start: 0.8021 (mmtt) cc_final: 0.7655 (mmpt) REVERT: B 1234 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.7613 (mp) REVERT: C 266 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7998 (pm20) REVERT: C 275 GLU cc_start: 0.7259 (tp30) cc_final: 0.7016 (tp30) REVERT: D 46 GLU cc_start: 0.7653 (tt0) cc_final: 0.7314 (tt0) REVERT: D 86 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7431 (tt0) REVERT: D 88 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8564 (mp) REVERT: D 108 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7952 (tp30) REVERT: D 123 TYR cc_start: 0.8635 (m-10) cc_final: 0.8402 (m-10) REVERT: E 64 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8437 (mt-10) REVERT: F 54 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.7341 (ptm-80) REVERT: F 133 GLN cc_start: 0.3466 (OUTLIER) cc_final: 0.2555 (mt0) REVERT: G 1 MET cc_start: 0.5186 (OUTLIER) cc_final: 0.4936 (tmm) REVERT: G 21 ILE cc_start: 0.7458 (OUTLIER) cc_final: 0.7102 (mm) REVERT: G 28 GLU cc_start: 0.7416 (tp30) cc_final: 0.7066 (tp30) outliers start: 125 outliers final: 55 residues processed: 442 average time/residue: 1.3404 time to fit residues: 698.8355 Evaluate side-chains 417 residues out of total 3077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 346 time to evaluate : 3.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1188 LYS Chi-restraints excluded: chain A residue 1205 ASN Chi-restraints excluded: chain A residue 1223 ILE Chi-restraints excluded: chain A residue 1252 ASP Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1346 LYS Chi-restraints excluded: chain A residue 1370 GLU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 479 ASN Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 1088 MET Chi-restraints excluded: chain B residue 1164 ILE Chi-restraints excluded: chain B residue 1198 CYS Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain B residue 1234 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 270 PHE Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain F residue 69 TYR Chi-restraints excluded: chain F residue 133 GLN Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 97 ARG Chi-restraints excluded: chain H residue 23 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 119 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 244 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 150 optimal weight: 5.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A1078 GLN A1161 ASN ** B 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 ASN ** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 GLN E 130 GLN G 19 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.136075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.098546 restraints weight = 35605.547| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.74 r_work: 0.3114 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 28210 Z= 0.175 Angle : 0.587 14.469 38174 Z= 0.298 Chirality : 0.046 0.237 4330 Planarity : 0.004 0.052 4906 Dihedral : 5.544 75.960 3799 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.82 % Favored : 95.89 % Rotamer: Outliers : 3.93 % Allowed : 17.84 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.14), residues: 3430 helix: 0.91 (0.14), residues: 1288 sheet: -0.45 (0.23), residues: 492 loop : 0.01 (0.16), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 466 HIS 0.007 0.001 HIS D 193 PHE 0.028 0.002 PHE A 918 TYR 0.023 0.001 TYR F 69 ARG 0.005 0.000 ARG H 67 Details of bonding type rmsd hydrogen bonds : bond 0.04141 ( 1203) hydrogen bonds : angle 5.02728 ( 3318) metal coordination : bond 0.00723 ( 24) metal coordination : angle 4.52091 ( 33) covalent geometry : bond 0.00409 (28186) covalent geometry : angle 0.57243 (38141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 364 time to evaluate : 3.422 Fit side-chains revert: symmetry clash REVERT: A 383 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7843 (pp) REVERT: A 396 ASP cc_start: 0.5644 (OUTLIER) cc_final: 0.5117 (t0) REVERT: A 424 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8339 (mp0) REVERT: A 1196 ILE cc_start: 0.8534 (mm) cc_final: 0.8294 (mm) REVERT: A 1370 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8242 (mm-30) REVERT: B 479 ASN cc_start: 0.5352 (OUTLIER) cc_final: 0.4964 (t0) REVERT: B 567 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.6878 (mmp) REVERT: B 643 LYS cc_start: 0.7858 (ptpt) cc_final: 0.7517 (pttt) REVERT: B 969 MET cc_start: 0.6736 (OUTLIER) cc_final: 0.6270 (mpt) REVERT: B 982 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7906 (ttm) REVERT: B 1113 LYS cc_start: 0.8018 (mmtt) cc_final: 0.7651 (mmpt) REVERT: B 1234 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.7590 (mp) REVERT: C 266 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8016 (pm20) REVERT: D 46 GLU cc_start: 0.7714 (tt0) cc_final: 0.7349 (tt0) REVERT: D 86 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7464 (tt0) REVERT: D 88 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8570 (mp) REVERT: D 108 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7965 (tp30) REVERT: E 64 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8433 (mt-10) REVERT: F 54 ARG cc_start: 0.9146 (OUTLIER) cc_final: 0.7598 (ptm-80) REVERT: F 133 GLN cc_start: 0.3426 (OUTLIER) cc_final: 0.2455 (mt0) REVERT: G 21 ILE cc_start: 0.7439 (OUTLIER) cc_final: 0.7069 (mm) REVERT: G 28 GLU cc_start: 0.7374 (tp30) cc_final: 0.6881 (tp30) outliers start: 121 outliers final: 63 residues processed: 440 average time/residue: 1.3737 time to fit residues: 714.3762 Evaluate side-chains 423 residues out of total 3077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 344 time to evaluate : 3.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1252 ASP Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1346 LYS Chi-restraints excluded: chain A residue 1370 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 410 ARG Chi-restraints excluded: chain B residue 479 ASN Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 567 MET Chi-restraints excluded: chain B residue 609 ARG Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 969 MET Chi-restraints excluded: chain B residue 982 MET Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1088 MET Chi-restraints excluded: chain B residue 1164 ILE Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain B residue 1234 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 270 PHE Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain F residue 69 TYR Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 133 GLN Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 97 ARG Chi-restraints excluded: chain G residue 103 ASN Chi-restraints excluded: chain H residue 23 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 101 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 305 optimal weight: 0.9990 chunk 266 optimal weight: 0.9990 chunk 150 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 307 optimal weight: 0.7980 chunk 206 optimal weight: 9.9990 chunk 197 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A1078 GLN A1161 ASN ** B 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 HIS B 364 GLN B 516 ASN B 845 ASN ** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN G 19 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.135998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.098662 restraints weight = 35624.668| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.73 r_work: 0.3119 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 28210 Z= 0.172 Angle : 0.587 14.658 38174 Z= 0.296 Chirality : 0.046 0.244 4330 Planarity : 0.004 0.052 4906 Dihedral : 5.453 76.667 3794 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.85 % Favored : 95.86 % Rotamer: Outliers : 3.83 % Allowed : 18.46 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.14), residues: 3430 helix: 0.94 (0.14), residues: 1285 sheet: -0.49 (0.22), residues: 486 loop : 0.01 (0.16), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1154 HIS 0.009 0.001 HIS D 193 PHE 0.028 0.002 PHE A 918 TYR 0.023 0.001 TYR F 69 ARG 0.005 0.000 ARG H 67 Details of bonding type rmsd hydrogen bonds : bond 0.04077 ( 1203) hydrogen bonds : angle 4.99511 ( 3318) metal coordination : bond 0.00728 ( 24) metal coordination : angle 4.46508 ( 33) covalent geometry : bond 0.00401 (28186) covalent geometry : angle 0.57249 (38141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 359 time to evaluate : 3.163 Fit side-chains revert: symmetry clash REVERT: A 34 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.6999 (mp) REVERT: A 383 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7844 (pp) REVERT: A 396 ASP cc_start: 0.5621 (OUTLIER) cc_final: 0.5103 (t0) REVERT: A 424 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8324 (mp0) REVERT: A 1196 ILE cc_start: 0.8581 (mm) cc_final: 0.8361 (mm) REVERT: A 1370 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8217 (mm-30) REVERT: B 279 PHE cc_start: 0.7215 (m-80) cc_final: 0.6923 (m-80) REVERT: B 479 ASN cc_start: 0.5350 (OUTLIER) cc_final: 0.4964 (t0) REVERT: B 643 LYS cc_start: 0.7871 (ptpt) cc_final: 0.7482 (pttt) REVERT: B 702 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7883 (tt0) REVERT: B 969 MET cc_start: 0.6674 (OUTLIER) cc_final: 0.6202 (mpt) REVERT: B 982 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7915 (ttm) REVERT: B 1234 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.7586 (mp) REVERT: C 266 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8012 (pm20) REVERT: C 330 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7169 (pp20) REVERT: D 46 GLU cc_start: 0.7670 (tt0) cc_final: 0.6930 (pt0) REVERT: D 86 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7462 (tt0) REVERT: D 88 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8572 (mp) REVERT: D 108 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7956 (tp30) REVERT: E 64 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8445 (mt-10) REVERT: F 54 ARG cc_start: 0.9147 (OUTLIER) cc_final: 0.7451 (ptm-80) REVERT: F 133 GLN cc_start: 0.3432 (OUTLIER) cc_final: 0.2424 (mt0) REVERT: G 21 ILE cc_start: 0.7520 (OUTLIER) cc_final: 0.7163 (mm) REVERT: G 28 GLU cc_start: 0.7313 (tp30) cc_final: 0.6893 (tp30) REVERT: G 81 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8321 (tp) outliers start: 118 outliers final: 66 residues processed: 435 average time/residue: 1.3518 time to fit residues: 690.4919 Evaluate side-chains 427 residues out of total 3077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 342 time to evaluate : 3.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1205 ASN Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1252 ASP Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1346 LYS Chi-restraints excluded: chain A residue 1370 GLU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 410 ARG Chi-restraints excluded: chain B residue 479 ASN Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 609 ARG Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 969 MET Chi-restraints excluded: chain B residue 982 MET Chi-restraints excluded: chain B residue 1088 MET Chi-restraints excluded: chain B residue 1164 ILE Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain B residue 1234 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 270 PHE Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain F residue 69 TYR Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 133 GLN Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 97 ARG Chi-restraints excluded: chain H residue 23 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 96 optimal weight: 1.9990 chunk 300 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 chunk 168 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 190 optimal weight: 0.8980 chunk 337 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1078 GLN A1161 ASN ** B 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 GLN B 516 ASN B 845 ASN ** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.135838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.098270 restraints weight = 35682.683| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.74 r_work: 0.3111 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 28210 Z= 0.187 Angle : 0.604 14.510 38174 Z= 0.305 Chirality : 0.046 0.263 4330 Planarity : 0.004 0.052 4906 Dihedral : 5.452 77.447 3792 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.88 % Favored : 95.83 % Rotamer: Outliers : 3.87 % Allowed : 18.78 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.14), residues: 3430 helix: 0.91 (0.14), residues: 1285 sheet: -0.51 (0.22), residues: 486 loop : -0.00 (0.16), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1154 HIS 0.012 0.001 HIS D 193 PHE 0.029 0.002 PHE A 918 TYR 0.024 0.002 TYR F 69 ARG 0.007 0.000 ARG A1124 Details of bonding type rmsd hydrogen bonds : bond 0.04139 ( 1203) hydrogen bonds : angle 5.00317 ( 3318) metal coordination : bond 0.00770 ( 24) metal coordination : angle 4.50805 ( 33) covalent geometry : bond 0.00440 (28186) covalent geometry : angle 0.58959 (38141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 354 time to evaluate : 3.027 Fit side-chains revert: symmetry clash REVERT: A 66 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.6818 (ttm-80) REVERT: A 171 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.6320 (ttp-170) REVERT: A 383 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7843 (pp) REVERT: A 396 ASP cc_start: 0.5600 (OUTLIER) cc_final: 0.5120 (t0) REVERT: A 400 GLU cc_start: 0.7271 (pp20) cc_final: 0.7065 (pp20) REVERT: A 424 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8303 (mp0) REVERT: A 1093 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7689 (mm-30) REVERT: A 1196 ILE cc_start: 0.8613 (mm) cc_final: 0.8363 (mm) REVERT: A 1228 ARG cc_start: 0.6417 (OUTLIER) cc_final: 0.6115 (mtp180) REVERT: A 1370 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8220 (mm-30) REVERT: B 279 PHE cc_start: 0.7170 (m-80) cc_final: 0.6303 (t80) REVERT: B 479 ASN cc_start: 0.5350 (OUTLIER) cc_final: 0.4960 (t0) REVERT: B 643 LYS cc_start: 0.7876 (ptpt) cc_final: 0.7368 (pttt) REVERT: B 702 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7872 (tt0) REVERT: B 969 MET cc_start: 0.6727 (OUTLIER) cc_final: 0.6233 (mpt) REVERT: B 982 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7921 (ttm) REVERT: B 1234 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.7602 (mp) REVERT: C 266 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8007 (pm20) REVERT: C 330 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7233 (pp20) REVERT: D 25 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7537 (mtmt) REVERT: D 46 GLU cc_start: 0.7674 (tt0) cc_final: 0.6929 (pt0) REVERT: D 86 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7438 (tt0) REVERT: D 88 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8558 (mp) REVERT: D 108 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7950 (tp30) REVERT: E 64 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8452 (mt-10) REVERT: F 54 ARG cc_start: 0.9170 (OUTLIER) cc_final: 0.7621 (ptm-80) REVERT: G 21 ILE cc_start: 0.7526 (OUTLIER) cc_final: 0.7144 (mm) REVERT: G 28 GLU cc_start: 0.7337 (tp30) cc_final: 0.6902 (tp30) outliers start: 119 outliers final: 67 residues processed: 433 average time/residue: 1.4030 time to fit residues: 717.3551 Evaluate side-chains 431 residues out of total 3077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 343 time to evaluate : 2.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1092 SER Chi-restraints excluded: chain A residue 1093 GLU Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1189 SER Chi-restraints excluded: chain A residue 1205 ASN Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1252 ASP Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1346 LYS Chi-restraints excluded: chain A residue 1370 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 410 ARG Chi-restraints excluded: chain B residue 479 ASN Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 609 ARG Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 969 MET Chi-restraints excluded: chain B residue 982 MET Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1088 MET Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain B residue 1234 LEU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 270 PHE Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain F residue 69 TYR Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 97 ARG Chi-restraints excluded: chain G residue 103 ASN Chi-restraints excluded: chain H residue 23 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 267 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 313 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 273 optimal weight: 4.9990 chunk 216 optimal weight: 0.1980 chunk 200 optimal weight: 0.7980 chunk 137 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A1078 GLN A1161 ASN ** B 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 GLN B 516 ASN B 845 ASN B1162 GLN ** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.136533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.099145 restraints weight = 35477.574| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.74 r_work: 0.3124 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 28210 Z= 0.159 Angle : 0.593 14.833 38174 Z= 0.299 Chirality : 0.046 0.268 4330 Planarity : 0.004 0.051 4906 Dihedral : 5.375 77.109 3792 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.94 % Favored : 95.77 % Rotamer: Outliers : 3.38 % Allowed : 19.50 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.14), residues: 3430 helix: 0.94 (0.14), residues: 1287 sheet: -0.52 (0.22), residues: 498 loop : 0.01 (0.16), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1154 HIS 0.015 0.001 HIS D 193 PHE 0.028 0.002 PHE A 918 TYR 0.023 0.001 TYR F 69 ARG 0.006 0.000 ARG A1124 Details of bonding type rmsd hydrogen bonds : bond 0.03970 ( 1203) hydrogen bonds : angle 4.96803 ( 3318) metal coordination : bond 0.00649 ( 24) metal coordination : angle 4.32818 ( 33) covalent geometry : bond 0.00372 (28186) covalent geometry : angle 0.57979 (38141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 360 time to evaluate : 3.339 Fit side-chains revert: symmetry clash REVERT: A 66 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.6776 (ttm-80) REVERT: A 171 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.6320 (ttp-170) REVERT: A 383 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7843 (pp) REVERT: A 424 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8289 (mp0) REVERT: A 1196 ILE cc_start: 0.8607 (mm) cc_final: 0.8350 (mm) REVERT: A 1228 ARG cc_start: 0.6390 (mmt90) cc_final: 0.6090 (mtp180) REVERT: A 1252 ASP cc_start: 0.8452 (OUTLIER) cc_final: 0.8184 (OUTLIER) REVERT: A 1370 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8205 (mm-30) REVERT: B 279 PHE cc_start: 0.7108 (m-80) cc_final: 0.6248 (t80) REVERT: B 378 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.6932 (mm110) REVERT: B 479 ASN cc_start: 0.5486 (OUTLIER) cc_final: 0.5015 (t0) REVERT: B 643 LYS cc_start: 0.7838 (ptpt) cc_final: 0.7470 (pttt) REVERT: B 702 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7836 (tt0) REVERT: B 956 MET cc_start: 0.7051 (tpt) cc_final: 0.6818 (tpt) REVERT: B 1234 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.7614 (mp) REVERT: C 266 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8007 (pm20) REVERT: C 330 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7199 (pp20) REVERT: D 25 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7487 (mtmt) REVERT: D 46 GLU cc_start: 0.7665 (tt0) cc_final: 0.7026 (pt0) REVERT: D 86 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7417 (tt0) REVERT: D 108 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7963 (tp30) REVERT: E 64 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8440 (mt-10) REVERT: F 1 MET cc_start: 0.4741 (pmm) cc_final: 0.4489 (pmm) REVERT: F 54 ARG cc_start: 0.9150 (OUTLIER) cc_final: 0.7590 (ptm-80) REVERT: G 28 GLU cc_start: 0.7282 (tp30) cc_final: 0.6695 (tp30) REVERT: G 81 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8308 (tp) outliers start: 104 outliers final: 63 residues processed: 429 average time/residue: 1.3921 time to fit residues: 701.7233 Evaluate side-chains 426 residues out of total 3077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 347 time to evaluate : 3.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1092 SER Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1205 ASN Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1252 ASP Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1346 LYS Chi-restraints excluded: chain A residue 1370 GLU Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 378 GLN Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 479 ASN Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 609 ARG Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1088 MET Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain B residue 1234 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 270 PHE Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain F residue 69 TYR Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 97 ARG Chi-restraints excluded: chain G residue 103 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 121 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 250 optimal weight: 4.9990 chunk 236 optimal weight: 4.9990 chunk 328 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 279 optimal weight: 1.9990 chunk 283 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 172 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1078 GLN A1161 ASN ** B 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 GLN B 845 ASN ** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN F 33 ASN G 19 ASN G 83 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.136478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.099052 restraints weight = 35638.810| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.73 r_work: 0.3122 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 28210 Z= 0.167 Angle : 0.606 14.743 38174 Z= 0.304 Chirality : 0.046 0.283 4330 Planarity : 0.004 0.051 4906 Dihedral : 5.296 77.277 3790 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.79 % Favored : 95.89 % Rotamer: Outliers : 3.18 % Allowed : 20.02 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.14), residues: 3430 helix: 0.94 (0.14), residues: 1287 sheet: -0.44 (0.22), residues: 488 loop : -0.02 (0.16), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1154 HIS 0.020 0.001 HIS D 193 PHE 0.028 0.002 PHE A 918 TYR 0.024 0.001 TYR F 69 ARG 0.007 0.000 ARG A1124 Details of bonding type rmsd hydrogen bonds : bond 0.03986 ( 1203) hydrogen bonds : angle 4.97929 ( 3318) metal coordination : bond 0.00676 ( 24) metal coordination : angle 4.39218 ( 33) covalent geometry : bond 0.00393 (28186) covalent geometry : angle 0.59194 (38141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 356 time to evaluate : 2.908 Fit side-chains revert: symmetry clash REVERT: A 34 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7102 (mp) REVERT: A 66 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.6782 (ttm-80) REVERT: A 78 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.7632 (mmm) REVERT: A 171 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.6303 (ttp-170) REVERT: A 383 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7842 (pp) REVERT: A 424 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8318 (mp0) REVERT: A 1196 ILE cc_start: 0.8613 (mm) cc_final: 0.8357 (mm) REVERT: A 1228 ARG cc_start: 0.6386 (OUTLIER) cc_final: 0.6095 (mtp180) REVERT: A 1252 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.8179 (OUTLIER) REVERT: A 1370 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8198 (mm-30) REVERT: B 19 GLU cc_start: 0.8058 (mp0) cc_final: 0.7736 (pp20) REVERT: B 279 PHE cc_start: 0.7104 (m-80) cc_final: 0.6276 (t80) REVERT: B 378 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.6928 (mm110) REVERT: B 479 ASN cc_start: 0.5520 (OUTLIER) cc_final: 0.5044 (t0) REVERT: B 643 LYS cc_start: 0.7827 (ptpt) cc_final: 0.7463 (pttt) REVERT: B 702 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7809 (tt0) REVERT: B 1234 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.7611 (mp) REVERT: C 266 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8009 (pm20) REVERT: C 330 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7212 (pp20) REVERT: D 1 MET cc_start: 0.5962 (mtp) cc_final: 0.5239 (mpt) REVERT: D 25 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7490 (mtmt) REVERT: D 46 GLU cc_start: 0.7626 (tt0) cc_final: 0.7012 (pt0) REVERT: D 86 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7404 (tt0) REVERT: D 88 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8553 (mp) REVERT: D 108 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7960 (tp30) REVERT: E 64 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8437 (mt-10) REVERT: F 33 ASN cc_start: 0.8050 (t0) cc_final: 0.7799 (t0) REVERT: F 54 ARG cc_start: 0.9172 (OUTLIER) cc_final: 0.7544 (ptm-80) REVERT: G 28 GLU cc_start: 0.7293 (tp30) cc_final: 0.6696 (tp30) REVERT: G 81 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8316 (tp) REVERT: H 28 TYR cc_start: 0.8626 (t80) cc_final: 0.8421 (t80) outliers start: 98 outliers final: 66 residues processed: 422 average time/residue: 1.4380 time to fit residues: 714.1829 Evaluate side-chains 434 residues out of total 3077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 348 time to evaluate : 3.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1092 SER Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1189 SER Chi-restraints excluded: chain A residue 1205 ASN Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1252 ASP Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1346 LYS Chi-restraints excluded: chain A residue 1370 GLU Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 378 GLN Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 479 ASN Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 609 ARG Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1088 MET Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain B residue 1234 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 270 PHE Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain F residue 69 TYR Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 97 ARG Chi-restraints excluded: chain G residue 103 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 303 optimal weight: 0.4980 chunk 268 optimal weight: 4.9990 chunk 281 optimal weight: 5.9990 chunk 214 optimal weight: 5.9990 chunk 174 optimal weight: 1.9990 chunk 277 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 312 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 233 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A1078 GLN A1111 GLN A1161 ASN ** B 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 GLN B 845 ASN ** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 ASN G 83 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.137821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.100459 restraints weight = 35489.995| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.74 r_work: 0.3145 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28210 Z= 0.135 Angle : 0.590 14.987 38174 Z= 0.296 Chirality : 0.045 0.279 4330 Planarity : 0.004 0.052 4906 Dihedral : 5.161 76.043 3790 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.91 % Favored : 95.80 % Rotamer: Outliers : 2.73 % Allowed : 20.67 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.14), residues: 3430 helix: 1.01 (0.14), residues: 1286 sheet: -0.42 (0.22), residues: 499 loop : 0.04 (0.16), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A1154 HIS 0.016 0.001 HIS D 193 PHE 0.026 0.001 PHE A 918 TYR 0.021 0.001 TYR B 250 ARG 0.007 0.000 ARG A1124 Details of bonding type rmsd hydrogen bonds : bond 0.03739 ( 1203) hydrogen bonds : angle 4.90984 ( 3318) metal coordination : bond 0.00525 ( 24) metal coordination : angle 4.14281 ( 33) covalent geometry : bond 0.00311 (28186) covalent geometry : angle 0.57716 (38141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 358 time to evaluate : 3.177 Fit side-chains revert: symmetry clash REVERT: A 34 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.7021 (mp) REVERT: A 66 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.6795 (ttm-80) REVERT: A 171 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.6317 (ttp-170) REVERT: A 383 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7823 (pp) REVERT: A 424 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8295 (mp0) REVERT: A 582 MET cc_start: 0.8789 (ptm) cc_final: 0.8564 (ptm) REVERT: A 1252 ASP cc_start: 0.8481 (t70) cc_final: 0.8237 (OUTLIER) REVERT: A 1370 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8143 (mm-30) REVERT: B 19 GLU cc_start: 0.8027 (mp0) cc_final: 0.7578 (pp20) REVERT: B 279 PHE cc_start: 0.7077 (m-80) cc_final: 0.6225 (t80) REVERT: B 479 ASN cc_start: 0.5413 (OUTLIER) cc_final: 0.4930 (t0) REVERT: B 643 LYS cc_start: 0.7777 (ptpt) cc_final: 0.7491 (pttt) REVERT: B 702 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7768 (tt0) REVERT: B 1234 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.7560 (mp) REVERT: C 266 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8007 (pm20) REVERT: C 330 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7182 (pp20) REVERT: D 1 MET cc_start: 0.5910 (mtp) cc_final: 0.5203 (mpt) REVERT: D 46 GLU cc_start: 0.7588 (tt0) cc_final: 0.7271 (tt0) REVERT: D 66 HIS cc_start: 0.7010 (m90) cc_final: 0.6219 (m-70) REVERT: D 86 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7274 (tt0) REVERT: D 88 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8521 (mp) REVERT: F 29 LYS cc_start: 0.8431 (ttmm) cc_final: 0.7403 (tptp) REVERT: F 33 ASN cc_start: 0.7992 (t0) cc_final: 0.7788 (t0) REVERT: F 54 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.7604 (ptm-80) REVERT: G 1 MET cc_start: 0.4026 (tmm) cc_final: 0.3675 (tmm) REVERT: G 28 GLU cc_start: 0.7223 (tp30) cc_final: 0.6653 (tp30) REVERT: G 81 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8293 (tp) REVERT: H 28 TYR cc_start: 0.8659 (t80) cc_final: 0.8448 (t80) outliers start: 84 outliers final: 57 residues processed: 418 average time/residue: 1.3651 time to fit residues: 669.6845 Evaluate side-chains 419 residues out of total 3077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 349 time to evaluate : 3.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1092 SER Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1189 SER Chi-restraints excluded: chain A residue 1205 ASN Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1346 LYS Chi-restraints excluded: chain A residue 1370 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 479 ASN Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 609 ARG Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 726 THR Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1088 MET Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain B residue 1234 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 270 PHE Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 54 ARG Chi-restraints excluded: chain F residue 69 TYR Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 81 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 129 optimal weight: 2.9990 chunk 145 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 252 optimal weight: 2.9990 chunk 187 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 232 optimal weight: 0.5980 chunk 156 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 246 optimal weight: 0.9980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1018 GLN A1078 GLN A1161 ASN ** B 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 ASN G 83 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.135863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.098475 restraints weight = 35716.304| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.72 r_work: 0.3114 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 28210 Z= 0.202 Angle : 0.635 14.232 38174 Z= 0.320 Chirality : 0.047 0.296 4330 Planarity : 0.004 0.052 4906 Dihedral : 5.291 77.830 3787 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.97 % Favored : 95.74 % Rotamer: Outliers : 2.70 % Allowed : 20.90 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.14), residues: 3430 helix: 0.90 (0.14), residues: 1287 sheet: -0.41 (0.22), residues: 484 loop : -0.03 (0.16), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A1154 HIS 0.017 0.001 HIS D 193 PHE 0.029 0.002 PHE A 918 TYR 0.026 0.002 TYR F 69 ARG 0.007 0.000 ARG F 73 Details of bonding type rmsd hydrogen bonds : bond 0.04119 ( 1203) hydrogen bonds : angle 5.00195 ( 3318) metal coordination : bond 0.00755 ( 24) metal coordination : angle 4.49621 ( 33) covalent geometry : bond 0.00480 (28186) covalent geometry : angle 0.62140 (38141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24970.48 seconds wall clock time: 432 minutes 27.59 seconds (25947.59 seconds total)