Starting phenix.real_space_refine on Sat Aug 8 08:30:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pdy_17626/08_2026/8pdy_17626.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pdy_17626/08_2026/8pdy_17626.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8pdy_17626/08_2026/8pdy_17626.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pdy_17626/08_2026/8pdy_17626.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pdy_17626/08_2026/8pdy_17626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pdy_17626/08_2026/8pdy_17626.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 81 5.49 5 Mg 1 5.21 5 S 107 5.16 5 C 16574 2.51 5 N 4763 2.21 5 O 5359 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26887 Number of models: 1 Model: "" Number of chains: 9 Chain: "G" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1786 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Chain: "H" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1780 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Chain: "I" Number of atoms: 10436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1323, 10436 Classifications: {'peptide': 1323} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1267} Chain breaks: 1 Chain: "J" Number of atoms: 10535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1355, 10535 Classifications: {'peptide': 1355} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1299} Chain breaks: 2 Chain: "K" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 655 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "R" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 260 Classifications: {'RNA': 12} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna2p': 2, 'rna3p': 9} Chain: "A" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 712 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "B" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 720 Classifications: {'DNA': 35} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 34} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14476 SG CYS J 70 23.352 70.678 82.864 1.00180.69 S ATOM 14490 SG CYS J 72 22.052 67.129 83.090 1.00176.87 S ATOM 14598 SG CYS J 85 21.006 69.752 85.675 1.00174.25 S ATOM 14622 SG CYS J 88 24.600 68.407 85.603 1.00172.72 S ATOM 20310 SG CYS J 814 56.622 125.576 93.193 1.00141.84 S ATOM 20875 SG CYS J 888 58.643 122.801 92.118 1.00137.40 S ATOM 20926 SG CYS J 895 57.631 125.695 89.565 1.00141.15 S ATOM 20947 SG CYS J 898 60.383 126.111 91.979 1.00136.40 S Time building chain proxies: 4.45, per 1000 atoms: 0.17 Number of scatterers: 26887 At special positions: 0 Unit cell: (139.776, 169.728, 158.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 107 16.00 P 81 15.00 Mg 1 11.99 O 5359 8.00 N 4763 7.00 C 16574 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 931.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1501 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 85 " pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 895 " Number of angles added : 12 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5948 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 46 sheets defined 39.6% alpha, 16.4% beta 36 base pairs and 52 stacking pairs defined. Time for finding SS restraints: 2.82 Creating SS restraints... Processing helix chain 'G' and resid 34 through 51 removed outlier: 3.859A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N MET G 51 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.594A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 154 through 160 Processing helix chain 'G' and resid 212 through 234 removed outlier: 4.040A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.707A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 88 Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 212 through 228 Processing helix chain 'H' and resid 229 through 232 removed outlier: 3.549A pdb=" N VAL H 232 " --> pdb=" O GLU H 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 229 through 232' Processing helix chain 'I' and resid 4 through 9 removed outlier: 3.778A pdb=" N LYS I 9 " --> pdb=" O TYR I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 40 Processing helix chain 'I' and resid 47 through 57 removed outlier: 3.850A pdb=" N ALA I 51 " --> pdb=" O TYR I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.885A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 233 through 236 Processing helix chain 'I' and resid 242 through 247 removed outlier: 3.553A pdb=" N ARG I 247 " --> pdb=" O GLU I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 318 through 329 Processing helix chain 'I' and resid 345 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 447 through 449 No H-bonds generated for 'chain 'I' and resid 447 through 449' Processing helix chain 'I' and resid 455 through 482 removed outlier: 3.531A pdb=" N MET I 459 " --> pdb=" O SER I 455 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 509 removed outlier: 3.764A pdb=" N SER I 509 " --> pdb=" O PHE I 505 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 545 through 549 Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.640A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 608 through 612 removed outlier: 3.926A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 612' Processing helix chain 'I' and resid 656 through 660 removed outlier: 4.256A pdb=" N VAL I 660 " --> pdb=" O THR I 657 " (cutoff:3.500A) Processing helix chain 'I' and resid 664 through 668 removed outlier: 3.522A pdb=" N LEU I 667 " --> pdb=" O GLY I 664 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 688 removed outlier: 3.669A pdb=" N GLN I 688 " --> pdb=" O ASN I 684 " (cutoff:3.500A) Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 738 through 741 removed outlier: 4.408A pdb=" N MET I 741 " --> pdb=" O GLU I 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 738 through 741' Processing helix chain 'I' and resid 820 through 826 Processing helix chain 'I' and resid 860 through 864 removed outlier: 3.592A pdb=" N LYS I 864 " --> pdb=" O ALA I 861 " (cutoff:3.500A) Processing helix chain 'I' and resid 942 through 983 removed outlier: 4.019A pdb=" N ILE I 966 " --> pdb=" O GLU I 962 " (cutoff:3.500A) Processing helix chain 'I' and resid 985 through 992 Processing helix chain 'I' and resid 993 through 999 removed outlier: 3.540A pdb=" N GLU I 999 " --> pdb=" O ASP I 995 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1038 removed outlier: 3.764A pdb=" N LEU I1011 " --> pdb=" O LYS I1007 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN I1017 " --> pdb=" O GLN I1013 " (cutoff:3.500A) Processing helix chain 'I' and resid 1081 through 1085 Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 4.484A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG I1106 " --> pdb=" O GLY I1102 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1101 through 1106' Processing helix chain 'I' and resid 1109 through 1134 Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.567A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1165 through 1176 Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1284 through 1292 Processing helix chain 'I' and resid 1297 through 1311 Processing helix chain 'I' and resid 1320 through 1332 removed outlier: 3.568A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.533A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 removed outlier: 3.568A pdb=" N SER J 119 " --> pdb=" O TRP J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 173 Processing helix chain 'J' and resid 181 through 192 Processing helix chain 'J' and resid 193 through 209 removed outlier: 4.284A pdb=" N ASN J 209 " --> pdb=" O LEU J 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 215 Processing helix chain 'J' and resid 216 through 230 removed outlier: 3.599A pdb=" N ARG J 220 " --> pdb=" O LYS J 216 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 285 Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 326 through 332 removed outlier: 3.580A pdb=" N MET J 330 " --> pdb=" O SER J 326 " (cutoff:3.500A) Processing helix chain 'J' and resid 336 through 341 removed outlier: 3.837A pdb=" N ASN J 341 " --> pdb=" O ARG J 337 " (cutoff:3.500A) Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 389 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 405 through 416 removed outlier: 3.946A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 450 through 458 removed outlier: 3.624A pdb=" N CYS J 454 " --> pdb=" O HIS J 450 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ALA J 455 " --> pdb=" O PRO J 451 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA J 456 " --> pdb=" O LEU J 452 " (cutoff:3.500A) Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 504 through 513 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 559 through 561 No H-bonds generated for 'chain 'J' and resid 559 through 561' Processing helix chain 'J' and resid 574 through 583 removed outlier: 3.674A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ILE J 582 " --> pdb=" O ILE J 578 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL J 583 " --> pdb=" O LEU J 579 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 592 Processing helix chain 'J' and resid 597 through 613 Processing helix chain 'J' and resid 613 through 636 removed outlier: 3.794A pdb=" N ILE J 619 " --> pdb=" O LYS J 615 " (cutoff:3.500A) Processing helix chain 'J' and resid 648 through 671 removed outlier: 4.423A pdb=" N GLU J 652 " --> pdb=" O GLU J 648 " (cutoff:3.500A) Processing helix chain 'J' and resid 674 through 703 removed outlier: 3.888A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 729 Processing helix chain 'J' and resid 733 through 742 Processing helix chain 'J' and resid 768 through 804 removed outlier: 3.722A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 removed outlier: 3.746A pdb=" N ARG J 838 " --> pdb=" O PRO J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 896 through 900 Processing helix chain 'J' and resid 914 through 925 removed outlier: 3.504A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 929 Processing helix chain 'J' and resid 1068 through 1074 Processing helix chain 'J' and resid 1137 through 1147 Processing helix chain 'J' and resid 1216 through 1224 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 3.511A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.128A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1296 Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1318 through 1325 Processing helix chain 'J' and resid 1330 through 1339 Processing helix chain 'J' and resid 1346 through 1354 Processing helix chain 'J' and resid 1361 through 1377 removed outlier: 4.128A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 17 through 32 Processing helix chain 'K' and resid 45 through 56 removed outlier: 3.517A pdb=" N ILE K 49 " --> pdb=" O LYS K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 84 Processing sheet with id=AA1, first strand: chain 'G' and resid 12 through 17 removed outlier: 4.943A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N HIS G 23 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N THR G 207 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL G 202 " --> pdb=" O ASN G 186 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 97 through 105 removed outlier: 7.475A pdb=" N SER G 141 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ILE G 61 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 90 through 91 Processing sheet with id=AA4, first strand: chain 'G' and resid 108 through 111 removed outlier: 6.448A pdb=" N GLY G 108 " --> pdb=" O HIS G 132 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N HIS G 132 " --> pdb=" O GLY G 108 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL G 110 " --> pdb=" O ILE G 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'H' and resid 15 through 17 removed outlier: 6.672A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP H 197 " --> pdb=" O ALA H 190 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ALA H 190 " --> pdb=" O ASP H 197 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASP H 199 " --> pdb=" O GLU H 188 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU H 188 " --> pdb=" O ASP H 199 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU H 201 " --> pdb=" O ASN H 186 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ASN H 186 " --> pdb=" O LEU H 201 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE H 203 " --> pdb=" O ALA H 184 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA H 184 " --> pdb=" O ILE H 203 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N MET H 205 " --> pdb=" O ARG H 182 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ARG H 182 " --> pdb=" O MET H 205 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N THR H 207 " --> pdb=" O VAL H 180 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL H 180 " --> pdb=" O THR H 207 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 98 through 105 removed outlier: 7.776A pdb=" N SER H 141 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ILE H 61 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 90 through 92 Processing sheet with id=AA9, first strand: chain 'H' and resid 108 through 111 Processing sheet with id=AB1, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.294A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 59 through 60 removed outlier: 4.018A pdb=" N LEU I 68 " --> pdb=" O ILE I 59 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 136 through 138 Processing sheet with id=AB5, first strand: chain 'I' and resid 451 through 454 removed outlier: 3.602A pdb=" N SER I 147 " --> pdb=" O ARG I 529 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 154 through 159 removed outlier: 4.929A pdb=" N TYR I 172 " --> pdb=" O PHE I 188 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 227 through 231 Processing sheet with id=AB8, first strand: chain 'I' and resid 239 through 240 Processing sheet with id=AB9, first strand: chain 'I' and resid 296 through 297 removed outlier: 3.833A pdb=" N MET I 315 " --> pdb=" O VAL I 297 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.379A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N THR I 595 " --> pdb=" O THR I 600 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N THR I 600 " --> pdb=" O THR I 595 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC3, first strand: chain 'I' and resid 634 through 638 Processing sheet with id=AC4, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.793A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AC6, first strand: chain 'I' and resid 768 through 769 Processing sheet with id=AC7, first strand: chain 'I' and resid 1097 through 1098 removed outlier: 8.071A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 816 through 819 removed outlier: 7.859A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'I' and resid 830 through 841 removed outlier: 4.065A pdb=" N LYS I1048 " --> pdb=" O SER I 840 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 849 through 850 removed outlier: 3.713A pdb=" N GLU I 849 " --> pdb=" O VAL I 887 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 882 through 884 removed outlier: 7.236A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 7.809A pdb=" N ILE J 447 " --> pdb=" O ARG J 352 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL J 354 " --> pdb=" O ILE J 447 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU J 449 " --> pdb=" O VAL J 354 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N THR J 356 " --> pdb=" O LEU J 449 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 1338 through 1339 removed outlier: 3.740A pdb=" N LYS J 21 " --> pdb=" O GLU I1338 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.454A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 9.998A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.769A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 144 through 145 Processing sheet with id=AD7, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AD8, first strand: chain 'J' and resid 706 through 708 Processing sheet with id=AD9, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AE1, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE2, first strand: chain 'J' and resid 825 through 826 removed outlier: 3.563A pdb=" N VAL J 825 " --> pdb=" O GLU J 833 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU J 833 " --> pdb=" O VAL J 825 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'J' and resid 848 through 849 Processing sheet with id=AE4, first strand: chain 'J' and resid 950 through 951 removed outlier: 3.861A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 957 through 961 removed outlier: 6.822A pdb=" N LEU J 982 " --> pdb=" O SER J 994 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N SER J 994 " --> pdb=" O LEU J 982 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU J 984 " --> pdb=" O LYS J 992 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 1024 through 1028 removed outlier: 6.115A pdb=" N MET J1025 " --> pdb=" O ARG J1123 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ARG J1123 " --> pdb=" O MET J1025 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL J1027 " --> pdb=" O LEU J1121 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 1098 through 1100 Processing sheet with id=AE8, first strand: chain 'J' and resid 1046 through 1051 Processing sheet with id=AE9, first strand: chain 'J' and resid 1189 through 1190 Processing sheet with id=AF1, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.452A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1076 hydrogen bonds defined for protein. 3030 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 92 hydrogen bonds 176 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 52 stacking parallelities Total time for adding SS restraints: 4.76 Time building geometry restraints manager: 2.87 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: 8865 1.34 - 1.46: 4278 1.46 - 1.58: 13969 1.58 - 1.70: 160 1.70 - 1.82: 186 Bond restraints: 27458 Sorted by residual: bond pdb=" C3' DA B 15 " pdb=" C2' DA B 15 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C3' DA A 34 " pdb=" C2' DA A 34 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DG A 17 " pdb=" C2' DG A 17 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.92e+00 bond pdb=" C3' DG B 1 " pdb=" C2' DG B 1 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.77e+00 bond pdb=" C3' DT A 29 " pdb=" C2' DT A 29 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.19e+00 ... (remaining 27453 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 37160 2.61 - 5.21: 251 5.21 - 7.82: 25 7.82 - 10.43: 8 10.43 - 13.03: 1 Bond angle restraints: 37445 Sorted by residual: angle pdb=" C ASP I1095 " pdb=" CA ASP I1095 " pdb=" CB ASP I1095 " ideal model delta sigma weight residual 117.23 110.88 6.35 1.36e+00 5.41e-01 2.18e+01 angle pdb=" CB MET J1370 " pdb=" CG MET J1370 " pdb=" SD MET J1370 " ideal model delta sigma weight residual 112.70 125.73 -13.03 3.00e+00 1.11e-01 1.89e+01 angle pdb=" N3 DT A 31 " pdb=" C4 DT A 31 " pdb=" O4 DT A 31 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT B 7 " pdb=" C4 DT B 7 " pdb=" O4 DT B 7 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 angle pdb=" N3 DT A 38 " pdb=" C4 DT A 38 " pdb=" O4 DT A 38 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+01 ... (remaining 37440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.40: 15861 35.40 - 70.79: 818 70.79 - 106.19: 37 106.19 - 141.58: 3 141.58 - 176.98: 1 Dihedral angle restraints: 16720 sinusoidal: 7474 harmonic: 9246 Sorted by residual: dihedral pdb=" CA LYS K 45 " pdb=" C LYS K 45 " pdb=" N THR K 46 " pdb=" CA THR K 46 " ideal model delta harmonic sigma weight residual 180.00 -159.02 -20.98 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA TYR J 140 " pdb=" C TYR J 140 " pdb=" N PHE J 141 " pdb=" CA PHE J 141 " ideal model delta harmonic sigma weight residual 180.00 159.34 20.66 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" C4' DG A 13 " pdb=" C3' DG A 13 " pdb=" O3' DG A 13 " pdb=" P DG A 14 " ideal model delta sinusoidal sigma weight residual -140.00 36.98 -176.98 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 16717 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2837 0.033 - 0.065: 932 0.065 - 0.098: 323 0.098 - 0.130: 170 0.130 - 0.163: 15 Chirality restraints: 4277 Sorted by residual: chirality pdb=" CB ILE I 177 " pdb=" CA ILE I 177 " pdb=" CG1 ILE I 177 " pdb=" CG2 ILE I 177 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.62e-01 chirality pdb=" C3' DG B 16 " pdb=" C4' DG B 16 " pdb=" O3' DG B 16 " pdb=" C2' DG B 16 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.86e-01 chirality pdb=" CA GLU J 925 " pdb=" N GLU J 925 " pdb=" C GLU J 925 " pdb=" CB GLU J 925 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.69e-01 ... (remaining 4274 not shown) Planarity restraints: 4620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE I 854 " -0.035 5.00e-02 4.00e+02 5.36e-02 4.60e+00 pdb=" N PRO I 855 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO I 855 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO I 855 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU I 813 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.60e+00 pdb=" C GLU I 813 " 0.037 2.00e-02 2.50e+03 pdb=" O GLU I 813 " -0.014 2.00e-02 2.50e+03 pdb=" N ASP I 814 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE J 416 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.39e+00 pdb=" C ILE J 416 " -0.032 2.00e-02 2.50e+03 pdb=" O ILE J 416 " 0.012 2.00e-02 2.50e+03 pdb=" N ARG J 417 " 0.011 2.00e-02 2.50e+03 ... (remaining 4617 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 372 2.64 - 3.20: 24547 3.20 - 3.77: 44580 3.77 - 4.33: 57468 4.33 - 4.90: 92603 Nonbonded interactions: 219570 Sorted by model distance: nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1503 " model vdw 2.070 2.170 nonbonded pdb=" O2 DC A 6 " pdb=" N2 DG B 35 " model vdw 2.070 2.496 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1503 " model vdw 2.073 2.170 nonbonded pdb=" OD2 ASP J 462 " pdb="MG MG J1503 " model vdw 2.076 2.170 nonbonded pdb=" OG SER J 326 " pdb=" OD2 ASP J 329 " model vdw 2.163 3.040 ... (remaining 219565 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'G' and resid 6 through 233) selection = (chain 'H' and resid 6 through 233) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.920 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:5.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 27466 Z= 0.195 Angle : 0.582 13.032 37457 Z= 0.359 Chirality : 0.041 0.163 4277 Planarity : 0.004 0.054 4620 Dihedral : 18.695 176.976 10772 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.75 % Favored : 97.22 % Rotamer: Outliers : 0.22 % Allowed : 23.06 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.15), residues: 3205 helix: 1.68 (0.16), residues: 1126 sheet: 0.11 (0.25), residues: 465 loop : -0.28 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 417 TYR 0.024 0.001 TYR G 152 PHE 0.010 0.001 PHE J 141 TRP 0.025 0.001 TRP J1020 HIS 0.004 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.20 (27458) covalent geometry : angle 0.57637 / 0.36 (37445) hydrogen bonds : bond 0.13830 / 9.19 ( 1166) hydrogen bonds : angle 5.81646 / 4.06 ( 3206) metal coordination : bond 0.00390 / 0.26 ( 8) metal coordination : angle 4.56577 / 2.46 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 195 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 105 TYR cc_start: 0.8507 (m-80) cc_final: 0.8275 (m-80) REVERT: J 697 MET cc_start: 0.8782 (tmm) cc_final: 0.8406 (tmm) REVERT: J 698 MET cc_start: 0.9439 (mmm) cc_final: 0.9209 (mmm) REVERT: J 913 GLU cc_start: 0.6718 (mp0) cc_final: 0.6411 (mp0) REVERT: J 1357 ILE cc_start: 0.9104 (pt) cc_final: 0.8865 (pp) REVERT: K 15 ASN cc_start: 0.8362 (t0) cc_final: 0.8146 (OUTLIER) REVERT: K 69 ARG cc_start: 0.9128 (mmm160) cc_final: 0.8922 (mmm160) REVERT: K 72 GLN cc_start: 0.9689 (tm-30) cc_final: 0.9460 (tm-30) outliers start: 6 outliers final: 5 residues processed: 199 average time/residue: 0.5635 time to fit residues: 131.8533 Evaluate side-chains 172 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 168 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1075 ARG Chi-restraints excluded: chain K residue 59 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 18 GLN ** I 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 510 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 659 GLN I 955 GLN ** I1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1218 HIS ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.052161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.037894 restraints weight = 124977.053| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 3.89 r_work: 0.2700 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 27466 Z= 0.218 Angle : 0.600 10.225 37457 Z= 0.311 Chirality : 0.042 0.264 4277 Planarity : 0.004 0.051 4620 Dihedral : 15.698 171.366 4482 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.12 % Favored : 96.85 % Rotamer: Outliers : 2.44 % Allowed : 21.56 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.15), residues: 3205 helix: 1.97 (0.16), residues: 1154 sheet: 0.14 (0.25), residues: 480 loop : -0.18 (0.16), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG H 12 TYR 0.018 0.001 TYR J 631 PHE 0.016 0.001 PHE I 405 TRP 0.013 0.001 TRP J1020 HIS 0.005 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.22 (27458) covalent geometry : angle 0.59172 / 0.31 (37445) hydrogen bonds : bond 0.04415 / 3.08 ( 1166) hydrogen bonds : angle 4.69607 / 3.30 ( 3206) metal coordination : bond 0.01597 / 1.00 ( 8) metal coordination : angle 5.46397 / 2.99 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 171 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 160 HIS cc_start: 0.8926 (OUTLIER) cc_final: 0.8681 (m-70) REVERT: I 105 TYR cc_start: 0.9072 (m-80) cc_final: 0.8782 (m-80) REVERT: I 161 LYS cc_start: 0.9349 (mmmt) cc_final: 0.8979 (mmmm) REVERT: I 163 LYS cc_start: 0.9321 (mmtm) cc_final: 0.9106 (pmtt) REVERT: I 239 MET cc_start: 0.7590 (ppp) cc_final: 0.7194 (ppp) REVERT: I 492 MET cc_start: 0.8816 (mpp) cc_final: 0.8477 (mpt) REVERT: I 562 GLU cc_start: 0.9014 (tm-30) cc_final: 0.8733 (tm-30) REVERT: I 1279 GLU cc_start: 0.9232 (mt-10) cc_final: 0.9005 (mt-10) REVERT: J 22 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8822 (pt) REVERT: J 298 MET cc_start: 0.9072 (ttp) cc_final: 0.8607 (ttp) REVERT: J 913 GLU cc_start: 0.7564 (mp0) cc_final: 0.7156 (mp0) REVERT: J 1040 MET cc_start: 0.5948 (OUTLIER) cc_final: 0.5530 (pmt) REVERT: J 1184 ASP cc_start: 0.9140 (OUTLIER) cc_final: 0.8251 (p0) REVERT: K 15 ASN cc_start: 0.8470 (t0) cc_final: 0.8154 (t0) REVERT: K 65 ASP cc_start: 0.9545 (p0) cc_final: 0.9314 (p0) REVERT: K 69 ARG cc_start: 0.9333 (mmm160) cc_final: 0.9008 (mmm160) outliers start: 67 outliers final: 26 residues processed: 219 average time/residue: 0.5421 time to fit residues: 140.5119 Evaluate side-chains 189 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 159 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 160 HIS Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1040 MET Chi-restraints excluded: chain J residue 1075 ARG Chi-restraints excluded: chain J residue 1184 ASP Chi-restraints excluded: chain J residue 1186 TYR Chi-restraints excluded: chain J residue 1352 ILE Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 64 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 116 optimal weight: 7.9990 chunk 243 optimal weight: 0.9990 chunk 245 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 302 optimal weight: 10.0000 chunk 314 optimal weight: 8.9990 chunk 114 optimal weight: 0.9990 chunk 327 optimal weight: 20.0000 chunk 284 optimal weight: 30.0000 chunk 247 optimal weight: 0.9990 chunk 321 optimal weight: 30.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 861 ASN J1114 GLN ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.051786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.037466 restraints weight = 124397.579| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 3.90 r_work: 0.2675 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 27466 Z= 0.201 Angle : 0.579 10.809 37457 Z= 0.300 Chirality : 0.041 0.224 4277 Planarity : 0.004 0.049 4620 Dihedral : 15.765 170.665 4480 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.00 % Favored : 96.97 % Rotamer: Outliers : 2.92 % Allowed : 22.58 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.15), residues: 3205 helix: 2.01 (0.16), residues: 1161 sheet: 0.13 (0.25), residues: 484 loop : -0.19 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 67 TYR 0.021 0.001 TYR J 140 PHE 0.014 0.001 PHE I 35 TRP 0.009 0.001 TRP J1020 HIS 0.005 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.20 (27458) covalent geometry : angle 0.57004 / 0.30 (37445) hydrogen bonds : bond 0.04222 / 2.94 ( 1166) hydrogen bonds : angle 4.52254 / 3.19 ( 3206) metal coordination : bond 0.01407 / 0.87 ( 8) metal coordination : angle 5.81529 / 3.19 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 174 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 51 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8420 (mmm) REVERT: H 160 HIS cc_start: 0.8880 (OUTLIER) cc_final: 0.8615 (m-70) REVERT: I 161 LYS cc_start: 0.9385 (mmmt) cc_final: 0.9159 (mmmt) REVERT: I 239 MET cc_start: 0.7698 (ppp) cc_final: 0.7338 (ppp) REVERT: I 492 MET cc_start: 0.8807 (mpp) cc_final: 0.8409 (mpt) REVERT: I 523 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8548 (mm-30) REVERT: I 562 GLU cc_start: 0.9070 (tm-30) cc_final: 0.8807 (tm-30) REVERT: J 298 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.8540 (ttp) REVERT: J 443 GLU cc_start: 0.9419 (OUTLIER) cc_final: 0.9183 (mm-30) REVERT: J 697 MET cc_start: 0.8982 (tmm) cc_final: 0.8512 (tmm) REVERT: J 698 MET cc_start: 0.9513 (tpt) cc_final: 0.9154 (mmm) REVERT: J 822 MET cc_start: 0.8827 (mmm) cc_final: 0.8521 (mmm) REVERT: J 913 GLU cc_start: 0.7661 (mp0) cc_final: 0.7257 (mp0) REVERT: K 15 ASN cc_start: 0.8497 (t0) cc_final: 0.8132 (t0) REVERT: K 65 ASP cc_start: 0.9526 (p0) cc_final: 0.9308 (p0) REVERT: K 69 ARG cc_start: 0.9312 (mmm160) cc_final: 0.9088 (mmm160) outliers start: 80 outliers final: 43 residues processed: 234 average time/residue: 0.4938 time to fit residues: 138.1915 Evaluate side-chains 208 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 160 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 160 HIS Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 421 SER Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 523 GLU Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 843 THR Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1180 MET Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 355 ILE Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 366 CYS Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 443 GLU Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 592 VAL Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 976 THR Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1075 ARG Chi-restraints excluded: chain J residue 1186 TYR Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 64 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 197 optimal weight: 6.9990 chunk 171 optimal weight: 2.9990 chunk 226 optimal weight: 0.3980 chunk 322 optimal weight: 50.0000 chunk 55 optimal weight: 7.9990 chunk 206 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 117 optimal weight: 9.9990 chunk 174 optimal weight: 0.9990 chunk 249 optimal weight: 1.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 688 GLN ** I1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 341 ASN J1019 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.051806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.037485 restraints weight = 124164.315| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 3.84 r_work: 0.2699 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27466 Z= 0.162 Angle : 0.562 10.376 37457 Z= 0.289 Chirality : 0.041 0.217 4277 Planarity : 0.004 0.052 4620 Dihedral : 15.798 170.874 4480 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.12 % Favored : 96.85 % Rotamer: Outliers : 2.99 % Allowed : 23.68 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.15), residues: 3205 helix: 2.04 (0.16), residues: 1152 sheet: 0.15 (0.25), residues: 474 loop : -0.19 (0.16), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 67 TYR 0.022 0.001 TYR J 140 PHE 0.014 0.001 PHE I 405 TRP 0.006 0.001 TRP J1020 HIS 0.004 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (27458) covalent geometry : angle 0.55224 / 0.29 (37445) hydrogen bonds : bond 0.04004 / 2.80 ( 1166) hydrogen bonds : angle 4.38065 / 3.10 ( 3206) metal coordination : bond 0.01176 / 0.72 ( 8) metal coordination : angle 5.73543 / 3.18 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 172 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 51 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8406 (mmm) REVERT: H 158 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7845 (mtm-85) REVERT: I 132 ASP cc_start: 0.9458 (OUTLIER) cc_final: 0.9038 (t0) REVERT: I 239 MET cc_start: 0.7793 (ppp) cc_final: 0.7425 (ppp) REVERT: I 492 MET cc_start: 0.8784 (mpp) cc_final: 0.8375 (mpt) REVERT: I 523 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8548 (mm-30) REVERT: I 530 ILE cc_start: 0.9416 (OUTLIER) cc_final: 0.8899 (pp) REVERT: I 562 GLU cc_start: 0.9082 (tm-30) cc_final: 0.8815 (tm-30) REVERT: I 813 GLU cc_start: 0.8374 (pp20) cc_final: 0.7847 (pp20) REVERT: I 814 ASP cc_start: 0.8979 (m-30) cc_final: 0.8779 (m-30) REVERT: I 1279 GLU cc_start: 0.9225 (mt-10) cc_final: 0.8853 (pt0) REVERT: J 298 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8551 (ttp) REVERT: J 697 MET cc_start: 0.8974 (tmm) cc_final: 0.8611 (tmm) REVERT: J 698 MET cc_start: 0.9509 (OUTLIER) cc_final: 0.9236 (mmm) REVERT: J 821 MET cc_start: 0.9021 (mmm) cc_final: 0.8684 (tpt) REVERT: J 913 GLU cc_start: 0.7643 (mp0) cc_final: 0.7195 (mp0) REVERT: J 963 VAL cc_start: 0.9104 (OUTLIER) cc_final: 0.8878 (t) REVERT: J 1184 ASP cc_start: 0.9140 (OUTLIER) cc_final: 0.8227 (p0) REVERT: K 15 ASN cc_start: 0.8462 (t0) cc_final: 0.8087 (t0) REVERT: K 65 ASP cc_start: 0.9531 (p0) cc_final: 0.9312 (p0) outliers start: 82 outliers final: 38 residues processed: 237 average time/residue: 0.4991 time to fit residues: 141.5249 Evaluate side-chains 208 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 161 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 158 ARG Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 523 GLU Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 843 THR Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1180 MET Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 355 ILE Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 528 THR Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 976 THR Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1184 ASP Chi-restraints excluded: chain J residue 1272 SER Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 64 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 215 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 chunk 190 optimal weight: 0.9990 chunk 317 optimal weight: 7.9990 chunk 289 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 246 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1135 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.050062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.035696 restraints weight = 125918.588| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 3.82 r_work: 0.2633 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8992 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 27466 Z= 0.311 Angle : 0.683 13.845 37457 Z= 0.345 Chirality : 0.043 0.215 4277 Planarity : 0.004 0.051 4620 Dihedral : 15.876 169.519 4476 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.37 % Favored : 96.60 % Rotamer: Outliers : 4.05 % Allowed : 23.97 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.15), residues: 3205 helix: 1.88 (0.15), residues: 1161 sheet: -0.06 (0.24), residues: 518 loop : -0.31 (0.16), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG K 69 TYR 0.023 0.002 TYR G 152 PHE 0.016 0.002 PHE I 35 TRP 0.006 0.001 TRP I 997 HIS 0.006 0.001 HIS J 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00665 / 0.31 (27458) covalent geometry : angle 0.67153 / 0.34 (37445) hydrogen bonds : bond 0.04563 / 3.19 ( 1166) hydrogen bonds : angle 4.58525 / 3.24 ( 3206) metal coordination : bond 0.02115 / 1.31 ( 8) metal coordination : angle 6.86563 / 3.69 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 160 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 51 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8496 (mmm) REVERT: H 111 THR cc_start: 0.9611 (OUTLIER) cc_final: 0.9254 (t) REVERT: H 158 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7281 (ptp90) REVERT: H 168 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8613 (tp) REVERT: I 132 ASP cc_start: 0.9477 (OUTLIER) cc_final: 0.9045 (t0) REVERT: I 239 MET cc_start: 0.7860 (ppp) cc_final: 0.7410 (ppp) REVERT: I 315 MET cc_start: 0.9303 (tpp) cc_final: 0.9031 (tpp) REVERT: I 492 MET cc_start: 0.8729 (mpp) cc_final: 0.8210 (mpt) REVERT: I 523 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8622 (mm-30) REVERT: I 530 ILE cc_start: 0.9441 (OUTLIER) cc_final: 0.8855 (pp) REVERT: I 562 GLU cc_start: 0.9139 (tm-30) cc_final: 0.8898 (tm-30) REVERT: I 704 MET cc_start: 0.8598 (mtp) cc_final: 0.8223 (mtm) REVERT: I 813 GLU cc_start: 0.8537 (pp20) cc_final: 0.8040 (pp20) REVERT: I 814 ASP cc_start: 0.9023 (m-30) cc_final: 0.8814 (m-30) REVERT: I 1279 GLU cc_start: 0.9241 (mt-10) cc_final: 0.8985 (mt-10) REVERT: J 298 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8584 (ttp) REVERT: J 443 GLU cc_start: 0.9377 (OUTLIER) cc_final: 0.9158 (mm-30) REVERT: J 644 MET cc_start: 0.9088 (mtm) cc_final: 0.8570 (mtm) REVERT: J 697 MET cc_start: 0.9042 (tmm) cc_final: 0.8781 (tmm) REVERT: J 913 GLU cc_start: 0.7840 (mp0) cc_final: 0.7370 (mp0) REVERT: J 963 VAL cc_start: 0.9117 (OUTLIER) cc_final: 0.8885 (t) REVERT: J 1184 ASP cc_start: 0.9159 (OUTLIER) cc_final: 0.8196 (p0) REVERT: J 1186 TYR cc_start: 0.9026 (m-80) cc_final: 0.8758 (t80) outliers start: 111 outliers final: 65 residues processed: 254 average time/residue: 0.5078 time to fit residues: 154.4983 Evaluate side-chains 227 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 151 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 158 ARG Chi-restraints excluded: chain H residue 168 ILE Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 421 SER Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 515 MET Chi-restraints excluded: chain I residue 523 GLU Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 654 ASP Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 843 THR Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1180 MET Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1235 LEU Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 72 CYS Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 355 ILE Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 366 CYS Chi-restraints excluded: chain J residue 443 GLU Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 592 VAL Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 976 THR Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1017 VAL Chi-restraints excluded: chain J residue 1019 ASN Chi-restraints excluded: chain J residue 1060 VAL Chi-restraints excluded: chain J residue 1184 ASP Chi-restraints excluded: chain J residue 1272 SER Chi-restraints excluded: chain J residue 1352 ILE Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 64 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 271 optimal weight: 9.9990 chunk 253 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 304 optimal weight: 4.9990 chunk 224 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 169 optimal weight: 0.6980 chunk 190 optimal weight: 0.9990 chunk 287 optimal weight: 8.9990 chunk 108 optimal weight: 6.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 314 ASN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 341 ASN ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.051606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.037233 restraints weight = 124065.487| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.85 r_work: 0.2690 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 27466 Z= 0.121 Angle : 0.576 10.651 37457 Z= 0.293 Chirality : 0.042 0.196 4277 Planarity : 0.004 0.053 4620 Dihedral : 15.858 172.006 4476 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.06 % Favored : 96.91 % Rotamer: Outliers : 2.81 % Allowed : 25.90 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.15), residues: 3205 helix: 1.98 (0.16), residues: 1157 sheet: 0.05 (0.24), residues: 481 loop : -0.27 (0.16), residues: 1567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 69 TYR 0.023 0.001 TYR G 152 PHE 0.013 0.001 PHE I 405 TRP 0.007 0.001 TRP J1020 HIS 0.004 0.001 HIS J1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (27458) covalent geometry : angle 0.56674 / 0.29 (37445) hydrogen bonds : bond 0.03947 / 2.76 ( 1166) hydrogen bonds : angle 4.27111 / 3.03 ( 3206) metal coordination : bond 0.00856 / 0.50 ( 8) metal coordination : angle 5.92122 / 3.32 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 172 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 51 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8494 (mmm) REVERT: H 158 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7898 (mtm-85) REVERT: I 132 ASP cc_start: 0.9470 (m-30) cc_final: 0.9011 (t0) REVERT: I 239 MET cc_start: 0.7947 (ppp) cc_final: 0.7487 (ppp) REVERT: I 492 MET cc_start: 0.8735 (mpp) cc_final: 0.8191 (mpt) REVERT: I 523 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8599 (mm-30) REVERT: I 530 ILE cc_start: 0.9422 (OUTLIER) cc_final: 0.8929 (pp) REVERT: I 562 GLU cc_start: 0.9121 (tm-30) cc_final: 0.8847 (tm-30) REVERT: I 813 GLU cc_start: 0.8406 (pp20) cc_final: 0.7832 (pp20) REVERT: I 814 ASP cc_start: 0.9008 (m-30) cc_final: 0.8778 (m-30) REVERT: I 1232 MET cc_start: 0.9295 (mtp) cc_final: 0.9002 (mmp) REVERT: I 1279 GLU cc_start: 0.9225 (mt-10) cc_final: 0.8851 (pt0) REVERT: J 298 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8552 (ttp) REVERT: J 443 GLU cc_start: 0.9405 (OUTLIER) cc_final: 0.9120 (mm-30) REVERT: J 697 MET cc_start: 0.9015 (tmm) cc_final: 0.8773 (tmm) REVERT: J 821 MET cc_start: 0.9337 (tpp) cc_final: 0.9002 (tpt) REVERT: J 913 GLU cc_start: 0.7694 (mp0) cc_final: 0.7270 (mp0) REVERT: J 963 VAL cc_start: 0.9157 (OUTLIER) cc_final: 0.8939 (t) REVERT: J 1040 MET cc_start: 0.5660 (pmm) cc_final: 0.5424 (pmt) REVERT: J 1184 ASP cc_start: 0.9137 (OUTLIER) cc_final: 0.8115 (p0) REVERT: K 15 ASN cc_start: 0.8363 (t0) cc_final: 0.7960 (t0) REVERT: K 65 ASP cc_start: 0.9501 (p0) cc_final: 0.9291 (p0) outliers start: 77 outliers final: 40 residues processed: 236 average time/residue: 0.5167 time to fit residues: 145.6574 Evaluate side-chains 206 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 158 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 158 ARG Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 523 GLU Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 355 ILE Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 366 CYS Chi-restraints excluded: chain J residue 443 GLU Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 528 THR Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1060 VAL Chi-restraints excluded: chain J residue 1184 ASP Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain K residue 64 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 103 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 260 optimal weight: 7.9990 chunk 206 optimal weight: 6.9990 chunk 228 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 187 optimal weight: 0.9990 chunk 269 optimal weight: 2.9990 chunk 267 optimal weight: 0.1980 chunk 299 optimal weight: 0.8980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 66 HIS ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 504 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.051569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.037219 restraints weight = 123320.928| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 3.85 r_work: 0.2689 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27466 Z= 0.137 Angle : 0.592 16.118 37457 Z= 0.299 Chirality : 0.041 0.244 4277 Planarity : 0.004 0.057 4620 Dihedral : 15.840 171.696 4476 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.12 % Favored : 96.85 % Rotamer: Outliers : 2.70 % Allowed : 26.30 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.15), residues: 3205 helix: 1.97 (0.15), residues: 1155 sheet: 0.02 (0.24), residues: 492 loop : -0.28 (0.16), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 67 TYR 0.023 0.001 TYR G 68 PHE 0.013 0.001 PHE J 141 TRP 0.007 0.001 TRP J 115 HIS 0.004 0.001 HIS J 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (27458) covalent geometry : angle 0.58374 / 0.30 (37445) hydrogen bonds : bond 0.03896 / 2.72 ( 1166) hydrogen bonds : angle 4.24959 / 3.02 ( 3206) metal coordination : bond 0.01026 / 0.64 ( 8) metal coordination : angle 5.55372 / 3.06 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 168 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 95 LYS cc_start: 0.9363 (ptpt) cc_final: 0.9152 (ptpt) REVERT: H 51 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8453 (mmm) REVERT: H 158 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7906 (mtm-85) REVERT: I 132 ASP cc_start: 0.9484 (m-30) cc_final: 0.8998 (t0) REVERT: I 239 MET cc_start: 0.7997 (ppp) cc_final: 0.7527 (ppp) REVERT: I 265 LYS cc_start: 0.9512 (OUTLIER) cc_final: 0.9292 (tptt) REVERT: I 315 MET cc_start: 0.9290 (tpp) cc_final: 0.8983 (tpp) REVERT: I 492 MET cc_start: 0.8743 (mpp) cc_final: 0.8161 (mpt) REVERT: I 523 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8557 (mm-30) REVERT: I 530 ILE cc_start: 0.9413 (OUTLIER) cc_final: 0.8884 (pp) REVERT: I 562 GLU cc_start: 0.9127 (tm-30) cc_final: 0.8826 (tm-30) REVERT: I 813 GLU cc_start: 0.8478 (pp20) cc_final: 0.7939 (pp20) REVERT: I 1232 MET cc_start: 0.9289 (mtp) cc_final: 0.8989 (mmp) REVERT: I 1279 GLU cc_start: 0.9234 (mt-10) cc_final: 0.8850 (pt0) REVERT: J 298 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8535 (ttp) REVERT: J 443 GLU cc_start: 0.9409 (OUTLIER) cc_final: 0.9135 (mm-30) REVERT: J 644 MET cc_start: 0.9057 (mtm) cc_final: 0.8484 (mtm) REVERT: J 697 MET cc_start: 0.9011 (tmm) cc_final: 0.8738 (tmm) REVERT: J 821 MET cc_start: 0.9281 (tpp) cc_final: 0.9012 (tpt) REVERT: J 913 GLU cc_start: 0.7758 (mp0) cc_final: 0.7301 (mp0) REVERT: J 963 VAL cc_start: 0.9166 (OUTLIER) cc_final: 0.8952 (t) REVERT: J 1040 MET cc_start: 0.5554 (pmm) cc_final: 0.5259 (pmt) REVERT: J 1184 ASP cc_start: 0.9146 (OUTLIER) cc_final: 0.8113 (p0) REVERT: K 15 ASN cc_start: 0.8376 (t0) cc_final: 0.7972 (t0) REVERT: K 35 LYS cc_start: 0.9469 (mmmm) cc_final: 0.9169 (mmmm) REVERT: K 65 ASP cc_start: 0.9504 (p0) cc_final: 0.9295 (p0) outliers start: 74 outliers final: 45 residues processed: 229 average time/residue: 0.5238 time to fit residues: 143.7797 Evaluate side-chains 215 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 161 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 158 ARG Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 265 LYS Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 421 SER Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 515 MET Chi-restraints excluded: chain I residue 523 GLU Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 72 CYS Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 355 ILE Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 366 CYS Chi-restraints excluded: chain J residue 443 GLU Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 528 THR Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 976 THR Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1060 VAL Chi-restraints excluded: chain J residue 1184 ASP Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain K residue 64 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 91 optimal weight: 6.9990 chunk 300 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 166 optimal weight: 4.9990 chunk 112 optimal weight: 0.0010 chunk 309 optimal weight: 3.9990 chunk 220 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 chunk 174 optimal weight: 3.9990 overall best weight: 3.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 504 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.050470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.036104 restraints weight = 125806.114| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 3.82 r_work: 0.2651 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 27466 Z= 0.228 Angle : 0.652 16.677 37457 Z= 0.327 Chirality : 0.042 0.215 4277 Planarity : 0.004 0.064 4620 Dihedral : 15.880 170.599 4476 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.59 % Favored : 96.38 % Rotamer: Outliers : 2.99 % Allowed : 26.27 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.15), residues: 3205 helix: 1.92 (0.16), residues: 1162 sheet: -0.05 (0.24), residues: 497 loop : -0.31 (0.16), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG K 67 TYR 0.022 0.001 TYR G 152 PHE 0.012 0.001 PHE J 141 TRP 0.010 0.001 TRP J 115 HIS 0.005 0.001 HIS J 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.23 (27458) covalent geometry : angle 0.64239 / 0.33 (37445) hydrogen bonds : bond 0.04201 / 2.93 ( 1166) hydrogen bonds : angle 4.36174 / 3.09 ( 3206) metal coordination : bond 0.01656 / 1.02 ( 8) metal coordination : angle 6.14401 / 3.33 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 163 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 95 LYS cc_start: 0.9386 (ptpt) cc_final: 0.9172 (ptpt) REVERT: H 51 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8498 (mmm) REVERT: H 158 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.8080 (mtm-85) REVERT: I 239 MET cc_start: 0.8081 (ppp) cc_final: 0.7593 (ppp) REVERT: I 265 LYS cc_start: 0.9516 (OUTLIER) cc_final: 0.9299 (tptt) REVERT: I 315 MET cc_start: 0.9300 (tpp) cc_final: 0.8997 (tpp) REVERT: I 492 MET cc_start: 0.8722 (mpp) cc_final: 0.8208 (mmt) REVERT: I 523 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8586 (mm-30) REVERT: I 530 ILE cc_start: 0.9437 (OUTLIER) cc_final: 0.8939 (pp) REVERT: I 562 GLU cc_start: 0.9132 (tm-30) cc_final: 0.8829 (tm-30) REVERT: I 813 GLU cc_start: 0.8511 (pp20) cc_final: 0.8022 (pp20) REVERT: I 1279 GLU cc_start: 0.9242 (mt-10) cc_final: 0.8967 (mt-10) REVERT: J 298 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8619 (ttp) REVERT: J 443 GLU cc_start: 0.9378 (OUTLIER) cc_final: 0.9110 (mm-30) REVERT: J 644 MET cc_start: 0.9200 (mtm) cc_final: 0.8707 (mtm) REVERT: J 697 MET cc_start: 0.9046 (tmm) cc_final: 0.8707 (tmm) REVERT: J 698 MET cc_start: 0.9504 (OUTLIER) cc_final: 0.9212 (mmm) REVERT: J 821 MET cc_start: 0.9358 (tpp) cc_final: 0.9023 (tpt) REVERT: J 913 GLU cc_start: 0.7815 (mp0) cc_final: 0.7337 (mp0) REVERT: J 925 GLU cc_start: 0.9526 (tm-30) cc_final: 0.9175 (pp20) REVERT: J 963 VAL cc_start: 0.9174 (OUTLIER) cc_final: 0.8956 (t) REVERT: J 1040 MET cc_start: 0.5555 (pmm) cc_final: 0.5201 (pmt) REVERT: J 1184 ASP cc_start: 0.9164 (OUTLIER) cc_final: 0.8179 (p0) REVERT: K 13 ILE cc_start: 0.9058 (mm) cc_final: 0.8686 (tt) REVERT: K 15 ASN cc_start: 0.8489 (t0) cc_final: 0.8100 (t0) REVERT: K 35 LYS cc_start: 0.9466 (mmmm) cc_final: 0.9173 (mmmm) REVERT: K 65 ASP cc_start: 0.9520 (p0) cc_final: 0.9305 (p0) outliers start: 82 outliers final: 56 residues processed: 230 average time/residue: 0.4947 time to fit residues: 135.8096 Evaluate side-chains 224 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 158 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 158 ARG Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 265 LYS Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 421 SER Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 515 MET Chi-restraints excluded: chain I residue 523 GLU Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 654 ASP Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 843 THR Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1235 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 72 CYS Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 355 ILE Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 366 CYS Chi-restraints excluded: chain J residue 443 GLU Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 499 ILE Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 528 THR Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 592 VAL Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 976 THR Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1060 VAL Chi-restraints excluded: chain J residue 1184 ASP Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain K residue 64 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 94 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 245 optimal weight: 6.9990 chunk 240 optimal weight: 3.9990 chunk 225 optimal weight: 8.9990 chunk 141 optimal weight: 2.9990 chunk 274 optimal weight: 0.0970 chunk 128 optimal weight: 5.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 31 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.050861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.036466 restraints weight = 126426.508| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 3.90 r_work: 0.2643 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 27466 Z= 0.190 Angle : 0.633 16.095 37457 Z= 0.318 Chirality : 0.042 0.215 4277 Planarity : 0.004 0.062 4620 Dihedral : 15.900 171.247 4476 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.56 % Favored : 96.41 % Rotamer: Outliers : 2.92 % Allowed : 26.63 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.15), residues: 3205 helix: 1.92 (0.16), residues: 1161 sheet: -0.12 (0.24), residues: 496 loop : -0.34 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG K 69 TYR 0.022 0.001 TYR G 152 PHE 0.012 0.001 PHE I 405 TRP 0.009 0.001 TRP J 115 HIS 0.004 0.001 HIS J 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.19 (27458) covalent geometry : angle 0.62358 / 0.32 (37445) hydrogen bonds : bond 0.04080 / 2.84 ( 1166) hydrogen bonds : angle 4.32294 / 3.07 ( 3206) metal coordination : bond 0.01407 / 0.86 ( 8) metal coordination : angle 6.05230 / 3.31 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 160 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 95 LYS cc_start: 0.9369 (ptpt) cc_final: 0.9157 (ptpt) REVERT: H 51 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8491 (mmm) REVERT: H 158 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7373 (ptp90) REVERT: I 132 ASP cc_start: 0.9486 (m-30) cc_final: 0.8980 (t0) REVERT: I 239 MET cc_start: 0.8088 (ppp) cc_final: 0.7591 (ppp) REVERT: I 265 LYS cc_start: 0.9520 (OUTLIER) cc_final: 0.9304 (tptt) REVERT: I 315 MET cc_start: 0.9352 (tpp) cc_final: 0.9062 (tpp) REVERT: I 492 MET cc_start: 0.8720 (mpp) cc_final: 0.8146 (mpt) REVERT: I 523 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.8570 (mm-30) REVERT: I 530 ILE cc_start: 0.9425 (OUTLIER) cc_final: 0.8929 (pp) REVERT: I 562 GLU cc_start: 0.9141 (tm-30) cc_final: 0.8849 (tm-30) REVERT: I 813 GLU cc_start: 0.8506 (pp20) cc_final: 0.7959 (pp20) REVERT: I 814 ASP cc_start: 0.9006 (m-30) cc_final: 0.8801 (m-30) REVERT: I 1232 MET cc_start: 0.9314 (mtp) cc_final: 0.9000 (mmp) REVERT: I 1279 GLU cc_start: 0.9243 (mt-10) cc_final: 0.8961 (mt-10) REVERT: J 298 MET cc_start: 0.9022 (OUTLIER) cc_final: 0.8578 (ttp) REVERT: J 330 MET cc_start: 0.8662 (ppp) cc_final: 0.8429 (ppp) REVERT: J 443 GLU cc_start: 0.9376 (OUTLIER) cc_final: 0.9146 (mm-30) REVERT: J 644 MET cc_start: 0.9264 (mtm) cc_final: 0.8626 (mtm) REVERT: J 697 MET cc_start: 0.9040 (tmm) cc_final: 0.8763 (tmm) REVERT: J 821 MET cc_start: 0.9312 (tpp) cc_final: 0.9006 (tpt) REVERT: J 913 GLU cc_start: 0.7838 (mp0) cc_final: 0.7364 (mp0) REVERT: J 963 VAL cc_start: 0.9186 (OUTLIER) cc_final: 0.8965 (t) REVERT: J 1040 MET cc_start: 0.5572 (pmm) cc_final: 0.5216 (pmt) REVERT: J 1184 ASP cc_start: 0.9159 (OUTLIER) cc_final: 0.8175 (p0) REVERT: K 13 ILE cc_start: 0.9054 (mm) cc_final: 0.8691 (tt) REVERT: K 15 ASN cc_start: 0.8442 (t0) cc_final: 0.8043 (t0) REVERT: K 35 LYS cc_start: 0.9476 (mmmm) cc_final: 0.9183 (mmmm) REVERT: K 65 ASP cc_start: 0.9514 (p0) cc_final: 0.9301 (p0) outliers start: 80 outliers final: 56 residues processed: 229 average time/residue: 0.4847 time to fit residues: 132.7428 Evaluate side-chains 221 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 156 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 158 ARG Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 265 LYS Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 421 SER Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 523 GLU Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 843 THR Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 72 CYS Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 355 ILE Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 366 CYS Chi-restraints excluded: chain J residue 443 GLU Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 499 ILE Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 528 THR Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 592 VAL Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 976 THR Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1060 VAL Chi-restraints excluded: chain J residue 1184 ASP Chi-restraints excluded: chain K residue 64 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 180 optimal weight: 3.9990 chunk 312 optimal weight: 7.9990 chunk 234 optimal weight: 6.9990 chunk 301 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 chunk 274 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 259 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 170 optimal weight: 0.4980 chunk 199 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 66 HIS ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1259 GLN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.051761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.037395 restraints weight = 124561.890| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 3.91 r_work: 0.2678 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27466 Z= 0.121 Angle : 0.625 17.398 37457 Z= 0.312 Chirality : 0.042 0.209 4277 Planarity : 0.004 0.064 4620 Dihedral : 15.874 172.069 4474 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.28 % Favored : 96.69 % Rotamer: Outliers : 2.26 % Allowed : 27.33 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.15), residues: 3205 helix: 2.01 (0.16), residues: 1149 sheet: 0.01 (0.24), residues: 478 loop : -0.29 (0.16), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG K 69 TYR 0.022 0.001 TYR G 152 PHE 0.015 0.001 PHE I 156 TRP 0.011 0.001 TRP J 115 HIS 0.003 0.001 HIS J1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (27458) covalent geometry : angle 0.61651 / 0.31 (37445) hydrogen bonds : bond 0.03873 / 2.69 ( 1166) hydrogen bonds : angle 4.20329 / 2.98 ( 3206) metal coordination : bond 0.00789 / 0.47 ( 8) metal coordination : angle 5.70390 / 3.17 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 173 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 95 LYS cc_start: 0.9350 (ptpt) cc_final: 0.9139 (ptpt) REVERT: G 166 ARG cc_start: 0.9156 (tpp80) cc_final: 0.8866 (mmm-85) REVERT: H 51 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8419 (mmm) REVERT: H 158 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7387 (ptp90) REVERT: I 124 MET cc_start: 0.9438 (ttp) cc_final: 0.9121 (ptm) REVERT: I 239 MET cc_start: 0.8081 (ppp) cc_final: 0.7579 (ppp) REVERT: I 315 MET cc_start: 0.9381 (tpp) cc_final: 0.9091 (tpp) REVERT: I 492 MET cc_start: 0.8733 (mpp) cc_final: 0.8387 (mpt) REVERT: I 523 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8620 (mm-30) REVERT: I 530 ILE cc_start: 0.9393 (OUTLIER) cc_final: 0.8893 (pp) REVERT: I 562 GLU cc_start: 0.9143 (tm-30) cc_final: 0.8832 (tm-30) REVERT: I 813 GLU cc_start: 0.8454 (pp20) cc_final: 0.7887 (pp20) REVERT: I 814 ASP cc_start: 0.8971 (m-30) cc_final: 0.8766 (m-30) REVERT: I 1232 MET cc_start: 0.9272 (mtp) cc_final: 0.8986 (mmp) REVERT: I 1279 GLU cc_start: 0.9238 (mt-10) cc_final: 0.8869 (pt0) REVERT: J 298 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8550 (ttp) REVERT: J 330 MET cc_start: 0.8634 (ppp) cc_final: 0.8373 (ppp) REVERT: J 443 GLU cc_start: 0.9397 (OUTLIER) cc_final: 0.9156 (mm-30) REVERT: J 644 MET cc_start: 0.9220 (mtm) cc_final: 0.8623 (mtm) REVERT: J 697 MET cc_start: 0.9028 (tmm) cc_final: 0.8368 (tmm) REVERT: J 821 MET cc_start: 0.9362 (tpp) cc_final: 0.9009 (tpt) REVERT: J 913 GLU cc_start: 0.7788 (mp0) cc_final: 0.7306 (mp0) REVERT: J 963 VAL cc_start: 0.9201 (OUTLIER) cc_final: 0.8984 (t) REVERT: J 1040 MET cc_start: 0.5511 (pmm) cc_final: 0.5150 (pmt) REVERT: J 1184 ASP cc_start: 0.9143 (OUTLIER) cc_final: 0.8146 (p0) REVERT: K 13 ILE cc_start: 0.9006 (mm) cc_final: 0.8537 (tt) REVERT: K 15 ASN cc_start: 0.8355 (t0) cc_final: 0.7967 (OUTLIER) REVERT: K 35 LYS cc_start: 0.9456 (mmmm) cc_final: 0.9165 (mmmm) REVERT: K 65 ASP cc_start: 0.9505 (p0) cc_final: 0.9290 (p0) outliers start: 62 outliers final: 49 residues processed: 226 average time/residue: 0.5140 time to fit residues: 138.3516 Evaluate side-chains 221 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 165 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 158 ARG Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 421 SER Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 523 GLU Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 843 THR Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 72 CYS Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 355 ILE Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 366 CYS Chi-restraints excluded: chain J residue 443 GLU Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 976 THR Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1017 VAL Chi-restraints excluded: chain J residue 1060 VAL Chi-restraints excluded: chain J residue 1184 ASP Chi-restraints excluded: chain K residue 64 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 162 optimal weight: 5.9990 chunk 204 optimal weight: 1.9990 chunk 83 optimal weight: 0.4980 chunk 213 optimal weight: 0.0020 chunk 274 optimal weight: 2.9990 chunk 271 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 163 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 242 optimal weight: 6.9990 chunk 302 optimal weight: 10.0000 overall best weight: 1.0592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.051912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.037585 restraints weight = 124149.151| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 3.90 r_work: 0.2696 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27466 Z= 0.125 Angle : 0.626 16.819 37457 Z= 0.312 Chirality : 0.042 0.281 4277 Planarity : 0.004 0.063 4620 Dihedral : 15.843 171.890 4474 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.40 % Favored : 96.57 % Rotamer: Outliers : 1.93 % Allowed : 27.87 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.15), residues: 3205 helix: 2.03 (0.16), residues: 1149 sheet: -0.01 (0.24), residues: 483 loop : -0.27 (0.16), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG K 67 TYR 0.019 0.001 TYR G 152 PHE 0.014 0.001 PHE I 156 TRP 0.013 0.001 TRP J 115 HIS 0.003 0.001 HIS J1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (27458) covalent geometry : angle 0.61857 / 0.31 (37445) hydrogen bonds : bond 0.03792 / 2.63 ( 1166) hydrogen bonds : angle 4.18275 / 2.97 ( 3206) metal coordination : bond 0.00860 / 0.53 ( 8) metal coordination : angle 5.43839 / 3.00 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6936.21 seconds wall clock time: 119 minutes 13.93 seconds (7153.93 seconds total)