Starting phenix.real_space_refine on Mon Aug 25 09:43:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pdy_17626/08_2025/8pdy_17626.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pdy_17626/08_2025/8pdy_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8pdy_17626/08_2025/8pdy_17626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pdy_17626/08_2025/8pdy_17626.map" model { file = "/net/cci-nas-00/data/ceres_data/8pdy_17626/08_2025/8pdy_17626.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pdy_17626/08_2025/8pdy_17626.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 5.16, per 1000 atoms: 0.19 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: 1.80 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 3.55 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: 5.54 Time building geometry restraints manager: 2.51 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=" CA ILE J 416 " pdb=" C ILE J 416 " ideal model delta sigma weight residual 1.518 1.535 -0.016 1.13e-02 7.83e+03 2.12e+00 bond pdb=" SD MET I 741 " pdb=" CE MET I 741 " ideal model delta sigma weight residual 1.791 1.762 0.029 2.50e-02 1.60e+03 1.35e+00 bond pdb=" C3' DG B 1 " pdb=" O3' DG B 1 " ideal model delta sigma weight residual 1.422 1.456 -0.034 3.00e-02 1.11e+03 1.32e+00 bond pdb=" CB GLU I 813 " pdb=" CG GLU I 813 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.20e+00 bond pdb=" C ASN I 519 " pdb=" N PRO I 520 " ideal model delta sigma weight residual 1.333 1.349 -0.016 1.44e-02 4.82e+03 1.18e+00 ... (remaining 27453 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 37183 2.61 - 5.21: 228 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=" CA GLU I 813 " pdb=" CB GLU I 813 " pdb=" CG GLU I 813 " ideal model delta sigma weight residual 114.10 121.48 -7.38 2.00e+00 2.50e-01 1.36e+01 angle pdb=" CB MET J 192 " pdb=" CG MET J 192 " pdb=" SD MET J 192 " ideal model delta sigma weight residual 112.70 123.02 -10.32 3.00e+00 1.11e-01 1.18e+01 angle pdb=" CB MET I 403 " pdb=" CG MET I 403 " pdb=" SD MET I 403 " ideal model delta sigma weight residual 112.70 122.59 -9.89 3.00e+00 1.11e-01 1.09e+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: 2934 0.033 - 0.065: 888 0.065 - 0.098: 292 0.098 - 0.130: 155 0.130 - 0.163: 8 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=" 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 chirality pdb=" CA ILE I 668 " pdb=" N ILE I 668 " pdb=" C ILE I 668 " pdb=" CB ILE I 668 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.94e-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: 3.880 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: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 28.020 Find NCS groups from input model: 0.240 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:5.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 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 : 0.002 0.034 27466 Z= 0.111 Angle : 0.554 13.032 37457 Z= 0.290 Chirality : 0.039 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 aren 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 covalent geometry : bond 0.00227 (27458) covalent geometry : angle 0.54778 (37445) hydrogen bonds : bond 0.13830 ( 1166) hydrogen bonds : angle 5.81646 ( 3206) metal coordination : bond 0.00390 ( 8) metal coordination : angle 4.56577 ( 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 : 0.890 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: 0.6003 time to fit residues: 139.7412 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 : 0.764 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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** J 861 ASN J1114 GLN J1218 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.051542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.037239 restraints weight = 125168.729| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 3.90 r_work: 0.2668 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 27466 Z= 0.220 Angle : 0.605 11.746 37457 Z= 0.306 Chirality : 0.041 0.209 4277 Planarity : 0.004 0.050 4620 Dihedral : 15.648 173.594 4482 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.31 % Favored : 96.66 % Rotamer: Outliers : 2.85 % Allowed : 21.34 % Favored : 75.81 % 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 aren not related in a simple way. whole: 0.93 (0.15), residues: 3205 helix: 1.95 (0.16), residues: 1159 sheet: 0.09 (0.24), residues: 486 loop : -0.17 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 67 TYR 0.018 0.001 TYR J 631 PHE 0.014 0.001 PHE I 405 TRP 0.011 0.001 TRP J1020 HIS 0.006 0.001 HIS J 777 Details of bonding type rmsd covalent geometry : bond 0.00482 (27458) covalent geometry : angle 0.59462 (37445) hydrogen bonds : bond 0.04293 ( 1166) hydrogen bonds : angle 4.52695 ( 3206) metal coordination : bond 0.01498 ( 8) metal coordination : angle 6.21962 ( 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 253 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 175 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 160 HIS cc_start: 0.8885 (OUTLIER) cc_final: 0.8627 (m-70) REVERT: I 105 TYR cc_start: 0.9074 (m-80) cc_final: 0.8804 (m-80) REVERT: I 161 LYS cc_start: 0.9381 (mmmt) cc_final: 0.8893 (mmmm) REVERT: I 163 LYS cc_start: 0.9330 (mmtm) cc_final: 0.9126 (pmtt) REVERT: I 239 MET cc_start: 0.7679 (ppp) cc_final: 0.7384 (ppp) REVERT: I 492 MET cc_start: 0.8783 (mpp) cc_final: 0.8449 (mpt) REVERT: I 515 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8478 (ptm) REVERT: I 523 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8569 (mm-30) REVERT: I 562 GLU cc_start: 0.9082 (tm-30) cc_final: 0.8829 (tm-30) REVERT: I 741 MET cc_start: 0.8941 (pmm) cc_final: 0.8737 (pmm) REVERT: I 1279 GLU cc_start: 0.9224 (mt-10) cc_final: 0.9014 (mt-10) REVERT: J 298 MET cc_start: 0.9070 (ttp) cc_final: 0.8568 (ttp) REVERT: J 304 ASP cc_start: 0.9033 (OUTLIER) cc_final: 0.8775 (m-30) REVERT: J 697 MET cc_start: 0.9022 (tmm) cc_final: 0.8674 (tmm) REVERT: J 913 GLU cc_start: 0.7684 (mp0) cc_final: 0.7236 (mp0) REVERT: J 1184 ASP cc_start: 0.9171 (OUTLIER) cc_final: 0.8263 (p0) REVERT: K 15 ASN cc_start: 0.8522 (t0) cc_final: 0.8241 (t0) REVERT: K 43 ASN cc_start: 0.9597 (t0) cc_final: 0.9388 (t0) REVERT: K 65 ASP cc_start: 0.9483 (p0) cc_final: 0.9250 (p0) REVERT: K 69 ARG cc_start: 0.9306 (mmm160) cc_final: 0.9059 (mmm160) outliers start: 78 outliers final: 30 residues processed: 234 average time/residue: 0.5590 time to fit residues: 154.5549 Evaluate side-chains 196 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 161 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 H residue 183 ILE Chi-restraints excluded: chain I residue 196 VAL 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 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 29 MET Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 366 CYS Chi-restraints excluded: chain J residue 429 LEU 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 931 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 997 VAL 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 1209 VAL 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: 10.0000 chunk 243 optimal weight: 3.9990 chunk 245 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 302 optimal weight: 10.0000 chunk 314 optimal weight: 0.1980 chunk 114 optimal weight: 1.9990 chunk 327 optimal weight: 10.0000 chunk 284 optimal weight: 4.9990 chunk 247 optimal weight: 0.0170 chunk 321 optimal weight: 10.0000 overall best weight: 0.8422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 688 GLN I 955 GLN ** I1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 341 ASN ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.052642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.038271 restraints weight = 123054.380| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 3.89 r_work: 0.2711 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 27466 Z= 0.109 Angle : 0.530 10.054 37457 Z= 0.271 Chirality : 0.040 0.194 4277 Planarity : 0.004 0.053 4620 Dihedral : 15.627 175.575 4480 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.87 % Favored : 97.10 % Rotamer: Outliers : 2.19 % Allowed : 23.46 % Favored : 74.35 % 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 aren not related in a simple way. whole: 1.03 (0.15), residues: 3205 helix: 2.11 (0.16), residues: 1147 sheet: 0.10 (0.25), residues: 484 loop : -0.14 (0.16), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 67 TYR 0.021 0.001 TYR G 152 PHE 0.011 0.001 PHE J 141 TRP 0.008 0.001 TRP J1020 HIS 0.004 0.001 HIS J 777 Details of bonding type rmsd covalent geometry : bond 0.00237 (27458) covalent geometry : angle 0.52148 (37445) hydrogen bonds : bond 0.03754 ( 1166) hydrogen bonds : angle 4.28221 ( 3206) metal coordination : bond 0.00716 ( 8) metal coordination : angle 5.34127 ( 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 245 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 185 time to evaluate : 1.078 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: 0.8780 (OUTLIER) cc_final: 0.8402 (mmm) REVERT: H 158 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7820 (mtm-85) REVERT: I 40 GLU cc_start: 0.8930 (pt0) cc_final: 0.8629 (pp20) REVERT: I 239 MET cc_start: 0.7769 (ppp) cc_final: 0.7367 (ppp) REVERT: I 315 MET cc_start: 0.9216 (tpp) cc_final: 0.8882 (tpp) REVERT: I 369 MET cc_start: 0.9341 (tmm) cc_final: 0.9140 (tmm) REVERT: I 370 MET cc_start: 0.9438 (mmm) cc_final: 0.9236 (mmm) REVERT: I 492 MET cc_start: 0.8804 (mpp) cc_final: 0.8373 (mpt) REVERT: I 562 GLU cc_start: 0.9085 (tm-30) cc_final: 0.8793 (tm-30) REVERT: I 741 MET cc_start: 0.8948 (pmm) cc_final: 0.8710 (pmm) REVERT: I 813 GLU cc_start: 0.8221 (pp20) cc_final: 0.7753 (pp20) REVERT: I 1232 MET cc_start: 0.9283 (mtp) cc_final: 0.8958 (mmp) REVERT: I 1279 GLU cc_start: 0.9211 (mt-10) cc_final: 0.8768 (pt0) REVERT: J 298 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8489 (ttp) REVERT: J 697 MET cc_start: 0.8978 (tmm) cc_final: 0.8666 (tmm) REVERT: J 698 MET cc_start: 0.9495 (tpt) cc_final: 0.9220 (mmm) REVERT: J 821 MET cc_start: 0.9027 (mmm) cc_final: 0.8647 (tpt) REVERT: J 913 GLU cc_start: 0.7622 (mp0) cc_final: 0.7145 (mp0) REVERT: J 1357 ILE cc_start: 0.9309 (pt) cc_final: 0.9062 (pp) REVERT: K 15 ASN cc_start: 0.8420 (t0) cc_final: 0.7987 (t0) REVERT: K 43 ASN cc_start: 0.9585 (t0) cc_final: 0.9338 (t0) REVERT: K 65 ASP cc_start: 0.9486 (p0) cc_final: 0.9276 (p0) REVERT: K 69 ARG cc_start: 0.9335 (mmm160) cc_final: 0.9032 (mmm160) outliers start: 60 outliers final: 32 residues processed: 230 average time/residue: 0.5780 time to fit residues: 156.8632 Evaluate side-chains 199 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 164 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 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 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 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 1235 LEU Chi-restraints excluded: chain J residue 22 ILE 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 429 LEU 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 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 K residue 32 VAL 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: 5.9990 chunk 226 optimal weight: 4.9990 chunk 322 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 206 optimal weight: 7.9990 chunk 80 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 chunk 174 optimal weight: 0.8980 chunk 249 optimal weight: 6.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 66 HIS ** I 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 955 GLN I1135 GLN ** I1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1019 ASN ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.050884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.036443 restraints weight = 124713.650| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 3.91 r_work: 0.2644 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1695 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= 0.209 Angle : 0.583 11.962 37457 Z= 0.295 Chirality : 0.040 0.186 4277 Planarity : 0.004 0.051 4620 Dihedral : 15.633 173.299 4476 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.12 % Favored : 96.85 % Rotamer: Outliers : 3.36 % Allowed : 23.50 % Favored : 73.15 % 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 aren not related in a simple way. whole: 0.96 (0.15), residues: 3205 helix: 2.04 (0.16), residues: 1159 sheet: 0.07 (0.24), residues: 494 loop : -0.21 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 67 TYR 0.021 0.001 TYR G 152 PHE 0.011 0.001 PHE I 405 TRP 0.005 0.001 TRP J 115 HIS 0.005 0.001 HIS J 777 Details of bonding type rmsd covalent geometry : bond 0.00458 (27458) covalent geometry : angle 0.57293 (37445) hydrogen bonds : bond 0.04134 ( 1166) hydrogen bonds : angle 4.30935 ( 3206) metal coordination : bond 0.01540 ( 8) metal coordination : angle 6.19196 ( 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 261 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 169 time to evaluate : 1.137 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: 0.8867 (OUTLIER) cc_final: 0.8415 (mmm) REVERT: H 158 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.8035 (mtm-85) REVERT: I 132 ASP cc_start: 0.9475 (OUTLIER) cc_final: 0.9015 (t0) REVERT: I 161 LYS cc_start: 0.9484 (mmmt) cc_final: 0.9140 (mmmt) REVERT: I 239 MET cc_start: 0.7859 (ppp) cc_final: 0.7431 (ppp) REVERT: I 492 MET cc_start: 0.8740 (mpp) cc_final: 0.8233 (mpt) REVERT: I 523 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8551 (mm-30) REVERT: I 530 ILE cc_start: 0.9429 (OUTLIER) cc_final: 0.8916 (pp) REVERT: I 562 GLU cc_start: 0.9125 (tm-30) cc_final: 0.8844 (tm-30) REVERT: I 741 MET cc_start: 0.8962 (pmm) cc_final: 0.8690 (pmm) REVERT: I 1279 GLU cc_start: 0.9247 (mt-10) cc_final: 0.8987 (mt-10) REVERT: J 298 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8569 (ttp) REVERT: J 304 ASP cc_start: 0.8967 (OUTLIER) cc_final: 0.8114 (m-30) REVERT: J 443 GLU cc_start: 0.9384 (OUTLIER) cc_final: 0.9110 (mm-30) REVERT: J 644 MET cc_start: 0.9066 (mtm) cc_final: 0.8566 (mtm) REVERT: J 697 MET cc_start: 0.9031 (tmm) cc_final: 0.8725 (tmm) REVERT: J 913 GLU cc_start: 0.7795 (mp0) cc_final: 0.7293 (mp0) REVERT: J 963 VAL cc_start: 0.9119 (OUTLIER) cc_final: 0.8901 (t) REVERT: J 1184 ASP cc_start: 0.9183 (OUTLIER) cc_final: 0.8270 (p0) REVERT: K 15 ASN cc_start: 0.8450 (t0) cc_final: 0.8035 (t0) REVERT: K 43 ASN cc_start: 0.9530 (t0) cc_final: 0.9222 (t0) REVERT: K 69 ARG cc_start: 0.9360 (mmm160) cc_final: 0.9082 (mmm160) outliers start: 92 outliers final: 48 residues processed: 245 average time/residue: 0.5848 time to fit residues: 170.1058 Evaluate side-chains 215 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 157 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 6 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 196 VAL 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 589 THR Chi-restraints excluded: chain I residue 630 VAL 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 768 MET 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 1225 VAL Chi-restraints excluded: chain J residue 22 ILE 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 304 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 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 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 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 1186 TYR Chi-restraints excluded: chain K residue 19 LEU 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: 4.9990 chunk 119 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 190 optimal weight: 2.9990 chunk 317 optimal weight: 2.9990 chunk 289 optimal weight: 0.0070 chunk 87 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 chunk 246 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 66 HIS ** 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 341 ASN K 70 GLN K 73 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.051325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.036923 restraints weight = 124257.236| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 3.93 r_work: 0.2670 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1780 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= 0.156 Angle : 0.558 10.806 37457 Z= 0.282 Chirality : 0.040 0.165 4277 Planarity : 0.004 0.055 4620 Dihedral : 15.646 175.157 4476 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.87 % Favored : 97.10 % Rotamer: Outliers : 3.76 % Allowed : 24.08 % Favored : 72.16 % 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 aren not related in a simple way. whole: 0.98 (0.15), residues: 3205 helix: 2.08 (0.16), residues: 1154 sheet: 0.15 (0.25), residues: 462 loop : -0.21 (0.16), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 67 TYR 0.022 0.001 TYR G 152 PHE 0.012 0.001 PHE J 141 TRP 0.006 0.001 TRP J 115 HIS 0.004 0.001 HIS I 165 Details of bonding type rmsd covalent geometry : bond 0.00346 (27458) covalent geometry : angle 0.54795 (37445) hydrogen bonds : bond 0.03809 ( 1166) hydrogen bonds : angle 4.20106 ( 3206) metal coordination : bond 0.01130 ( 8) metal coordination : angle 5.78997 ( 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 276 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 173 time to evaluate : 0.931 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: 0.8831 (OUTLIER) cc_final: 0.8491 (mmm) REVERT: H 158 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.8060 (mtm-85) REVERT: H 160 HIS cc_start: 0.8833 (OUTLIER) cc_final: 0.8507 (m-70) REVERT: I 132 ASP cc_start: 0.9461 (m-30) cc_final: 0.8996 (t0) REVERT: I 239 MET cc_start: 0.7886 (ppp) cc_final: 0.7394 (ppp) REVERT: I 315 MET cc_start: 0.9192 (tpp) cc_final: 0.8942 (tpp) REVERT: I 369 MET cc_start: 0.9320 (tmm) cc_final: 0.9109 (tmm) REVERT: I 492 MET cc_start: 0.8749 (mpp) cc_final: 0.8174 (mpt) REVERT: I 523 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8581 (mm-30) REVERT: I 530 ILE cc_start: 0.9427 (OUTLIER) cc_final: 0.8891 (pp) REVERT: I 562 GLU cc_start: 0.9138 (tm-30) cc_final: 0.8838 (tm-30) REVERT: I 741 MET cc_start: 0.8980 (pmm) cc_final: 0.8689 (pmm) REVERT: I 813 GLU cc_start: 0.8440 (pp20) cc_final: 0.7938 (pp20) REVERT: I 1232 MET cc_start: 0.9332 (mtp) cc_final: 0.8975 (mmp) REVERT: I 1279 GLU cc_start: 0.9225 (mt-10) cc_final: 0.8851 (pt0) REVERT: J 298 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.8603 (ttp) REVERT: J 443 GLU cc_start: 0.9370 (OUTLIER) cc_final: 0.9100 (mm-30) REVERT: J 644 MET cc_start: 0.9109 (mtm) cc_final: 0.8655 (mtm) REVERT: J 697 MET cc_start: 0.9042 (tmm) cc_final: 0.8748 (tmm) REVERT: J 821 MET cc_start: 0.9291 (tpp) cc_final: 0.8958 (tpt) REVERT: J 913 GLU cc_start: 0.7759 (mp0) cc_final: 0.7278 (mp0) REVERT: J 963 VAL cc_start: 0.9175 (OUTLIER) cc_final: 0.8963 (t) REVERT: J 1040 MET cc_start: 0.5679 (pmm) cc_final: 0.5422 (pmt) REVERT: J 1184 ASP cc_start: 0.9171 (OUTLIER) cc_final: 0.8264 (p0) REVERT: K 13 ILE cc_start: 0.9034 (mm) cc_final: 0.8669 (tt) REVERT: K 15 ASN cc_start: 0.8381 (t0) cc_final: 0.7964 (t0) REVERT: K 35 LYS cc_start: 0.9471 (mmmm) cc_final: 0.9169 (mmmm) REVERT: K 43 ASN cc_start: 0.9570 (t0) cc_final: 0.9216 (t0) REVERT: K 65 ASP cc_start: 0.9496 (p0) cc_final: 0.9286 (p0) REVERT: K 69 ARG cc_start: 0.9377 (mmm160) cc_final: 0.9123 (mmm160) outliers start: 103 outliers final: 48 residues processed: 256 average time/residue: 0.5178 time to fit residues: 157.8171 Evaluate side-chains 218 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 161 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 158 ARG 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 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 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 964 LEU Chi-restraints excluded: chain I residue 984 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 363 LEU 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 579 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 271 optimal weight: 5.9990 chunk 253 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 304 optimal weight: 0.9980 chunk 224 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 287 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 66 HIS I 31 GLN I 314 ASN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 504 GLN ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.051393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.036974 restraints weight = 124395.499| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 3.92 r_work: 0.2673 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.1914 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= 0.149 Angle : 0.566 11.375 37457 Z= 0.285 Chirality : 0.040 0.262 4277 Planarity : 0.004 0.056 4620 Dihedral : 15.640 175.158 4476 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.34 % Favored : 96.63 % Rotamer: Outliers : 3.32 % Allowed : 25.21 % Favored : 71.47 % 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 aren not related in a simple way. whole: 0.97 (0.15), residues: 3205 helix: 2.10 (0.16), residues: 1153 sheet: 0.13 (0.25), residues: 462 loop : -0.25 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 322 TYR 0.023 0.001 TYR G 152 PHE 0.012 0.001 PHE I 405 TRP 0.007 0.001 TRP J 115 HIS 0.004 0.001 HIS J 450 Details of bonding type rmsd covalent geometry : bond 0.00329 (27458) covalent geometry : angle 0.55660 (37445) hydrogen bonds : bond 0.03791 ( 1166) hydrogen bonds : angle 4.15489 ( 3206) metal coordination : bond 0.01035 ( 8) metal coordination : angle 5.62987 ( 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 263 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 172 time to evaluate : 1.053 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: 0.8853 (OUTLIER) cc_final: 0.8515 (mmm) REVERT: H 158 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7377 (ptp90) REVERT: H 160 HIS cc_start: 0.8837 (OUTLIER) cc_final: 0.8512 (m-70) REVERT: I 132 ASP cc_start: 0.9465 (m-30) cc_final: 0.8965 (t0) REVERT: I 239 MET cc_start: 0.7905 (ppp) cc_final: 0.7408 (ppp) REVERT: I 265 LYS cc_start: 0.9528 (OUTLIER) cc_final: 0.9313 (tptt) REVERT: I 315 MET cc_start: 0.9329 (tpp) cc_final: 0.9044 (tpp) REVERT: I 492 MET cc_start: 0.8742 (mpp) cc_final: 0.8234 (mmt) REVERT: I 523 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8551 (mm-30) REVERT: I 530 ILE cc_start: 0.9416 (OUTLIER) cc_final: 0.8927 (pp) REVERT: I 562 GLU cc_start: 0.9140 (tm-30) cc_final: 0.8806 (tm-30) REVERT: I 741 MET cc_start: 0.8983 (pmm) cc_final: 0.8724 (pmm) REVERT: I 813 GLU cc_start: 0.8505 (pp20) cc_final: 0.7955 (pp20) REVERT: I 1232 MET cc_start: 0.9320 (mtp) cc_final: 0.8996 (mmp) REVERT: I 1279 GLU cc_start: 0.9220 (mt-10) cc_final: 0.8855 (pt0) REVERT: J 298 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8560 (ttp) REVERT: J 443 GLU cc_start: 0.9371 (OUTLIER) cc_final: 0.9115 (mm-30) REVERT: J 644 MET cc_start: 0.9160 (mtm) cc_final: 0.8724 (mtm) REVERT: J 697 MET cc_start: 0.9032 (tmm) cc_final: 0.8722 (tmm) REVERT: J 698 MET cc_start: 0.9517 (OUTLIER) cc_final: 0.9238 (mmm) REVERT: J 821 MET cc_start: 0.9260 (tpp) cc_final: 0.8960 (tpt) REVERT: J 913 GLU cc_start: 0.7757 (mp0) cc_final: 0.7276 (mp0) REVERT: J 963 VAL cc_start: 0.9172 (OUTLIER) cc_final: 0.8967 (t) REVERT: J 1040 MET cc_start: 0.5576 (pmm) cc_final: 0.5303 (pmt) REVERT: J 1184 ASP cc_start: 0.9158 (OUTLIER) cc_final: 0.8245 (p0) REVERT: K 13 ILE cc_start: 0.9011 (mm) cc_final: 0.8664 (tt) REVERT: K 15 ASN cc_start: 0.8375 (t0) cc_final: 0.7964 (t0) REVERT: K 35 LYS cc_start: 0.9470 (mmmm) cc_final: 0.9176 (mmmm) REVERT: K 43 ASN cc_start: 0.9569 (t0) cc_final: 0.9173 (t0) REVERT: K 65 ASP cc_start: 0.9491 (p0) cc_final: 0.9267 (p0) REVERT: K 69 ARG cc_start: 0.9405 (mmm160) cc_final: 0.9163 (mmm160) outliers start: 91 outliers final: 51 residues processed: 247 average time/residue: 0.5718 time to fit residues: 169.3779 Evaluate side-chains 225 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 163 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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 160 HIS Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 265 LYS Chi-restraints excluded: chain I residue 400 VAL 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 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 888 THR 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 1253 LEU Chi-restraints excluded: chain I residue 1290 MET 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 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 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 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 J residue 1248 ILE Chi-restraints excluded: chain K residue 19 LEU 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: 0.6980 chunk 260 optimal weight: 6.9990 chunk 206 optimal weight: 7.9990 chunk 228 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 42 optimal weight: 0.6980 chunk 187 optimal weight: 0.7980 chunk 269 optimal weight: 3.9990 chunk 267 optimal weight: 9.9990 chunk 299 optimal weight: 5.9990 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 66 HIS ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 504 GLN ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3290 r_free = 0.3290 target = 0.050944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.036545 restraints weight = 123885.337| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 3.90 r_work: 0.2647 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.2039 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= 0.182 Angle : 0.596 15.629 37457 Z= 0.297 Chirality : 0.040 0.214 4277 Planarity : 0.004 0.055 4620 Dihedral : 15.642 174.616 4476 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.37 % Favored : 96.60 % Rotamer: Outliers : 3.32 % Allowed : 25.68 % 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 aren not related in a simple way. whole: 0.93 (0.15), residues: 3205 helix: 2.07 (0.16), residues: 1158 sheet: 0.12 (0.25), residues: 468 loop : -0.29 (0.16), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 67 TYR 0.023 0.001 TYR G 152 PHE 0.019 0.001 PHE I 405 TRP 0.008 0.001 TRP J 115 HIS 0.006 0.001 HIS J 450 Details of bonding type rmsd covalent geometry : bond 0.00404 (27458) covalent geometry : angle 0.58727 (37445) hydrogen bonds : bond 0.03877 ( 1166) hydrogen bonds : angle 4.19164 ( 3206) metal coordination : bond 0.01333 ( 8) metal coordination : angle 5.73251 ( 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 252 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 161 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 166 ARG cc_start: 0.9145 (tpp80) cc_final: 0.8865 (mmm-85) REVERT: H 51 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.8545 (mmm) REVERT: H 158 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7395 (ptp90) REVERT: I 239 MET cc_start: 0.7930 (ppp) cc_final: 0.7394 (ppp) REVERT: I 265 LYS cc_start: 0.9526 (OUTLIER) cc_final: 0.9312 (tptt) REVERT: I 492 MET cc_start: 0.8721 (mpp) cc_final: 0.8220 (mmt) REVERT: I 523 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8532 (mm-30) REVERT: I 530 ILE cc_start: 0.9415 (OUTLIER) cc_final: 0.8913 (pp) REVERT: I 562 GLU cc_start: 0.9156 (tm-30) cc_final: 0.8904 (tm-30) REVERT: I 741 MET cc_start: 0.8971 (pmm) cc_final: 0.8690 (pmm) REVERT: I 813 GLU cc_start: 0.8537 (pp20) cc_final: 0.7949 (pp20) REVERT: I 814 ASP cc_start: 0.8879 (m-30) cc_final: 0.8647 (m-30) REVERT: I 834 GLN cc_start: 0.9223 (tt0) cc_final: 0.8913 (mm-40) REVERT: I 1232 MET cc_start: 0.9333 (mtp) cc_final: 0.8978 (mmp) REVERT: I 1279 GLU cc_start: 0.9218 (mt-10) cc_final: 0.8921 (mt-10) REVERT: J 298 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8601 (ttp) REVERT: J 443 GLU cc_start: 0.9359 (OUTLIER) cc_final: 0.9110 (mm-30) REVERT: J 466 MET cc_start: 0.9203 (mmm) cc_final: 0.8952 (mmm) REVERT: J 644 MET cc_start: 0.9212 (mtm) cc_final: 0.8812 (mtm) REVERT: J 697 MET cc_start: 0.9062 (tmm) cc_final: 0.8806 (tmm) REVERT: J 821 MET cc_start: 0.9346 (tpp) cc_final: 0.8969 (tpt) REVERT: J 913 GLU cc_start: 0.7785 (mp0) cc_final: 0.7284 (mp0) REVERT: J 1040 MET cc_start: 0.5759 (pmm) cc_final: 0.5338 (pmt) REVERT: J 1184 ASP cc_start: 0.9169 (OUTLIER) cc_final: 0.8243 (p0) REVERT: K 13 ILE cc_start: 0.8990 (mm) cc_final: 0.8660 (tt) REVERT: K 15 ASN cc_start: 0.8344 (t0) cc_final: 0.7938 (t0) REVERT: K 35 LYS cc_start: 0.9458 (mmmm) cc_final: 0.9171 (mmmm) REVERT: K 43 ASN cc_start: 0.9584 (t0) cc_final: 0.9200 (t0) REVERT: K 69 ARG cc_start: 0.9408 (mmm160) cc_final: 0.9189 (mmm160) outliers start: 91 outliers final: 59 residues processed: 238 average time/residue: 0.6116 time to fit residues: 174.3302 Evaluate side-chains 226 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 159 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL 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 137 ASN 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 589 THR 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 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 1253 LEU Chi-restraints excluded: chain I residue 1290 MET 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 363 LEU Chi-restraints excluded: chain J residue 366 CYS Chi-restraints excluded: chain J residue 415 VAL 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 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 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 J residue 1248 ILE Chi-restraints excluded: chain J residue 1368 ASP 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: 5.9990 chunk 300 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 166 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 309 optimal weight: 3.9990 chunk 220 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 chunk 97 optimal weight: 0.2980 chunk 174 optimal weight: 2.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.050469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.035994 restraints weight = 125218.304| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 3.91 r_work: 0.2632 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27466 Z= 0.196 Angle : 0.617 13.642 37457 Z= 0.306 Chirality : 0.041 0.202 4277 Planarity : 0.004 0.055 4620 Dihedral : 15.687 174.393 4476 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.81 % Favored : 96.16 % Rotamer: Outliers : 3.47 % Allowed : 25.98 % Favored : 70.56 % 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 aren not related in a simple way. whole: 0.85 (0.15), residues: 3205 helix: 2.01 (0.16), residues: 1162 sheet: 0.05 (0.25), residues: 468 loop : -0.34 (0.16), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 67 TYR 0.024 0.001 TYR G 152 PHE 0.021 0.001 PHE I 405 TRP 0.011 0.001 TRP J 115 HIS 0.006 0.001 HIS J 450 Details of bonding type rmsd covalent geometry : bond 0.00431 (27458) covalent geometry : angle 0.60712 (37445) hydrogen bonds : bond 0.03997 ( 1166) hydrogen bonds : angle 4.21810 ( 3206) metal coordination : bond 0.01454 ( 8) metal coordination : angle 6.01863 ( 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 261 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 166 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 51 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8521 (mmm) REVERT: H 65 LEU cc_start: 0.9546 (OUTLIER) cc_final: 0.9035 (tp) REVERT: H 158 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7418 (ptp90) REVERT: I 132 ASP cc_start: 0.9509 (m-30) cc_final: 0.8933 (t0) REVERT: I 239 MET cc_start: 0.7943 (ppp) cc_final: 0.7395 (ppp) REVERT: I 492 MET cc_start: 0.8711 (mpp) cc_final: 0.8179 (mmt) REVERT: I 523 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8564 (mm-30) REVERT: I 530 ILE cc_start: 0.9392 (OUTLIER) cc_final: 0.8771 (pp) REVERT: I 562 GLU cc_start: 0.9163 (tm-30) cc_final: 0.8805 (tm-30) REVERT: I 741 MET cc_start: 0.8938 (pmm) cc_final: 0.8637 (pmm) REVERT: I 813 GLU cc_start: 0.8593 (pp20) cc_final: 0.7990 (pp20) REVERT: I 814 ASP cc_start: 0.8797 (m-30) cc_final: 0.8577 (m-30) REVERT: I 834 GLN cc_start: 0.9230 (tt0) cc_final: 0.8904 (mm-40) REVERT: I 1279 GLU cc_start: 0.9241 (mt-10) cc_final: 0.8715 (mp0) REVERT: J 298 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8572 (ttp) REVERT: J 443 GLU cc_start: 0.9371 (OUTLIER) cc_final: 0.9132 (mm-30) REVERT: J 644 MET cc_start: 0.9296 (mtm) cc_final: 0.8677 (mtm) REVERT: J 697 MET cc_start: 0.9077 (tmm) cc_final: 0.8846 (tmm) REVERT: J 821 MET cc_start: 0.9267 (tpp) cc_final: 0.8986 (tpt) REVERT: J 913 GLU cc_start: 0.7840 (mp0) cc_final: 0.7283 (mp0) REVERT: J 1040 MET cc_start: 0.5703 (pmm) cc_final: 0.5460 (pmt) REVERT: J 1184 ASP cc_start: 0.9189 (OUTLIER) cc_final: 0.8193 (p0) REVERT: K 13 ILE cc_start: 0.8950 (mm) cc_final: 0.8618 (tt) REVERT: K 15 ASN cc_start: 0.8337 (t0) cc_final: 0.7949 (OUTLIER) REVERT: K 35 LYS cc_start: 0.9418 (mmmm) cc_final: 0.9050 (mmmm) REVERT: K 43 ASN cc_start: 0.9555 (t0) cc_final: 0.9158 (t0) REVERT: K 69 ARG cc_start: 0.9442 (mmm160) cc_final: 0.9211 (mmm160) outliers start: 95 outliers final: 58 residues processed: 247 average time/residue: 0.6257 time to fit residues: 183.8282 Evaluate side-chains 223 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 158 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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 65 LEU Chi-restraints excluded: chain H residue 74 VAL 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 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 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 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 1253 LEU Chi-restraints excluded: chain I residue 1290 MET 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 363 LEU Chi-restraints excluded: chain J residue 366 CYS Chi-restraints excluded: chain J residue 415 VAL 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 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 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 J residue 1248 ILE Chi-restraints excluded: chain J residue 1368 ASP 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: 6.9990 chunk 150 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 245 optimal weight: 6.9990 chunk 240 optimal weight: 6.9990 chunk 225 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 274 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 73 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 = 0.3265 r_free = 0.3265 target = 0.050112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.035659 restraints weight = 125757.490| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 3.92 r_work: 0.2621 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 27466 Z= 0.218 Angle : 0.653 17.268 37457 Z= 0.323 Chirality : 0.041 0.195 4277 Planarity : 0.004 0.061 4620 Dihedral : 15.716 174.233 4474 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.87 % Favored : 96.10 % Rotamer: Outliers : 2.88 % Allowed : 26.96 % Favored : 70.16 % 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 aren not related in a simple way. whole: 0.77 (0.15), residues: 3205 helix: 1.97 (0.16), residues: 1161 sheet: -0.08 (0.25), residues: 468 loop : -0.37 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 67 TYR 0.023 0.001 TYR G 152 PHE 0.020 0.001 PHE I 405 TRP 0.013 0.001 TRP J 115 HIS 0.005 0.001 HIS J 777 Details of bonding type rmsd covalent geometry : bond 0.00482 (27458) covalent geometry : angle 0.64407 (37445) hydrogen bonds : bond 0.04115 ( 1166) hydrogen bonds : angle 4.27842 ( 3206) metal coordination : bond 0.01594 ( 8) metal coordination : angle 6.15712 ( 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 241 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 162 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 51 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8561 (mmm) REVERT: H 65 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.9031 (tp) REVERT: H 158 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7427 (ptp90) REVERT: I 124 MET cc_start: 0.9463 (ttp) cc_final: 0.9097 (ptm) REVERT: I 132 ASP cc_start: 0.9501 (m-30) cc_final: 0.8880 (t0) REVERT: I 239 MET cc_start: 0.7969 (ppp) cc_final: 0.7502 (ppp) REVERT: I 446 ASP cc_start: 0.9179 (m-30) cc_final: 0.8724 (t0) REVERT: I 492 MET cc_start: 0.8702 (mpp) cc_final: 0.8167 (mmt) REVERT: I 523 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8609 (mm-30) REVERT: I 530 ILE cc_start: 0.9404 (OUTLIER) cc_final: 0.8764 (pp) REVERT: I 546 GLU cc_start: 0.8984 (pm20) cc_final: 0.8712 (tm-30) REVERT: I 562 GLU cc_start: 0.9179 (tm-30) cc_final: 0.8813 (tm-30) REVERT: I 741 MET cc_start: 0.8929 (pmm) cc_final: 0.8638 (pmm) REVERT: I 813 GLU cc_start: 0.8622 (pp20) cc_final: 0.8033 (pp20) REVERT: I 834 GLN cc_start: 0.9232 (tt0) cc_final: 0.8910 (mm-40) REVERT: I 877 VAL cc_start: 0.9458 (OUTLIER) cc_final: 0.9230 (p) REVERT: I 1279 GLU cc_start: 0.9230 (mt-10) cc_final: 0.8933 (mt-10) REVERT: J 298 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8565 (ttp) REVERT: J 443 GLU cc_start: 0.9340 (OUTLIER) cc_final: 0.9137 (mm-30) REVERT: J 644 MET cc_start: 0.9322 (mtm) cc_final: 0.8745 (mtm) REVERT: J 697 MET cc_start: 0.9092 (tmm) cc_final: 0.8854 (tmm) REVERT: J 821 MET cc_start: 0.9315 (tpp) cc_final: 0.8950 (tpt) REVERT: J 913 GLU cc_start: 0.7889 (mp0) cc_final: 0.7314 (mp0) REVERT: J 925 GLU cc_start: 0.9526 (tm-30) cc_final: 0.9096 (pp20) REVERT: J 1040 MET cc_start: 0.5706 (pmm) cc_final: 0.5469 (pmt) REVERT: J 1184 ASP cc_start: 0.9155 (OUTLIER) cc_final: 0.8200 (p0) REVERT: J 1186 TYR cc_start: 0.8829 (t80) cc_final: 0.8549 (t80) REVERT: K 13 ILE cc_start: 0.8938 (mm) cc_final: 0.8625 (tt) REVERT: K 15 ASN cc_start: 0.8385 (t0) cc_final: 0.8009 (OUTLIER) REVERT: K 35 LYS cc_start: 0.9409 (mmmm) cc_final: 0.9045 (mmmm) REVERT: K 43 ASN cc_start: 0.9564 (t0) cc_final: 0.9168 (t0) outliers start: 79 outliers final: 56 residues processed: 228 average time/residue: 0.6156 time to fit residues: 168.4743 Evaluate side-chains 217 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 153 time to evaluate : 1.136 ------------------------------------------------------------------------------- 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 65 LEU Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 137 ASN 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 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 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 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 877 VAL 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 1253 LEU 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 363 LEU Chi-restraints excluded: chain J residue 366 CYS Chi-restraints excluded: chain J residue 415 VAL 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 592 VAL Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 674 THR 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 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 J residue 1368 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: 0.4980 chunk 312 optimal weight: 0.9980 chunk 234 optimal weight: 0.9980 chunk 301 optimal weight: 0.9980 chunk 158 optimal weight: 3.9990 chunk 274 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 259 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 170 optimal weight: 1.9990 chunk 199 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** J 777 HIS J1259 GLN ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3302 r_free = 0.3302 target = 0.051450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.037082 restraints weight = 123784.787| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 3.92 r_work: 0.2673 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.2322 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= 0.118 Angle : 0.624 16.588 37457 Z= 0.307 Chirality : 0.041 0.200 4277 Planarity : 0.004 0.058 4620 Dihedral : 15.675 176.185 4474 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.21 % Favored : 96.76 % Rotamer: Outliers : 2.19 % Allowed : 27.87 % Favored : 69.94 % 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 aren not related in a simple way. whole: 0.88 (0.15), residues: 3205 helix: 2.07 (0.16), residues: 1143 sheet: -0.06 (0.24), residues: 476 loop : -0.28 (0.16), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG K 69 TYR 0.022 0.001 TYR G 152 PHE 0.015 0.001 PHE I 405 TRP 0.013 0.001 TRP J 115 HIS 0.005 0.001 HIS J 450 Details of bonding type rmsd covalent geometry : bond 0.00268 (27458) covalent geometry : angle 0.61649 (37445) hydrogen bonds : bond 0.03720 ( 1166) hydrogen bonds : angle 4.13757 ( 3206) metal coordination : bond 0.00787 ( 8) metal coordination : angle 5.54000 ( 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 231 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 171 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 51 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8453 (mmm) REVERT: H 65 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9001 (tp) REVERT: H 158 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7465 (ptp90) REVERT: I 124 MET cc_start: 0.9440 (ttp) cc_final: 0.9168 (ptm) REVERT: I 132 ASP cc_start: 0.9491 (m-30) cc_final: 0.8897 (t0) REVERT: I 239 MET cc_start: 0.7949 (ppp) cc_final: 0.7390 (ppp) REVERT: I 446 ASP cc_start: 0.9128 (m-30) cc_final: 0.8625 (t0) REVERT: I 492 MET cc_start: 0.8728 (mpp) cc_final: 0.8289 (mpt) REVERT: I 523 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8547 (mm-30) REVERT: I 530 ILE cc_start: 0.9374 (OUTLIER) cc_final: 0.8879 (pp) REVERT: I 546 GLU cc_start: 0.8994 (pm20) cc_final: 0.8701 (tm-30) REVERT: I 562 GLU cc_start: 0.9176 (tm-30) cc_final: 0.8892 (tm-30) REVERT: I 741 MET cc_start: 0.8927 (pmm) cc_final: 0.8652 (pmm) REVERT: I 813 GLU cc_start: 0.8523 (pp20) cc_final: 0.7978 (pp20) REVERT: I 820 GLU cc_start: 0.9154 (tm-30) cc_final: 0.8758 (tm-30) REVERT: I 1232 MET cc_start: 0.9281 (mtp) cc_final: 0.8981 (mmp) REVERT: I 1279 GLU cc_start: 0.9205 (mt-10) cc_final: 0.8820 (pt0) REVERT: J 17 PHE cc_start: 0.8311 (t80) cc_final: 0.8012 (t80) REVERT: J 298 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.8528 (ttp) REVERT: J 400 MET cc_start: 0.9145 (ttm) cc_final: 0.8749 (mtm) REVERT: J 403 ARG cc_start: 0.9483 (mtp85) cc_final: 0.9245 (mmm160) REVERT: J 644 MET cc_start: 0.9255 (mtm) cc_final: 0.8724 (mtm) REVERT: J 821 MET cc_start: 0.9295 (tpp) cc_final: 0.8968 (tpt) REVERT: J 913 GLU cc_start: 0.7845 (mp0) cc_final: 0.7281 (mp0) REVERT: J 1040 MET cc_start: 0.5657 (pmm) cc_final: 0.5292 (pmt) REVERT: J 1184 ASP cc_start: 0.9153 (OUTLIER) cc_final: 0.8189 (p0) REVERT: J 1186 TYR cc_start: 0.8716 (t80) cc_final: 0.8476 (t80) REVERT: J 1195 GLN cc_start: 0.9255 (OUTLIER) cc_final: 0.9040 (tm-30) REVERT: K 13 ILE cc_start: 0.8892 (mm) cc_final: 0.8510 (tt) REVERT: K 15 ASN cc_start: 0.8254 (t0) cc_final: 0.7860 (OUTLIER) REVERT: K 35 LYS cc_start: 0.9413 (mmmm) cc_final: 0.9068 (mmmm) REVERT: K 43 ASN cc_start: 0.9591 (t0) cc_final: 0.9234 (t0) outliers start: 60 outliers final: 45 residues processed: 222 average time/residue: 0.5245 time to fit residues: 138.8631 Evaluate side-chains 214 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 162 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 70 THR 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 65 LEU Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 158 ARG Chi-restraints excluded: chain I residue 6 THR 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 635 THR 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 888 THR 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 1253 LEU 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 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 825 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 J residue 1195 GLN Chi-restraints excluded: chain J residue 1368 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: 4.9990 chunk 204 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 213 optimal weight: 0.0870 chunk 274 optimal weight: 10.0000 chunk 271 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 163 optimal weight: 0.0970 chunk 176 optimal weight: 0.0020 chunk 242 optimal weight: 6.9990 chunk 302 optimal weight: 9.9990 overall best weight: 1.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 504 GLN ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 GLN 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 = 0.051719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.037388 restraints weight = 123372.639| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 3.94 r_work: 0.2675 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27466 Z= 0.123 Angle : 0.629 15.859 37457 Z= 0.307 Chirality : 0.041 0.207 4277 Planarity : 0.004 0.067 4620 Dihedral : 15.599 175.478 4474 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.46 % Favored : 96.51 % Rotamer: Outliers : 2.23 % Allowed : 27.98 % Favored : 69.79 % 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 aren not related in a simple way. whole: 0.91 (0.15), residues: 3205 helix: 2.08 (0.16), residues: 1144 sheet: 0.01 (0.25), residues: 463 loop : -0.26 (0.16), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG K 69 TYR 0.021 0.001 TYR G 152 PHE 0.021 0.001 PHE I 156 TRP 0.015 0.001 TRP J 115 HIS 0.006 0.001 HIS J 450 Details of bonding type rmsd covalent geometry : bond 0.00281 (27458) covalent geometry : angle 0.62159 (37445) hydrogen bonds : bond 0.03671 ( 1166) hydrogen bonds : angle 4.10872 ( 3206) metal coordination : bond 0.00805 ( 8) metal coordination : angle 5.36033 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7597.70 seconds wall clock time: 130 minutes 41.96 seconds (7841.96 seconds total)