Starting phenix.real_space_refine on Mon Jun 23 09:39:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pdy_17626/06_2025/8pdy_17626.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pdy_17626/06_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_17626/06_2025/8pdy_17626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pdy_17626/06_2025/8pdy_17626.map" model { file = "/net/cci-nas-00/data/ceres_data/8pdy_17626/06_2025/8pdy_17626.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pdy_17626/06_2025/8pdy_17626.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.49, per 1000 atoms: 0.58 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: 6.47 Conformation dependent library (CDL) restraints added in 3.0 seconds 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: 8.71 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: 12.62 Time building geometry restraints manager: 7.31 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: 4.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.010 Check model and map are aligned: 0.210 Set scattering table: 0.240 Process input model: 70.720 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.440 ------------------------------------------------------------------------------- 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 : 10.32 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (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 TRP 0.025 0.001 TRP J1020 HIS 0.004 0.001 HIS J 777 PHE 0.010 0.001 PHE J 141 TYR 0.024 0.001 TYR G 152 ARG 0.004 0.000 ARG J 417 Details of bonding type rmsd hydrogen bonds : bond 0.13830 ( 1166) hydrogen bonds : angle 5.81646 ( 3206) metal coordination : bond 0.00390 ( 8) metal coordination : angle 4.56577 ( 12) covalent geometry : bond 0.00227 (27458) covalent geometry : angle 0.54778 (37445) *********************** 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 : 2.784 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: 1.3490 time to fit residues: 314.4650 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 : 2.769 ------------------------------------------------------------------------------- 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 276 optimal weight: 20.0000 chunk 248 optimal weight: 9.9990 chunk 137 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 167 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 257 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 156 optimal weight: 3.9990 chunk 191 optimal weight: 0.9980 chunk 297 optimal weight: 3.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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 J1218 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.050149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.035807 restraints weight = 126168.703| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 3.88 r_work: 0.2625 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 27466 Z= 0.319 Angle : 0.677 14.691 37457 Z= 0.343 Chirality : 0.042 0.209 4277 Planarity : 0.004 0.050 4620 Dihedral : 15.716 172.146 4482 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.62 % Favored : 96.35 % Rotamer: Outliers : 3.14 % Allowed : 21.34 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.15), residues: 3205 helix: 1.87 (0.15), residues: 1156 sheet: 0.03 (0.24), residues: 497 loop : -0.23 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP J1020 HIS 0.006 0.001 HIS J 777 PHE 0.018 0.002 PHE J 17 TYR 0.019 0.002 TYR J 631 ARG 0.006 0.001 ARG H 12 Details of bonding type rmsd hydrogen bonds : bond 0.04825 ( 1166) hydrogen bonds : angle 4.74985 ( 3206) metal coordination : bond 0.02243 ( 8) metal coordination : angle 7.22727 ( 12) covalent geometry : bond 0.00692 (27458) covalent geometry : angle 0.66493 (37445) *********************** 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 252 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 166 time to evaluate : 2.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 160 HIS cc_start: 0.8838 (OUTLIER) cc_final: 0.8573 (m-70) REVERT: I 161 LYS cc_start: 0.9404 (mmmt) cc_final: 0.9098 (mmmm) REVERT: I 239 MET cc_start: 0.7799 (ppp) cc_final: 0.7420 (ppp) REVERT: I 420 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9118 (tt) REVERT: I 492 MET cc_start: 0.8771 (mpp) cc_final: 0.8457 (mpt) REVERT: I 504 GLU cc_start: 0.9440 (tm-30) cc_final: 0.9178 (tm-30) REVERT: I 562 GLU cc_start: 0.9134 (tm-30) cc_final: 0.8919 (tm-30) REVERT: J 298 MET cc_start: 0.9101 (ttp) cc_final: 0.8602 (ttp) REVERT: J 304 ASP cc_start: 0.9060 (OUTLIER) cc_final: 0.8797 (m-30) REVERT: J 330 MET cc_start: 0.8996 (ppp) cc_final: 0.8759 (ppp) REVERT: J 697 MET cc_start: 0.9046 (tmm) cc_final: 0.8760 (tmm) REVERT: J 822 MET cc_start: 0.9018 (mmm) cc_final: 0.8691 (mmm) REVERT: J 913 GLU cc_start: 0.7760 (mp0) cc_final: 0.7254 (mp0) REVERT: J 1184 ASP cc_start: 0.9223 (OUTLIER) cc_final: 0.8301 (p0) REVERT: K 43 ASN cc_start: 0.9604 (t0) cc_final: 0.9375 (t0) REVERT: K 65 ASP cc_start: 0.9530 (p0) cc_final: 0.9296 (p0) REVERT: K 69 ARG cc_start: 0.9298 (mmm160) cc_final: 0.9045 (mmm160) outliers start: 86 outliers final: 35 residues processed: 233 average time/residue: 1.2605 time to fit residues: 349.9488 Evaluate side-chains 191 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 152 time to evaluate : 2.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 160 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 6 THR 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 420 LEU 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 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 I residue 1293 VAL Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 366 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 862 THR 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 1209 VAL Chi-restraints excluded: chain J residue 1352 ILE Chi-restraints excluded: chain K residue 21 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 285 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 162 optimal weight: 0.0670 chunk 110 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 276 optimal weight: 20.0000 chunk 259 optimal weight: 1.9990 chunk 320 optimal weight: 9.9990 chunk 173 optimal weight: 0.8980 chunk 298 optimal weight: 4.9990 overall best weight: 1.3924 ------------------------------------------------------------------------------- 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 ** I1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 341 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.051706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.037323 restraints weight = 122928.681| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 3.87 r_work: 0.2676 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27466 Z= 0.130 Angle : 0.543 11.163 37457 Z= 0.278 Chirality : 0.040 0.198 4277 Planarity : 0.004 0.053 4620 Dihedral : 15.704 174.959 4480 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.96 % Favored : 97.00 % Rotamer: Outliers : 2.26 % Allowed : 23.53 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.15), residues: 3205 helix: 2.06 (0.16), residues: 1152 sheet: 0.07 (0.24), residues: 489 loop : -0.25 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J1020 HIS 0.004 0.001 HIS J 777 PHE 0.018 0.001 PHE J 17 TYR 0.014 0.001 TYR J 140 ARG 0.007 0.000 ARG K 67 Details of bonding type rmsd hydrogen bonds : bond 0.03953 ( 1166) hydrogen bonds : angle 4.37624 ( 3206) metal coordination : bond 0.00954 ( 8) metal coordination : angle 6.03472 ( 12) covalent geometry : bond 0.00286 (27458) covalent geometry : angle 0.53262 (37445) *********************** 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 243 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 181 time to evaluate : 2.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 51 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8542 (mmm) REVERT: H 158 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7811 (mtm-85) REVERT: H 160 HIS cc_start: 0.8908 (OUTLIER) cc_final: 0.8651 (m-70) REVERT: I 132 ASP cc_start: 0.9471 (m-30) cc_final: 0.9031 (t0) REVERT: I 161 LYS cc_start: 0.9446 (mmmt) cc_final: 0.8996 (mmmm) REVERT: I 239 MET cc_start: 0.7778 (ppp) cc_final: 0.7391 (ppp) REVERT: I 492 MET cc_start: 0.8789 (mpp) cc_final: 0.8362 (mpt) REVERT: I 523 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8598 (mm-30) REVERT: I 530 ILE cc_start: 0.9411 (OUTLIER) cc_final: 0.8911 (pp) REVERT: I 562 GLU cc_start: 0.9121 (tm-30) cc_final: 0.8868 (tm-30) REVERT: I 813 GLU cc_start: 0.8344 (pp20) cc_final: 0.7823 (pp20) REVERT: I 834 GLN cc_start: 0.9179 (tt0) cc_final: 0.8853 (mm-40) REVERT: J 298 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8549 (ttp) REVERT: J 304 ASP cc_start: 0.8966 (OUTLIER) cc_final: 0.8098 (m-30) REVERT: J 330 MET cc_start: 0.8924 (ppp) cc_final: 0.8693 (ppp) REVERT: J 443 GLU cc_start: 0.9412 (OUTLIER) cc_final: 0.9121 (mm-30) REVERT: J 697 MET cc_start: 0.9008 (tmm) cc_final: 0.8289 (tmm) REVERT: J 698 MET cc_start: 0.9529 (OUTLIER) cc_final: 0.9199 (mmm) REVERT: J 913 GLU cc_start: 0.7700 (mp0) cc_final: 0.7206 (mp0) REVERT: K 15 ASN cc_start: 0.8466 (t0) cc_final: 0.8111 (t0) REVERT: K 43 ASN cc_start: 0.9589 (t0) cc_final: 0.9314 (t0) REVERT: K 65 ASP cc_start: 0.9485 (p0) cc_final: 0.9247 (p0) REVERT: K 69 ARG cc_start: 0.9324 (mmm160) cc_final: 0.9078 (mmm160) outliers start: 62 outliers final: 26 residues processed: 228 average time/residue: 1.5113 time to fit residues: 408.0242 Evaluate side-chains 198 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 163 time to evaluate : 2.924 ------------------------------------------------------------------------------- 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 158 ARG Chi-restraints excluded: chain H residue 160 HIS Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 523 GLU Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1235 LEU Chi-restraints excluded: chain I residue 1291 LEU 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 357 VAL Chi-restraints excluded: chain J residue 443 GLU Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 976 THR Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1060 VAL Chi-restraints excluded: chain J residue 1075 ARG Chi-restraints excluded: chain K residue 59 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 200 optimal weight: 0.9990 chunk 120 optimal weight: 0.0980 chunk 154 optimal weight: 3.9990 chunk 327 optimal weight: 10.0000 chunk 213 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 chunk 118 optimal weight: 7.9990 chunk 305 optimal weight: 9.9990 chunk 284 optimal weight: 30.0000 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 GLN ** I 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1135 GLN ** I1313 HIS ** 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 = 0.3277 r_free = 0.3277 target = 0.050571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.036171 restraints weight = 125329.775| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 3.90 r_work: 0.2637 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 27466 Z= 0.208 Angle : 0.582 12.281 37457 Z= 0.295 Chirality : 0.040 0.179 4277 Planarity : 0.004 0.052 4620 Dihedral : 15.722 173.723 4478 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.15 % Favored : 96.82 % Rotamer: Outliers : 3.47 % Allowed : 24.44 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.15), residues: 3205 helix: 2.08 (0.16), residues: 1152 sheet: 0.08 (0.24), residues: 485 loop : -0.25 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 115 HIS 0.004 0.001 HIS J 777 PHE 0.014 0.001 PHE J 17 TYR 0.022 0.001 TYR G 152 ARG 0.009 0.000 ARG K 67 Details of bonding type rmsd hydrogen bonds : bond 0.04119 ( 1166) hydrogen bonds : angle 4.37949 ( 3206) metal coordination : bond 0.01486 ( 8) metal coordination : angle 6.28051 ( 12) covalent geometry : bond 0.00455 (27458) covalent geometry : angle 0.57080 (37445) *********************** 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 262 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 167 time to evaluate : 2.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 51 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8518 (mmm) REVERT: H 158 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7875 (mtm-85) REVERT: H 160 HIS cc_start: 0.8831 (OUTLIER) cc_final: 0.8533 (m-70) REVERT: I 132 ASP cc_start: 0.9455 (m-30) cc_final: 0.9003 (t0) REVERT: I 239 MET cc_start: 0.7856 (ppp) cc_final: 0.7456 (ppp) REVERT: I 492 MET cc_start: 0.8737 (mpp) cc_final: 0.8227 (mpt) REVERT: I 523 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8607 (mm-30) REVERT: I 530 ILE cc_start: 0.9453 (OUTLIER) cc_final: 0.8899 (pp) REVERT: I 562 GLU cc_start: 0.9133 (tm-30) cc_final: 0.8867 (tm-30) REVERT: I 813 GLU cc_start: 0.8500 (pp20) cc_final: 0.7958 (pp20) REVERT: I 1232 MET cc_start: 0.9333 (mtp) cc_final: 0.8999 (mmp) REVERT: J 39 LYS cc_start: 0.9470 (OUTLIER) cc_final: 0.9120 (mtmm) REVERT: J 180 MET cc_start: 0.8428 (tpp) cc_final: 0.8168 (tpp) REVERT: J 298 MET cc_start: 0.9035 (OUTLIER) cc_final: 0.8581 (ttp) REVERT: J 304 ASP cc_start: 0.8990 (OUTLIER) cc_final: 0.8133 (m-30) REVERT: J 330 MET cc_start: 0.8861 (ppp) cc_final: 0.8651 (ppp) REVERT: J 443 GLU cc_start: 0.9380 (OUTLIER) cc_final: 0.9102 (mm-30) REVERT: J 644 MET cc_start: 0.9131 (mtm) cc_final: 0.8603 (mtm) REVERT: J 697 MET cc_start: 0.9048 (tmm) cc_final: 0.8719 (tmm) REVERT: J 821 MET cc_start: 0.9071 (mmm) cc_final: 0.8657 (tpt) REVERT: J 822 MET cc_start: 0.8996 (mmm) cc_final: 0.8649 (mmm) REVERT: J 913 GLU cc_start: 0.7836 (mp0) cc_final: 0.7338 (mp0) REVERT: J 963 VAL cc_start: 0.9141 (OUTLIER) cc_final: 0.8920 (t) REVERT: J 1184 ASP cc_start: 0.9175 (OUTLIER) cc_final: 0.8202 (p0) REVERT: K 15 ASN cc_start: 0.8520 (t0) cc_final: 0.8154 (t0) REVERT: K 43 ASN cc_start: 0.9562 (t0) cc_final: 0.9254 (t0) REVERT: K 69 ARG cc_start: 0.9335 (mmm160) cc_final: 0.9135 (mmm160) outliers start: 95 outliers final: 46 residues processed: 248 average time/residue: 1.1977 time to fit residues: 355.3112 Evaluate side-chains 212 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 155 time to evaluate : 2.871 ------------------------------------------------------------------------------- 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 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 158 ARG Chi-restraints excluded: chain H residue 160 HIS Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 135 THR 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 635 THR 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 964 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 39 LYS 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 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 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 1017 VAL Chi-restraints excluded: chain J residue 1060 VAL Chi-restraints excluded: chain J residue 1184 ASP Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 64 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 34 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 280 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 322 optimal weight: 10.0000 chunk 259 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 307 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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** J1019 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.049519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.035176 restraints weight = 126319.693| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 3.86 r_work: 0.2595 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 27466 Z= 0.290 Angle : 0.659 16.089 37457 Z= 0.332 Chirality : 0.042 0.190 4277 Planarity : 0.004 0.052 4620 Dihedral : 15.806 173.347 4474 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.56 % Favored : 96.41 % Rotamer: Outliers : 4.30 % Allowed : 24.41 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.15), residues: 3205 helix: 1.91 (0.16), residues: 1158 sheet: -0.01 (0.24), residues: 488 loop : -0.36 (0.16), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 115 HIS 0.005 0.001 HIS J 777 PHE 0.020 0.002 PHE J 17 TYR 0.022 0.002 TYR G 152 ARG 0.009 0.000 ARG K 67 Details of bonding type rmsd hydrogen bonds : bond 0.04521 ( 1166) hydrogen bonds : angle 4.54617 ( 3206) metal coordination : bond 0.01922 ( 8) metal coordination : angle 7.26465 ( 12) covalent geometry : bond 0.00631 (27458) covalent geometry : angle 0.64583 (37445) *********************** 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 283 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 165 time to evaluate : 3.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 95 LYS cc_start: 0.9392 (ptpt) cc_final: 0.9160 (ptpt) REVERT: H 51 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8575 (mmm) REVERT: H 111 THR cc_start: 0.9586 (OUTLIER) cc_final: 0.9204 (t) REVERT: H 158 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7912 (mtm-85) REVERT: H 160 HIS cc_start: 0.8879 (OUTLIER) cc_final: 0.8555 (m-70) REVERT: I 132 ASP cc_start: 0.9483 (OUTLIER) cc_final: 0.8948 (t0) REVERT: I 239 MET cc_start: 0.7900 (ppp) cc_final: 0.7442 (ppp) REVERT: I 315 MET cc_start: 0.9242 (tpp) cc_final: 0.8989 (tpp) REVERT: I 446 ASP cc_start: 0.9190 (m-30) cc_final: 0.8764 (t0) REVERT: I 492 MET cc_start: 0.8683 (mpp) cc_final: 0.8070 (mpt) REVERT: I 523 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8601 (mm-30) REVERT: I 530 ILE cc_start: 0.9455 (OUTLIER) cc_final: 0.8802 (pp) REVERT: I 546 GLU cc_start: 0.8979 (pm20) cc_final: 0.8772 (tm-30) REVERT: I 562 GLU cc_start: 0.9165 (tm-30) cc_final: 0.8888 (tm-30) REVERT: I 685 MET cc_start: 0.9001 (ptp) cc_final: 0.8798 (mtm) REVERT: I 834 GLN cc_start: 0.9226 (tt0) cc_final: 0.8982 (mm-40) REVERT: I 1232 MET cc_start: 0.9339 (mtp) cc_final: 0.8985 (mmp) REVERT: J 39 LYS cc_start: 0.9493 (OUTLIER) cc_final: 0.9086 (mtmm) REVERT: J 304 ASP cc_start: 0.9082 (OUTLIER) cc_final: 0.8257 (m-30) REVERT: J 330 MET cc_start: 0.8784 (ppp) cc_final: 0.8448 (ppp) REVERT: J 443 GLU cc_start: 0.9360 (OUTLIER) cc_final: 0.9157 (mm-30) REVERT: J 644 MET cc_start: 0.9332 (mtm) cc_final: 0.8632 (mtm) REVERT: J 697 MET cc_start: 0.9095 (tmm) cc_final: 0.8812 (tmm) REVERT: J 913 GLU cc_start: 0.7870 (mp0) cc_final: 0.7337 (mp0) REVERT: J 1184 ASP cc_start: 0.9220 (OUTLIER) cc_final: 0.8286 (p0) REVERT: J 1186 TYR cc_start: 0.9036 (OUTLIER) cc_final: 0.8794 (t80) REVERT: K 13 ILE cc_start: 0.9037 (mm) cc_final: 0.8683 (tt) REVERT: K 19 LEU cc_start: 0.8805 (tt) cc_final: 0.8597 (tm) REVERT: K 35 LYS cc_start: 0.9441 (mmmm) cc_final: 0.9018 (mmmm) REVERT: K 43 ASN cc_start: 0.9548 (t0) cc_final: 0.9145 (t0) outliers start: 118 outliers final: 57 residues processed: 263 average time/residue: 1.2566 time to fit residues: 393.5001 Evaluate side-chains 223 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 154 time to evaluate : 2.831 ------------------------------------------------------------------------------- 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 74 VAL Chi-restraints excluded: chain H residue 111 THR 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 132 ASP Chi-restraints excluded: chain I residue 135 THR 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 515 MET Chi-restraints excluded: chain I residue 523 GLU Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 654 ASP Chi-restraints excluded: chain I residue 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 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 1092 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 39 LYS Chi-restraints excluded: chain J residue 72 CYS 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 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 1186 TYR Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 64 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 123 optimal weight: 6.9990 chunk 149 optimal weight: 3.9990 chunk 293 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 310 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 287 optimal weight: 10.0000 chunk 96 optimal weight: 0.8980 chunk 142 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 314 ASN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 504 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.050973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.036602 restraints weight = 124605.153| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 3.91 r_work: 0.2647 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.2158 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= 0.128 Angle : 0.574 15.533 37457 Z= 0.290 Chirality : 0.041 0.267 4277 Planarity : 0.004 0.055 4620 Dihedral : 15.765 175.826 4474 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.18 % Favored : 96.79 % Rotamer: Outliers : 3.14 % Allowed : 26.52 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.15), residues: 3205 helix: 1.98 (0.16), residues: 1162 sheet: 0.00 (0.25), residues: 467 loop : -0.34 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J1020 HIS 0.003 0.001 HIS J1366 PHE 0.013 0.001 PHE J 141 TYR 0.023 0.001 TYR G 152 ARG 0.019 0.000 ARG K 69 Details of bonding type rmsd hydrogen bonds : bond 0.03923 ( 1166) hydrogen bonds : angle 4.24430 ( 3206) metal coordination : bond 0.00967 ( 8) metal coordination : angle 6.10889 ( 12) covalent geometry : bond 0.00286 (27458) covalent geometry : angle 0.56316 (37445) *********************** 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 262 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 176 time to evaluate : 8.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 95 LYS cc_start: 0.9366 (ptpt) cc_final: 0.9135 (ptpt) REVERT: H 51 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8458 (mmm) REVERT: H 158 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7401 (ptp90) REVERT: H 160 HIS cc_start: 0.8849 (OUTLIER) cc_final: 0.8509 (m-70) REVERT: I 124 MET cc_start: 0.9458 (ttp) cc_final: 0.9138 (ptm) REVERT: I 132 ASP cc_start: 0.9473 (m-30) cc_final: 0.8954 (t0) REVERT: I 239 MET cc_start: 0.7890 (ppp) cc_final: 0.7411 (ppp) REVERT: I 315 MET cc_start: 0.9270 (tpp) cc_final: 0.9070 (tpp) REVERT: I 446 ASP cc_start: 0.9166 (m-30) cc_final: 0.8704 (t0) REVERT: I 492 MET cc_start: 0.8727 (mpp) cc_final: 0.8190 (mmt) REVERT: I 503 LYS cc_start: 0.9431 (tppp) cc_final: 0.9191 (ptpt) REVERT: I 523 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8542 (mm-30) REVERT: I 530 ILE cc_start: 0.9433 (OUTLIER) cc_final: 0.8884 (pp) REVERT: I 546 GLU cc_start: 0.8999 (pm20) cc_final: 0.8758 (tm-30) REVERT: I 562 GLU cc_start: 0.9145 (tm-30) cc_final: 0.8845 (tm-30) REVERT: I 813 GLU cc_start: 0.8468 (pp20) cc_final: 0.7951 (pp20) REVERT: I 834 GLN cc_start: 0.9200 (tt0) cc_final: 0.8962 (mm-40) REVERT: I 1232 MET cc_start: 0.9313 (mtp) cc_final: 0.9051 (mmp) REVERT: J 298 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8582 (ttp) REVERT: J 443 GLU cc_start: 0.9357 (OUTLIER) cc_final: 0.9148 (mm-30) REVERT: J 644 MET cc_start: 0.9289 (mtm) cc_final: 0.8662 (mtm) REVERT: J 697 MET cc_start: 0.9052 (tmm) cc_final: 0.8823 (tmm) REVERT: J 913 GLU cc_start: 0.7874 (mp0) cc_final: 0.7367 (mp0) REVERT: J 925 GLU cc_start: 0.9517 (tm-30) cc_final: 0.9166 (pp20) REVERT: J 1040 MET cc_start: 0.5956 (pmm) cc_final: 0.5613 (pmt) REVERT: J 1184 ASP cc_start: 0.9198 (OUTLIER) cc_final: 0.8256 (p0) REVERT: K 13 ILE cc_start: 0.8960 (mm) cc_final: 0.8530 (tt) REVERT: K 15 ASN cc_start: 0.8391 (t0) cc_final: 0.7964 (t0) REVERT: K 19 LEU cc_start: 0.8688 (tt) cc_final: 0.8443 (tm) REVERT: K 35 LYS cc_start: 0.9462 (mmmm) cc_final: 0.9157 (mmmm) REVERT: K 43 ASN cc_start: 0.9572 (t0) cc_final: 0.9167 (t0) outliers start: 86 outliers final: 43 residues processed: 247 average time/residue: 1.7431 time to fit residues: 515.8460 Evaluate side-chains 215 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 164 time to evaluate : 2.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain H residue 5 VAL 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 158 ARG Chi-restraints excluded: chain H residue 160 HIS Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 421 SER Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 523 GLU Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 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 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 825 VAL 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 1060 VAL Chi-restraints excluded: chain J residue 1151 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 247 optimal weight: 0.6980 chunk 15 optimal weight: 20.0000 chunk 40 optimal weight: 8.9990 chunk 115 optimal weight: 0.9980 chunk 260 optimal weight: 7.9990 chunk 312 optimal weight: 6.9990 chunk 111 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 36 optimal weight: 20.0000 chunk 287 optimal weight: 10.0000 chunk 172 optimal weight: 4.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.050412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.036099 restraints weight = 125572.934| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 3.91 r_work: 0.2626 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 27466 Z= 0.190 Angle : 0.602 16.090 37457 Z= 0.303 Chirality : 0.041 0.210 4277 Planarity : 0.004 0.054 4620 Dihedral : 15.741 174.575 4474 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.62 % Favored : 96.35 % Rotamer: Outliers : 3.43 % Allowed : 26.85 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.15), residues: 3205 helix: 2.00 (0.16), residues: 1156 sheet: 0.00 (0.25), residues: 467 loop : -0.34 (0.16), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 115 HIS 0.005 0.001 HIS J 450 PHE 0.014 0.001 PHE I 405 TYR 0.023 0.001 TYR G 152 ARG 0.012 0.000 ARG K 69 Details of bonding type rmsd hydrogen bonds : bond 0.04065 ( 1166) hydrogen bonds : angle 4.27414 ( 3206) metal coordination : bond 0.01405 ( 8) metal coordination : angle 6.15887 ( 12) covalent geometry : bond 0.00420 (27458) covalent geometry : angle 0.59153 (37445) *********************** 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 262 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 168 time to evaluate : 2.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 166 ARG cc_start: 0.9147 (tpp80) cc_final: 0.8477 (mtp85) REVERT: H 51 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8478 (mmm) REVERT: H 158 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7403 (ptp90) REVERT: I 239 MET cc_start: 0.7940 (ppp) cc_final: 0.7414 (ppp) REVERT: I 265 LYS cc_start: 0.9543 (OUTLIER) cc_final: 0.9337 (tptt) REVERT: I 446 ASP cc_start: 0.9173 (m-30) cc_final: 0.8760 (t0) REVERT: I 492 MET cc_start: 0.8724 (mpp) cc_final: 0.8163 (mmt) REVERT: I 523 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8582 (mm-30) REVERT: I 530 ILE cc_start: 0.9435 (OUTLIER) cc_final: 0.8874 (pp) REVERT: I 546 GLU cc_start: 0.9057 (pm20) cc_final: 0.8788 (tm-30) REVERT: I 562 GLU cc_start: 0.9138 (tm-30) cc_final: 0.8808 (tm-30) REVERT: I 681 MET cc_start: 0.8906 (ptp) cc_final: 0.8701 (ptp) REVERT: I 813 GLU cc_start: 0.8550 (pp20) cc_final: 0.8007 (pp20) REVERT: I 834 GLN cc_start: 0.9213 (tt0) cc_final: 0.8982 (mm-40) REVERT: I 1232 MET cc_start: 0.9335 (mtp) cc_final: 0.9004 (mmp) REVERT: J 298 MET cc_start: 0.9046 (OUTLIER) cc_final: 0.8616 (ttp) REVERT: J 443 GLU cc_start: 0.9351 (OUTLIER) cc_final: 0.9139 (mm-30) REVERT: J 644 MET cc_start: 0.9328 (mtm) cc_final: 0.8670 (mtm) REVERT: J 697 MET cc_start: 0.9096 (tmm) cc_final: 0.8849 (tmm) REVERT: J 821 MET cc_start: 0.9305 (tpp) cc_final: 0.8903 (tpt) REVERT: J 822 MET cc_start: 0.9052 (mmm) cc_final: 0.8694 (mmm) REVERT: J 913 GLU cc_start: 0.7911 (mp0) cc_final: 0.7382 (mp0) REVERT: J 1040 MET cc_start: 0.5743 (pmm) cc_final: 0.5331 (pmt) REVERT: J 1184 ASP cc_start: 0.9197 (OUTLIER) cc_final: 0.8269 (p0) REVERT: J 1186 TYR cc_start: 0.8827 (t80) cc_final: 0.8514 (t80) REVERT: K 13 ILE cc_start: 0.9004 (mm) cc_final: 0.8692 (tt) REVERT: K 19 LEU cc_start: 0.8674 (tt) cc_final: 0.8450 (tm) REVERT: K 35 LYS cc_start: 0.9438 (mmmm) cc_final: 0.9039 (mmmm) REVERT: K 43 ASN cc_start: 0.9567 (t0) cc_final: 0.9164 (t0) outliers start: 94 outliers final: 53 residues processed: 248 average time/residue: 1.5135 time to fit residues: 447.8652 Evaluate side-chains 219 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 158 time to evaluate : 3.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain H residue 5 VAL 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 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 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 1290 MET 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 177 ASP 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 573 THR Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 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 1151 LYS Chi-restraints excluded: chain J residue 1184 ASP Chi-restraints excluded: chain J residue 1368 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 240 optimal weight: 7.9990 chunk 233 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 216 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 237 optimal weight: 5.9990 chunk 198 optimal weight: 10.0000 chunk 83 optimal weight: 0.7980 chunk 294 optimal weight: 5.9990 chunk 125 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.050470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.036049 restraints weight = 124882.736| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 3.92 r_work: 0.2633 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 27466 Z= 0.169 Angle : 0.609 15.366 37457 Z= 0.304 Chirality : 0.041 0.205 4277 Planarity : 0.004 0.055 4620 Dihedral : 15.735 175.079 4474 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.65 % Favored : 96.32 % Rotamer: Outliers : 3.25 % Allowed : 27.47 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.15), residues: 3205 helix: 1.98 (0.16), residues: 1155 sheet: 0.06 (0.25), residues: 457 loop : -0.35 (0.16), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 115 HIS 0.007 0.001 HIS J 450 PHE 0.013 0.001 PHE I 405 TYR 0.025 0.001 TYR G 152 ARG 0.014 0.000 ARG K 69 Details of bonding type rmsd hydrogen bonds : bond 0.03951 ( 1166) hydrogen bonds : angle 4.22095 ( 3206) metal coordination : bond 0.01265 ( 8) metal coordination : angle 5.98068 ( 12) covalent geometry : bond 0.00376 (27458) covalent geometry : angle 0.59960 (37445) *********************** 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: 89 poor density : 172 time to evaluate : 3.288 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: 0.9167 (tpp80) cc_final: 0.8515 (mtp85) REVERT: H 51 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8469 (mmm) REVERT: H 65 LEU cc_start: 0.9536 (OUTLIER) cc_final: 0.9038 (tp) REVERT: H 158 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7431 (ptp90) REVERT: I 124 MET cc_start: 0.9473 (ttp) cc_final: 0.9109 (ptm) REVERT: I 132 ASP cc_start: 0.9501 (m-30) cc_final: 0.8921 (t0) REVERT: I 239 MET cc_start: 0.7993 (ppp) cc_final: 0.7451 (ppp) REVERT: I 446 ASP cc_start: 0.9166 (m-30) cc_final: 0.8750 (t0) REVERT: I 492 MET cc_start: 0.8712 (mpp) cc_final: 0.8124 (mmt) REVERT: I 523 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8573 (mm-30) REVERT: I 530 ILE cc_start: 0.9424 (OUTLIER) cc_final: 0.8934 (pp) REVERT: I 546 GLU cc_start: 0.9065 (pm20) cc_final: 0.8771 (tm-30) REVERT: I 562 GLU cc_start: 0.9155 (tm-30) cc_final: 0.8809 (tm-30) REVERT: I 813 GLU cc_start: 0.8576 (pp20) cc_final: 0.8020 (pp20) REVERT: I 820 GLU cc_start: 0.9193 (tm-30) cc_final: 0.8785 (tm-30) REVERT: I 834 GLN cc_start: 0.9198 (tt0) cc_final: 0.8957 (mm-40) REVERT: I 1232 MET cc_start: 0.9319 (mtp) cc_final: 0.8996 (mmp) REVERT: I 1279 GLU cc_start: 0.9261 (mt-10) cc_final: 0.8783 (pm20) REVERT: J 298 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8583 (ttp) REVERT: J 443 GLU cc_start: 0.9360 (OUTLIER) cc_final: 0.9141 (mm-30) REVERT: J 644 MET cc_start: 0.9323 (mtm) cc_final: 0.8693 (mtm) REVERT: J 697 MET cc_start: 0.9071 (tmm) cc_final: 0.8849 (tmm) REVERT: J 821 MET cc_start: 0.9307 (tpp) cc_final: 0.8958 (tpt) REVERT: J 913 GLU cc_start: 0.7951 (mp0) cc_final: 0.7409 (mp0) REVERT: J 1040 MET cc_start: 0.5604 (pmm) cc_final: 0.5312 (pmt) REVERT: J 1184 ASP cc_start: 0.9200 (OUTLIER) cc_final: 0.8285 (p0) REVERT: J 1186 TYR cc_start: 0.8838 (t80) cc_final: 0.8495 (t80) REVERT: K 13 ILE cc_start: 0.8974 (mm) cc_final: 0.8575 (tt) REVERT: K 15 ASN cc_start: 0.8388 (t0) cc_final: 0.8016 (OUTLIER) REVERT: K 19 LEU cc_start: 0.8683 (tt) cc_final: 0.8447 (tm) REVERT: K 35 LYS cc_start: 0.9432 (mmmm) cc_final: 0.9041 (mmmm) REVERT: K 43 ASN cc_start: 0.9572 (t0) cc_final: 0.9171 (t0) outliers start: 89 outliers final: 56 residues processed: 248 average time/residue: 1.4345 time to fit residues: 426.3698 Evaluate side-chains 227 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 164 time to evaluate : 2.713 ------------------------------------------------------------------------------- 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 5 VAL 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 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 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 1092 THR Chi-restraints excluded: chain I residue 1225 VAL 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 177 ASP Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 355 ILE Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 366 CYS Chi-restraints excluded: chain J residue 443 GLU Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 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 1368 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 149 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 274 optimal weight: 8.9990 chunk 281 optimal weight: 9.9990 chunk 204 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 31 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 504 GLN J1259 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.050769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.036386 restraints weight = 125038.256| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 3.94 r_work: 0.2638 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 27466 Z= 0.160 Angle : 0.626 16.649 37457 Z= 0.310 Chirality : 0.041 0.198 4277 Planarity : 0.004 0.060 4620 Dihedral : 15.724 175.153 4474 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.56 % Favored : 96.41 % Rotamer: Outliers : 2.96 % Allowed : 27.73 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.15), residues: 3205 helix: 1.98 (0.16), residues: 1157 sheet: 0.01 (0.25), residues: 469 loop : -0.34 (0.16), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 115 HIS 0.007 0.001 HIS J 450 PHE 0.018 0.001 PHE I 405 TYR 0.025 0.001 TYR G 152 ARG 0.012 0.000 ARG K 67 Details of bonding type rmsd hydrogen bonds : bond 0.03909 ( 1166) hydrogen bonds : angle 4.22269 ( 3206) metal coordination : bond 0.01193 ( 8) metal coordination : angle 5.84658 ( 12) covalent geometry : bond 0.00358 (27458) covalent geometry : angle 0.61679 (37445) *********************** 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 253 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 172 time to evaluate : 3.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 166 ARG cc_start: 0.9169 (tpp80) cc_final: 0.8520 (mtp85) REVERT: H 51 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8470 (mmm) REVERT: H 65 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9033 (tp) REVERT: H 158 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7418 (ptp90) REVERT: I 124 MET cc_start: 0.9464 (ttp) cc_final: 0.9116 (ptm) REVERT: I 132 ASP cc_start: 0.9507 (m-30) cc_final: 0.8929 (t0) REVERT: I 239 MET cc_start: 0.8037 (ppp) cc_final: 0.7497 (ppp) REVERT: I 492 MET cc_start: 0.8754 (mpp) cc_final: 0.8081 (mpt) REVERT: I 523 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8573 (mm-30) REVERT: I 530 ILE cc_start: 0.9413 (OUTLIER) cc_final: 0.8887 (pp) REVERT: I 562 GLU cc_start: 0.9170 (tm-30) cc_final: 0.8806 (tm-30) REVERT: I 685 MET cc_start: 0.9058 (mtm) cc_final: 0.8801 (mtm) REVERT: I 813 GLU cc_start: 0.8545 (pp20) cc_final: 0.7983 (pp20) REVERT: I 820 GLU cc_start: 0.9185 (tm-30) cc_final: 0.8788 (tm-30) REVERT: I 834 GLN cc_start: 0.9199 (tt0) cc_final: 0.8960 (mm-40) REVERT: I 1232 MET cc_start: 0.9326 (mtp) cc_final: 0.9001 (mmp) REVERT: I 1279 GLU cc_start: 0.9237 (mt-10) cc_final: 0.8752 (pm20) REVERT: J 179 LYS cc_start: 0.9584 (OUTLIER) cc_final: 0.9115 (mmpt) REVERT: J 298 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8573 (ttp) REVERT: J 403 ARG cc_start: 0.9464 (mtp85) cc_final: 0.9235 (mmm160) REVERT: J 644 MET cc_start: 0.9327 (mtm) cc_final: 0.8700 (mtm) REVERT: J 821 MET cc_start: 0.9294 (tpp) cc_final: 0.8980 (tpt) REVERT: J 913 GLU cc_start: 0.7971 (mp0) cc_final: 0.7420 (mp0) REVERT: J 1040 MET cc_start: 0.5490 (pmm) cc_final: 0.5207 (pmt) REVERT: J 1143 ASP cc_start: 0.9132 (t0) cc_final: 0.8877 (t0) REVERT: J 1184 ASP cc_start: 0.9190 (OUTLIER) cc_final: 0.8258 (p0) REVERT: J 1186 TYR cc_start: 0.8809 (OUTLIER) cc_final: 0.8452 (t80) REVERT: K 13 ILE cc_start: 0.8952 (mm) cc_final: 0.8579 (tt) REVERT: K 15 ASN cc_start: 0.8387 (t0) cc_final: 0.8012 (OUTLIER) REVERT: K 19 LEU cc_start: 0.8680 (tt) cc_final: 0.8431 (tm) REVERT: K 35 LYS cc_start: 0.9420 (mmmm) cc_final: 0.9042 (mmmm) REVERT: K 43 ASN cc_start: 0.9584 (t0) cc_final: 0.9193 (t0) outliers start: 81 outliers final: 59 residues processed: 242 average time/residue: 1.2463 time to fit residues: 359.1579 Evaluate side-chains 231 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 164 time to evaluate : 2.786 ------------------------------------------------------------------------------- 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 5 VAL 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 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 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 1092 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain I residue 1339 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 177 ASP Chi-restraints excluded: chain J residue 179 LYS Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 355 ILE Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 363 LEU Chi-restraints excluded: chain J residue 366 CYS Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 888 CYS 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 1186 TYR Chi-restraints excluded: chain J residue 1368 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 45 optimal weight: 1.9990 chunk 250 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 52 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 306 optimal weight: 2.9990 chunk 305 optimal weight: 8.9990 chunk 319 optimal weight: 7.9990 chunk 228 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.050513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.036134 restraints weight = 125300.805| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 3.90 r_work: 0.2638 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 27466 Z= 0.174 Angle : 0.657 16.836 37457 Z= 0.323 Chirality : 0.041 0.197 4277 Planarity : 0.004 0.071 4620 Dihedral : 15.725 174.963 4474 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.65 % Favored : 96.32 % Rotamer: Outliers : 3.06 % Allowed : 27.69 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.15), residues: 3205 helix: 2.01 (0.16), residues: 1150 sheet: -0.07 (0.25), residues: 474 loop : -0.31 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 115 HIS 0.007 0.001 HIS J 450 PHE 0.019 0.001 PHE I 405 TYR 0.025 0.001 TYR G 152 ARG 0.015 0.000 ARG K 69 Details of bonding type rmsd hydrogen bonds : bond 0.03933 ( 1166) hydrogen bonds : angle 4.23306 ( 3206) metal coordination : bond 0.01262 ( 8) metal coordination : angle 5.87653 ( 12) covalent geometry : bond 0.00390 (27458) covalent geometry : angle 0.64826 (37445) ********************** 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 254 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 170 time to evaluate : 4.487 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: 0.9182 (tpp80) cc_final: 0.8528 (mtp85) REVERT: H 7 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8132 (pp20) REVERT: H 51 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8593 (mmm) REVERT: H 65 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9000 (tp) REVERT: H 158 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7419 (ptp90) REVERT: I 124 MET cc_start: 0.9485 (ttp) cc_final: 0.9110 (ptm) REVERT: I 239 MET cc_start: 0.8039 (ppp) cc_final: 0.7497 (ppp) REVERT: I 492 MET cc_start: 0.8718 (mpp) cc_final: 0.8054 (mpt) REVERT: I 523 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8580 (mm-30) REVERT: I 530 ILE cc_start: 0.9407 (OUTLIER) cc_final: 0.8856 (pp) REVERT: I 562 GLU cc_start: 0.9172 (tm-30) cc_final: 0.8793 (tm-30) REVERT: I 813 GLU cc_start: 0.8559 (pp20) cc_final: 0.7982 (pp20) REVERT: I 820 GLU cc_start: 0.9166 (tm-30) cc_final: 0.8765 (tm-30) REVERT: I 834 GLN cc_start: 0.9201 (tt0) cc_final: 0.8950 (mm-40) REVERT: I 1232 MET cc_start: 0.9327 (mtp) cc_final: 0.8988 (mmp) REVERT: I 1279 GLU cc_start: 0.9252 (mt-10) cc_final: 0.8756 (pm20) REVERT: J 17 PHE cc_start: 0.8324 (t80) cc_final: 0.8050 (t80) REVERT: J 179 LYS cc_start: 0.9586 (OUTLIER) cc_final: 0.9103 (mmpt) REVERT: J 298 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8579 (ttp) REVERT: J 338 PHE cc_start: 0.9293 (OUTLIER) cc_final: 0.8583 (t80) REVERT: J 403 ARG cc_start: 0.9467 (mtp85) cc_final: 0.9245 (mmm160) REVERT: J 644 MET cc_start: 0.9348 (mtm) cc_final: 0.8691 (mtm) REVERT: J 821 MET cc_start: 0.9309 (tpp) cc_final: 0.8980 (tpt) REVERT: J 913 GLU cc_start: 0.7981 (mp0) cc_final: 0.7387 (mp0) REVERT: J 1040 MET cc_start: 0.5487 (pmm) cc_final: 0.5193 (pmt) REVERT: J 1143 ASP cc_start: 0.9143 (t0) cc_final: 0.8902 (t0) REVERT: J 1184 ASP cc_start: 0.9203 (OUTLIER) cc_final: 0.8286 (p0) REVERT: J 1186 TYR cc_start: 0.8810 (OUTLIER) cc_final: 0.8475 (t80) REVERT: K 13 ILE cc_start: 0.8940 (mm) cc_final: 0.8566 (tt) REVERT: K 15 ASN cc_start: 0.8370 (t0) cc_final: 0.8002 (OUTLIER) REVERT: K 19 LEU cc_start: 0.8712 (tt) cc_final: 0.8459 (tm) REVERT: K 35 LYS cc_start: 0.9410 (mmmm) cc_final: 0.9041 (mmmm) REVERT: K 43 ASN cc_start: 0.9590 (t0) cc_final: 0.9210 (t0) outliers start: 84 outliers final: 60 residues processed: 239 average time/residue: 1.2651 time to fit residues: 361.8635 Evaluate side-chains 233 residues out of total 2741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 163 time to evaluate : 2.907 ------------------------------------------------------------------------------- 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 5 VAL Chi-restraints excluded: chain H residue 7 GLU 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 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 1092 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain I residue 1339 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 177 ASP Chi-restraints excluded: chain J residue 179 LYS Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 338 PHE Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 355 ILE Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 366 CYS Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 888 CYS 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 1151 LYS Chi-restraints excluded: chain J residue 1184 ASP Chi-restraints excluded: chain J residue 1186 TYR Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1368 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 154 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 190 optimal weight: 5.9990 chunk 242 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 284 optimal weight: 30.0000 chunk 283 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 228 optimal weight: 7.9990 chunk 172 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.051230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.036865 restraints weight = 124003.524| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 3.94 r_work: 0.2659 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.2446 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= 0.131 Angle : 0.634 16.570 37457 Z= 0.313 Chirality : 0.041 0.344 4277 Planarity : 0.004 0.061 4620 Dihedral : 15.684 175.891 4474 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.49 % Favored : 96.47 % Rotamer: Outliers : 2.59 % Allowed : 28.06 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.15), residues: 3205 helix: 2.05 (0.16), residues: 1143 sheet: -0.08 (0.24), residues: 480 loop : -0.27 (0.16), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 115 HIS 0.006 0.001 HIS J 450 PHE 0.017 0.001 PHE I 405 TYR 0.025 0.001 TYR G 152 ARG 0.014 0.000 ARG K 69 Details of bonding type rmsd hydrogen bonds : bond 0.03720 ( 1166) hydrogen bonds : angle 4.17990 ( 3206) metal coordination : bond 0.00908 ( 8) metal coordination : angle 5.51550 ( 12) covalent geometry : bond 0.00298 (27458) covalent geometry : angle 0.62591 (37445) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20501.48 seconds wall clock time: 360 minutes 38.09 seconds (21638.09 seconds total)