Starting phenix.real_space_refine on Sun Jun 7 01:04:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yn0_73131/06_2026/9yn0_73131.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yn0_73131/06_2026/9yn0_73131.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9yn0_73131/06_2026/9yn0_73131.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yn0_73131/06_2026/9yn0_73131.map" model { file = "/net/cci-nas-00/data/ceres_data/9yn0_73131/06_2026/9yn0_73131.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yn0_73131/06_2026/9yn0_73131.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.020 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 117 5.49 5 Mg 1 5.21 5 S 131 5.16 5 C 19548 2.51 5 N 5617 2.21 5 O 6688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32104 Number of models: 1 Model: "" Number of chains: 20 Chain: "I" Number of atoms: 10567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10567 Classifications: {'peptide': 1340} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Chain: "K" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 610 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "P" Number of atoms: 1178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1178 Classifications: {'DNA': 57} Link IDs: {'rna3p': 56} Chain breaks: 1 Chain: "G" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1709 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 211} Chain breaks: 1 Chain: "H" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1710 Classifications: {'peptide': 222} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 212} Chain breaks: 1 Chain: "J" Number of atoms: 10386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1336, 10386 Classifications: {'peptide': 1336} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1280} Chain breaks: 2 Chain: "L" Number of atoms: 4416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4416 Classifications: {'peptide': 553} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 17, 'TRANS': 535} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 34 Chain: "Q" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 1116 Classifications: {'DNA': 55} Link IDs: {'rna3p': 54} Chain breaks: 1 Chain: "R" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna3p': 2} Chain: "I" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'POP': 1} Classifications: {'undetermined': 1} 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} Chain: "I" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 148 Classifications: {'water': 148} Link IDs: {None: 147} Chain: "K" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "P" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "G" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "H" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "J" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 122 Classifications: {'water': 122} Link IDs: {None: 121} Chain: "L" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "Q" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16223 SG CYS J 70 51.197 53.562 117.233 1.00100.53 S ATOM 16237 SG CYS J 72 53.189 52.451 120.168 1.00 99.15 S ATOM 16345 SG CYS J 85 49.588 52.836 120.520 1.00113.04 S ATOM 16369 SG CYS J 88 51.736 55.879 120.216 1.00111.93 S ATOM 22057 SG CYS J 814 23.818 109.143 86.883 1.00 90.99 S ATOM 22622 SG CYS J 888 27.272 107.943 87.816 1.00 74.85 S ATOM 22673 SG CYS J 895 25.612 106.672 84.733 1.00 75.29 S ATOM 22694 SG CYS J 898 26.805 110.192 84.842 1.00 93.66 S Time building chain proxies: 7.28, per 1000 atoms: 0.23 Number of scatterers: 32104 At special positions: 0 Unit cell: (154.8, 184.9, 196.08, 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 131 16.00 P 117 15.00 Mg 1 11.99 O 6688 8.00 N 5617 7.00 C 19548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.90 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " Number of angles added : 12 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6962 Finding SS restraints... Secondary structure from input PDB file: 143 helices and 48 sheets defined 45.2% alpha, 16.0% beta 48 base pairs and 94 stacking pairs defined. Time for finding SS restraints: 4.38 Creating SS restraints... Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.541A pdb=" N LEU I 32 " --> pdb=" O LEU I 28 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 57 removed outlier: 3.827A pdb=" N ALA I 51 " --> pdb=" O TYR I 47 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL I 56 " --> pdb=" O ALA I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.815A 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 242 through 247 Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 289 through 293 removed outlier: 3.638A pdb=" N ILE I 292 " --> pdb=" O VAL I 289 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 327 removed outlier: 3.891A pdb=" N GLN I 327 " --> pdb=" O ALA I 323 " (cutoff:3.500A) 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 removed outlier: 3.826A pdb=" N ALA I 381 " --> pdb=" O THR I 377 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU I 382 " --> pdb=" O ARG I 378 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 397 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 455 through 482 removed outlier: 3.535A pdb=" N GLN I 463 " --> pdb=" O MET I 459 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG I 470 " --> pdb=" O VAL I 466 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER I 480 " --> pdb=" O LYS I 476 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU I 481 " --> pdb=" O GLU I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 488 through 493 removed outlier: 3.867A pdb=" N MET I 492 " --> pdb=" O MET I 488 " (cutoff:3.500A) Processing helix chain 'I' and resid 494 through 509 removed outlier: 4.429A pdb=" N ILE I 498 " --> pdb=" O ASN I 494 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA I 501 " --> pdb=" O PRO I 497 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL I 502 " --> pdb=" O ILE I 498 " (cutoff:3.500A) removed outlier: 3.558A 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: 3.507A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 608 through 612 removed outlier: 3.708A 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 648 through 650 No H-bonds generated for 'chain 'I' and resid 648 through 650' Processing helix chain 'I' and resid 664 through 668 removed outlier: 3.644A pdb=" N LEU I 667 " --> pdb=" O GLY I 664 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE I 668 " --> pdb=" O ALA I 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 664 through 668' Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 686 Processing helix chain 'I' and resid 704 through 713 removed outlier: 4.147A pdb=" N GLY I 713 " --> pdb=" O ALA I 709 " (cutoff:3.500A) Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 896 through 907 Processing helix chain 'I' and resid 942 through 976 removed outlier: 3.951A pdb=" N ARG I 974 " --> pdb=" O GLY I 970 " (cutoff:3.500A) Processing helix chain 'I' and resid 977 through 981 Processing helix chain 'I' and resid 985 through 990 removed outlier: 4.651A pdb=" N ASP I 990 " --> pdb=" O ALA I 986 " (cutoff:3.500A) Processing helix chain 'I' and resid 993 through 1000 removed outlier: 3.991A pdb=" N LEU I 998 " --> pdb=" O ASP I 995 " (cutoff:3.500A) Processing helix chain 'I' and resid 1001 through 1005 Processing helix chain 'I' and resid 1006 through 1037 Processing helix chain 'I' and resid 1081 through 1085 removed outlier: 3.789A pdb=" N MET I1085 " --> pdb=" O ILE I1082 " (cutoff:3.500A) Processing helix chain 'I' and resid 1099 through 1103 removed outlier: 3.650A pdb=" N GLY I1102 " --> pdb=" O ASN I1099 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL I1103 " --> pdb=" O PRO I1100 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1099 through 1103' Processing helix chain 'I' and resid 1109 through 1134 Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.675A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU I1151 " --> pdb=" O ARG I1147 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1176 Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1242 Processing helix chain 'I' and resid 1271 through 1282 Processing helix chain 'I' and resid 1283 through 1292 Processing helix chain 'I' and resid 1297 through 1311 removed outlier: 3.797A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1332 removed outlier: 3.803A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 15 through 33 removed outlier: 3.679A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 57 Processing helix chain 'K' and resid 60 through 78 Processing helix chain 'G' and resid 34 through 48 removed outlier: 3.846A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 86 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 158 Processing helix chain 'G' and resid 212 through 228 Processing helix chain 'G' and resid 228 through 233 Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.670A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 removed outlier: 3.753A pdb=" N GLY H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) 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 227 Processing helix chain 'J' and resid 26 through 34 removed outlier: 3.531A pdb=" N SER J 34 " --> pdb=" O ILE J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 63 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 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 180 through 191 removed outlier: 3.579A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 207 Processing helix chain 'J' and resid 210 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 264 through 286 removed outlier: 3.742A pdb=" N LEU J 268 " --> pdb=" O ASP J 264 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 326 through 332 Processing helix chain 'J' and resid 336 through 342 Processing helix chain 'J' and resid 370 through 377 removed outlier: 3.744A pdb=" N GLU J 375 " --> pdb=" O LYS J 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 405 through 416 removed outlier: 4.134A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (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 453 through 458 Processing helix chain 'J' and resid 473 through 484 Processing helix chain 'J' and resid 504 through 514 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 580 Processing helix chain 'J' and resid 581 through 583 No H-bonds generated for 'chain 'J' and resid 581 through 583' Processing helix chain 'J' and resid 588 through 593 removed outlier: 3.655A pdb=" N ILE J 591 " --> pdb=" O PRO J 588 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN J 593 " --> pdb=" O SER J 590 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 612 Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.918A pdb=" N ASP J 622 " --> pdb=" O VAL J 618 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 671 Processing helix chain 'J' and resid 674 through 702 Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 removed outlier: 3.743A pdb=" N GLN J 739 " --> pdb=" O ALA J 735 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 805 removed outlier: 4.142A pdb=" N LYS J 781 " --> pdb=" O HIS J 777 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY J 782 " --> pdb=" O GLY J 778 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N THR J 790 " --> pdb=" O THR J 786 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) Processing helix chain 'J' and resid 835 through 840 Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 884 through 888 Processing helix chain 'J' and resid 896 through 900 removed outlier: 3.523A pdb=" N GLY J 900 " --> pdb=" O ALA J 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 896 through 900' Processing helix chain 'J' and resid 914 through 925 removed outlier: 3.691A 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 1146 Processing helix chain 'J' and resid 1216 through 1224 Processing helix chain 'J' and resid 1225 through 1243 removed outlier: 3.567A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU J1243 " --> pdb=" O ASP J1239 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.454A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 removed outlier: 3.595A pdb=" N ALA J1294 " --> pdb=" O ARG J1290 " (cutoff:3.500A) Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1318 through 1326 Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1347 through 1353 Processing helix chain 'J' and resid 1359 through 1361 No H-bonds generated for 'chain 'J' and resid 1359 through 1361' Processing helix chain 'J' and resid 1362 through 1374 Processing helix chain 'L' and resid 8 through 20 Processing helix chain 'L' and resid 23 through 30 Processing helix chain 'L' and resid 37 through 51 removed outlier: 3.813A pdb=" N ILE L 41 " --> pdb=" O ASP L 37 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN L 49 " --> pdb=" O ILE L 45 " (cutoff:3.500A) Processing helix chain 'L' and resid 66 through 83 Processing helix chain 'L' and resid 96 through 106 Processing helix chain 'L' and resid 112 through 136 removed outlier: 3.960A pdb=" N ILE L 117 " --> pdb=" O ARG L 113 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU L 136 " --> pdb=" O CYS L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 153 Processing helix chain 'L' and resid 157 through 162 Processing helix chain 'L' and resid 215 through 235 removed outlier: 3.880A pdb=" N ASP L 233 " --> pdb=" O VAL L 229 " (cutoff:3.500A) Processing helix chain 'L' and resid 245 through 257 removed outlier: 4.278A pdb=" N ILE L 249 " --> pdb=" O ALA L 245 " (cutoff:3.500A) Processing helix chain 'L' and resid 262 through 296 removed outlier: 3.730A pdb=" N CYS L 291 " --> pdb=" O ILE L 287 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLN L 294 " --> pdb=" O LEU L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 307 removed outlier: 3.529A pdb=" N PHE L 302 " --> pdb=" O PRO L 298 " (cutoff:3.500A) Processing helix chain 'L' and resid 313 through 319 Processing helix chain 'L' and resid 320 through 323 removed outlier: 3.992A pdb=" N ASN L 323 " --> pdb=" O ILE L 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 320 through 323' Processing helix chain 'L' and resid 324 through 330 Processing helix chain 'L' and resid 333 through 352 Processing helix chain 'L' and resid 354 through 382 removed outlier: 3.800A pdb=" N VAL L 358 " --> pdb=" O THR L 354 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN L 362 " --> pdb=" O VAL L 358 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG L 363 " --> pdb=" O LYS L 359 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE L 367 " --> pdb=" O ARG L 363 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY L 368 " --> pdb=" O ARG L 364 " (cutoff:3.500A) Processing helix chain 'L' and resid 383 through 393 removed outlier: 4.266A pdb=" N VAL L 387 " --> pdb=" O ASN L 383 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 418 removed outlier: 3.638A pdb=" N ILE L 410 " --> pdb=" O GLN L 406 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY L 411 " --> pdb=" O GLU L 407 " (cutoff:3.500A) Processing helix chain 'L' and resid 420 through 424 removed outlier: 3.599A pdb=" N ARG L 423 " --> pdb=" O GLU L 420 " (cutoff:3.500A) Processing helix chain 'L' and resid 426 through 447 removed outlier: 4.001A pdb=" N TYR L 430 " --> pdb=" O LYS L 426 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N TRP L 433 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TRP L 434 " --> pdb=" O TYR L 430 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA L 447 " --> pdb=" O ILE L 443 " (cutoff:3.500A) Processing helix chain 'L' and resid 453 through 475 Processing helix chain 'L' and resid 479 through 488 Processing helix chain 'L' and resid 490 through 500 Processing helix chain 'L' and resid 518 through 523 removed outlier: 3.768A pdb=" N PHE L 522 " --> pdb=" O LEU L 519 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE L 523 " --> pdb=" O GLY L 520 " (cutoff:3.500A) Processing helix chain 'L' and resid 530 through 550 removed outlier: 3.845A pdb=" N GLY L 550 " --> pdb=" O ASP L 546 " (cutoff:3.500A) Processing helix chain 'L' and resid 552 through 564 Processing helix chain 'L' and resid 572 through 581 Processing helix chain 'L' and resid 583 through 599 Processing helix chain 'L' and resid 600 through 604 Processing helix chain 'L' and resid 606 through 611 removed outlier: 3.637A pdb=" N PHE L 610 " --> pdb=" O LEU L 607 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.583A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 59 through 60 removed outlier: 6.695A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA I 94 " --> pdb=" O GLY I 125 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLY I 125 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU I 96 " --> pdb=" O TYR I 123 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N TYR I 123 " --> pdb=" O LEU I 96 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL I 98 " --> pdb=" O GLU I 121 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU I 121 " --> pdb=" O VAL I 98 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEU I 100 " --> pdb=" O GLU I 119 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLU I 119 " --> pdb=" O LEU I 100 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU I 102 " --> pdb=" O ILE I 117 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE I 117 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE I 104 " --> pdb=" O LYS I 115 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 136 through 138 Processing sheet with id=AA4, first strand: chain 'I' and resid 451 through 454 removed outlier: 3.703A pdb=" N SER I 147 " --> pdb=" O ARG I 529 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 154 through 159 removed outlier: 3.568A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 285 through 287 removed outlier: 4.419A pdb=" N LEU I 237 " --> pdb=" O VAL I 287 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 255 through 257 removed outlier: 7.141A pdb=" N ILE I 255 " --> pdb=" O TYR I 262 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 296 through 297 removed outlier: 3.971A pdb=" N MET I 315 " --> pdb=" O VAL I 297 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 301 through 303 removed outlier: 6.044A pdb=" N ASP I 303 " --> pdb=" O LEU I 309 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LEU I 309 " --> pdb=" O ASP I 303 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.425A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N THR I 595 " --> pdb=" O THR I 600 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N THR I 600 " --> pdb=" O THR I 595 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AB3, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.528A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.731A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AB6, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AB7, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.335A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 830 through 841 removed outlier: 6.309A pdb=" N THR I 830 " --> pdb=" O LYS I1057 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS I1057 " --> pdb=" O THR I 830 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N HIS I 832 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA I1055 " --> pdb=" O HIS I 832 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLN I 834 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TYR I1053 " --> pdb=" O GLN I 834 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU I 836 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS I1051 " --> pdb=" O LEU I 836 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N CYS I 838 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ILE I1049 " --> pdb=" O CYS I 838 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N SER I 840 " --> pdb=" O LEU I1047 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.831A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 887 through 889 Processing sheet with id=AC2, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 6.552A pdb=" N CYS J 366 " --> pdb=" O VAL J 440 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE J 442 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU J 368 " --> pdb=" O ILE J 442 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 1268 through 1270 removed outlier: 3.789A pdb=" N GLN I1268 " --> pdb=" O VAL J 347 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 1335 through 1340 removed outlier: 3.879A pdb=" N ALA J 19 " --> pdb=" O GLU I1340 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 12 through 20 removed outlier: 6.729A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLN G 18 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N HIS G 23 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.709A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLY G 149 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N CYS G 54 " --> pdb=" O GLY G 149 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AC8, first strand: chain 'G' and resid 108 through 111 removed outlier: 6.575A pdb=" N GLY G 108 " --> pdb=" O HIS G 132 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N HIS G 132 " --> pdb=" O GLY G 108 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL G 110 " --> pdb=" O ILE G 130 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 152 through 153 Processing sheet with id=AD1, first strand: chain 'H' and resid 13 through 18 removed outlier: 6.641A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N THR H 196 " --> pdb=" O VAL H 192 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL H 192 " --> pdb=" O THR H 196 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU H 198 " --> pdb=" O ALA H 190 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 97 through 105 removed outlier: 6.567A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 90 through 92 Processing sheet with id=AD4, first strand: chain 'H' and resid 108 through 111 removed outlier: 3.714A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AD6, first strand: chain 'J' and resid 103 through 112 removed outlier: 9.917A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.271A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 159 through 160 removed outlier: 6.960A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 252 through 254 removed outlier: 6.734A pdb=" N PHE J 260 " --> pdb=" O ILE L 505 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AE1, first strand: chain 'J' and resid 703 through 707 Processing sheet with id=AE2, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AE3, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE4, first strand: chain 'J' and resid 825 through 826 removed outlier: 6.938A pdb=" N VAL J 825 " --> pdb=" O LYS J 832 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 848 through 849 removed outlier: 6.960A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 949 through 952 removed outlier: 4.414A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL J 952 " --> pdb=" O THR J1016 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N THR J1016 " --> pdb=" O VAL J 952 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 991 through 996 removed outlier: 3.839A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 1025 through 1028 removed outlier: 5.115A pdb=" N MET J1025 " --> pdb=" O ARG J1123 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG J1123 " --> pdb=" O MET J1025 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL J1027 " --> pdb=" O LEU J1121 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 1034 through 1038 removed outlier: 3.877A pdb=" N LYS J1079 " --> pdb=" O ARG J1036 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR J1038 " --> pdb=" O ALA J1077 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 1046 through 1051 removed outlier: 3.696A pdb=" N VAL J1060 " --> pdb=" O THR J1047 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN J1049 " --> pdb=" O SER J1058 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 1186 through 1191 Processing sheet with id=AF3, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 6.765A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1369 hydrogen bonds defined for protein. 3849 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 118 hydrogen bonds 236 hydrogen bond angles 0 basepair planarities 48 basepair parallelities 94 stacking parallelities Total time for adding SS restraints: 10.20 Time building geometry restraints manager: 3.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9206 1.33 - 1.45: 5043 1.45 - 1.57: 17761 1.57 - 1.69: 227 1.69 - 1.81: 231 Bond restraints: 32468 Sorted by residual: bond pdb=" O POP I1401 " pdb=" P2 POP I1401 " ideal model delta sigma weight residual 1.661 1.611 0.050 2.00e-02 2.50e+03 6.17e+00 bond pdb=" O POP I1401 " pdb=" P1 POP I1401 " ideal model delta sigma weight residual 1.660 1.612 0.048 2.00e-02 2.50e+03 5.84e+00 bond pdb=" C3' DA Q 54 " pdb=" O3' DA Q 54 " ideal model delta sigma weight residual 1.422 1.459 -0.037 3.00e-02 1.11e+03 1.56e+00 bond pdb=" O1 POP I1401 " pdb=" P1 POP I1401 " ideal model delta sigma weight residual 1.531 1.510 0.021 2.00e-02 2.50e+03 1.15e+00 bond pdb=" O2 POP I1401 " pdb=" P1 POP I1401 " ideal model delta sigma weight residual 1.531 1.510 0.021 2.00e-02 2.50e+03 1.11e+00 ... (remaining 32463 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.53: 44289 3.53 - 7.06: 31 7.06 - 10.59: 5 10.59 - 14.13: 1 14.13 - 17.66: 1 Bond angle restraints: 44327 Sorted by residual: angle pdb=" P1 POP I1401 " pdb=" O POP I1401 " pdb=" P2 POP I1401 " ideal model delta sigma weight residual 139.66 122.00 17.66 3.00e+00 1.11e-01 3.46e+01 angle pdb=" C LYS I 17 " pdb=" N ARG I 18 " pdb=" CA ARG I 18 " ideal model delta sigma weight residual 121.95 111.33 10.62 3.74e+00 7.15e-02 8.07e+00 angle pdb=" O POP I1401 " pdb=" P1 POP I1401 " pdb=" O2 POP I1401 " ideal model delta sigma weight residual 102.11 110.07 -7.96 3.00e+00 1.11e-01 7.04e+00 angle pdb=" O POP I1401 " pdb=" P2 POP I1401 " pdb=" O4 POP I1401 " ideal model delta sigma weight residual 102.05 109.24 -7.19 3.00e+00 1.11e-01 5.75e+00 angle pdb=" N GLY G 106 " pdb=" CA GLY G 106 " pdb=" C GLY G 106 " ideal model delta sigma weight residual 111.56 113.89 -2.33 1.01e+00 9.80e-01 5.34e+00 ... (remaining 44322 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.22: 19072 35.22 - 70.43: 639 70.43 - 105.65: 14 105.65 - 140.87: 0 140.87 - 176.09: 1 Dihedral angle restraints: 19726 sinusoidal: 8929 harmonic: 10797 Sorted by residual: dihedral pdb=" C4' DA Q 54 " pdb=" C3' DA Q 54 " pdb=" O3' DA Q 54 " pdb=" P DG Q 55 " ideal model delta sinusoidal sigma weight residual 220.00 43.91 176.09 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA PHE I1164 " pdb=" C PHE I1164 " pdb=" N SER I1165 " pdb=" CA SER I1165 " ideal model delta harmonic sigma weight residual -180.00 -161.57 -18.43 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA TRP J 33 " pdb=" C TRP J 33 " pdb=" N SER J 34 " pdb=" CA SER J 34 " ideal model delta harmonic sigma weight residual 180.00 -162.02 -17.98 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 19723 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 3054 0.028 - 0.056: 1282 0.056 - 0.084: 411 0.084 - 0.112: 234 0.112 - 0.140: 82 Chirality restraints: 5063 Sorted by residual: chirality pdb=" CA ILE J 105 " pdb=" N ILE J 105 " pdb=" C ILE J 105 " pdb=" CB ILE J 105 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-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 4.83e-01 chirality pdb=" CA VAL I 690 " pdb=" N VAL I 690 " pdb=" C VAL I 690 " pdb=" CB VAL I 690 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 5060 not shown) Planarity restraints: 5391 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL J 858 " -0.031 5.00e-02 4.00e+02 4.76e-02 3.62e+00 pdb=" N PRO J 859 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO J 859 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO J 859 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR I 589 " 0.031 5.00e-02 4.00e+02 4.71e-02 3.56e+00 pdb=" N PRO I 590 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO I 590 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO I 590 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS I 551 " -0.027 5.00e-02 4.00e+02 4.04e-02 2.62e+00 pdb=" N PRO I 552 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO I 552 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO I 552 " -0.023 5.00e-02 4.00e+02 ... (remaining 5388 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 42 2.61 - 3.18: 26253 3.18 - 3.76: 47330 3.76 - 4.33: 67847 4.33 - 4.90: 112419 Nonbonded interactions: 253891 Sorted by model distance: nonbonded pdb="MG MG J1501 " pdb=" O HOH R 101 " model vdw 2.040 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1501 " model vdw 2.062 2.170 nonbonded pdb=" OP1 C R 3 " pdb="MG MG J1501 " model vdw 2.190 2.170 nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1501 " model vdw 2.226 2.170 nonbonded pdb=" O3' U R 2 " pdb="MG MG J1501 " model vdw 2.246 2.170 ... (remaining 253886 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 7 through 158 or resid 167 through 233)) selection = (chain 'H' and resid 7 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: 4.520 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: 0.030 Extract box with map and model: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 40.320 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 32476 Z= 0.132 Angle : 0.504 17.657 44339 Z= 0.278 Chirality : 0.040 0.140 5063 Planarity : 0.004 0.048 5391 Dihedral : 14.922 176.087 12764 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.28 % Allowed : 5.83 % Favored : 92.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.14), residues: 3725 helix: 1.36 (0.14), residues: 1479 sheet: -0.03 (0.23), residues: 485 loop : -0.59 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 278 TYR 0.011 0.001 TYR J 679 PHE 0.010 0.001 PHE I 514 TRP 0.009 0.001 TRP L 326 HIS 0.004 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (32468) covalent geometry : angle 0.50393 / 0.28 (44327) hydrogen bonds : bond 0.13375 / 8.66 ( 1485) hydrogen bonds : angle 5.42575 / 3.77 ( 4085) metal coordination : bond 0.05929 / 2.56 ( 8) metal coordination : angle 0.07401 / 0.04 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 394 time to evaluate : 1.235 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: I 160 ASP cc_start: 0.8607 (t0) cc_final: 0.8364 (t0) REVERT: I 321 LEU cc_start: 0.9610 (mp) cc_final: 0.9259 (mp) REVERT: I 546 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8559 (tp30) REVERT: I 950 GLU cc_start: 0.8931 (tp30) cc_final: 0.8616 (tp30) REVERT: K 43 ASN cc_start: 0.8816 (t0) cc_final: 0.8471 (t0) REVERT: K 72 GLN cc_start: 0.9001 (tp40) cc_final: 0.8701 (tm-30) REVERT: J 227 PHE cc_start: 0.9133 (OUTLIER) cc_final: 0.8672 (t80) REVERT: J 802 ASP cc_start: 0.8621 (OUTLIER) cc_final: 0.8318 (m-30) REVERT: J 1165 PHE cc_start: 0.7532 (OUTLIER) cc_final: 0.5974 (m-10) REVERT: J 1208 ASP cc_start: 0.8554 (m-30) cc_final: 0.8251 (m-30) REVERT: J 1370 MET cc_start: 0.9055 (mtt) cc_final: 0.8814 (mtp) REVERT: L 268 TYR cc_start: 0.9339 (t80) cc_final: 0.8953 (t80) REVERT: L 322 MET cc_start: 0.3989 (ptp) cc_final: 0.2129 (tmt) REVERT: L 331 HIS cc_start: 0.8875 (m90) cc_final: 0.8674 (m90) outliers start: 41 outliers final: 8 residues processed: 430 average time/residue: 0.9288 time to fit residues: 455.9984 Evaluate side-chains 259 residues out of total 3207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 248 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 388 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.0980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.3980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.0170 chunk 298 optimal weight: 50.0000 overall best weight: 1.1022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 387 ASN G 137 ASN J 430 HIS L 49 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.107720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.064039 restraints weight = 71266.440| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.87 r_work: 0.2730 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32476 Z= 0.127 Angle : 0.544 12.714 44339 Z= 0.287 Chirality : 0.041 0.153 5063 Planarity : 0.004 0.092 5391 Dihedral : 15.717 174.143 5405 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.63 % Allowed : 11.53 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.14), residues: 3725 helix: 1.84 (0.14), residues: 1509 sheet: 0.28 (0.23), residues: 486 loop : -0.40 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 394 TYR 0.014 0.001 TYR J 631 PHE 0.019 0.001 PHE L 256 TRP 0.008 0.001 TRP J1020 HIS 0.004 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (32468) covalent geometry : angle 0.54379 / 0.29 (44327) hydrogen bonds : bond 0.04081 / 2.67 ( 1485) hydrogen bonds : angle 4.24434 / 2.98 ( 4085) metal coordination : bond 0.00700 / 0.33 ( 8) metal coordination : angle 1.75658 / 0.84 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 272 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 20 GLN cc_start: 0.9116 (mt0) cc_final: 0.8913 (mt0) REVERT: I 160 ASP cc_start: 0.8782 (t0) cc_final: 0.8219 (t0) REVERT: I 163 LYS cc_start: 0.8469 (mmmt) cc_final: 0.8184 (mmmt) REVERT: I 321 LEU cc_start: 0.9559 (mp) cc_final: 0.9314 (mp) REVERT: I 378 ARG cc_start: 0.8685 (tmt170) cc_final: 0.8365 (tmt170) REVERT: I 481 LEU cc_start: 0.9055 (mp) cc_final: 0.8481 (pp) REVERT: I 485 ASP cc_start: 0.8772 (m-30) cc_final: 0.7998 (m-30) REVERT: I 545 PHE cc_start: 0.8152 (m-80) cc_final: 0.7884 (m-10) REVERT: I 546 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8169 (tp30) REVERT: I 642 SER cc_start: 0.9195 (p) cc_final: 0.8935 (t) REVERT: I 741 MET cc_start: 0.8760 (mmt) cc_final: 0.8316 (mmm) REVERT: I 909 LYS cc_start: 0.8371 (pptt) cc_final: 0.8142 (pptt) REVERT: I 950 GLU cc_start: 0.9209 (tp30) cc_final: 0.8825 (tp30) REVERT: I 951 MET cc_start: 0.8932 (tmm) cc_final: 0.8662 (mtp) REVERT: I 965 GLN cc_start: 0.9156 (tp40) cc_final: 0.8931 (tm-30) REVERT: I 1243 MET cc_start: 0.9415 (ttp) cc_final: 0.9191 (ttp) REVERT: K 16 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.6965 (ptp90) REVERT: K 43 ASN cc_start: 0.8607 (t0) cc_final: 0.8205 (t0) REVERT: K 58 LEU cc_start: 0.9150 (mt) cc_final: 0.8946 (mp) REVERT: G 33 ARG cc_start: 0.8859 (tpt170) cc_final: 0.8321 (mmt180) REVERT: G 181 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7990 (mt-10) REVERT: H 125 LYS cc_start: 0.8618 (tmtm) cc_final: 0.8320 (tmtm) REVERT: J 29 MET cc_start: 0.8595 (tpp) cc_final: 0.8192 (ttp) REVERT: J 180 MET cc_start: 0.8624 (mtm) cc_final: 0.8317 (mtt) REVERT: J 213 LYS cc_start: 0.8432 (mtmt) cc_final: 0.8120 (mtmt) REVERT: J 227 PHE cc_start: 0.9028 (OUTLIER) cc_final: 0.8475 (t80) REVERT: J 802 ASP cc_start: 0.8817 (OUTLIER) cc_final: 0.8595 (m-30) REVERT: J 1025 MET cc_start: 0.8586 (tpp) cc_final: 0.7626 (tmt) REVERT: J 1165 PHE cc_start: 0.7418 (OUTLIER) cc_final: 0.6391 (m-10) REVERT: J 1370 MET cc_start: 0.8779 (mtt) cc_final: 0.8520 (mtp) REVERT: L 54 GLN cc_start: 0.8526 (tp40) cc_final: 0.7979 (pp30) REVERT: L 55 VAL cc_start: 0.6356 (OUTLIER) cc_final: 0.5947 (t) REVERT: L 121 LYS cc_start: 0.9449 (mtmt) cc_final: 0.9202 (mtmp) REVERT: L 268 TYR cc_start: 0.9471 (t80) cc_final: 0.9067 (t80) REVERT: L 322 MET cc_start: 0.4422 (ptp) cc_final: 0.2626 (tmt) REVERT: L 489 MET cc_start: 0.7963 (mtp) cc_final: 0.7729 (ttt) outliers start: 52 outliers final: 13 residues processed: 308 average time/residue: 0.8361 time to fit residues: 297.3177 Evaluate side-chains 251 residues out of total 3207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 233 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain K residue 16 ARG Chi-restraints excluded: chain H residue 25 LYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 822 MET Chi-restraints excluded: chain J residue 1016 THR Chi-restraints excluded: chain J residue 1028 ILE Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1250 ASP Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 256 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 319 optimal weight: 5.9990 chunk 138 optimal weight: 0.0170 chunk 317 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 25 optimal weight: 0.3980 chunk 277 optimal weight: 0.2980 chunk 326 optimal weight: 2.9990 chunk 204 optimal weight: 4.9990 chunk 176 optimal weight: 4.9990 chunk 152 optimal weight: 7.9990 overall best weight: 1.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 65 ASN G 186 ASN J 430 HIS J 777 HIS ** L 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.107633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.063692 restraints weight = 71010.880| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.88 r_work: 0.2731 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 32476 Z= 0.124 Angle : 0.519 11.898 44339 Z= 0.274 Chirality : 0.040 0.146 5063 Planarity : 0.004 0.054 5391 Dihedral : 15.658 174.441 5397 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.91 % Allowed : 12.53 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.14), residues: 3725 helix: 2.06 (0.14), residues: 1503 sheet: 0.42 (0.24), residues: 467 loop : -0.39 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 540 TYR 0.012 0.001 TYR J 631 PHE 0.032 0.001 PHE L 256 TRP 0.011 0.001 TRP J1020 HIS 0.003 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (32468) covalent geometry : angle 0.51896 / 0.27 (44327) hydrogen bonds : bond 0.03763 / 2.46 ( 1485) hydrogen bonds : angle 4.08292 / 2.88 ( 4085) metal coordination : bond 0.00600 / 0.30 ( 8) metal coordination : angle 1.52622 / 0.74 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 249 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 160 ASP cc_start: 0.8805 (t0) cc_final: 0.8225 (t0) REVERT: I 163 LYS cc_start: 0.8494 (mmmt) cc_final: 0.8231 (mmmt) REVERT: I 247 ARG cc_start: 0.9142 (ttp80) cc_final: 0.8780 (ttp80) REVERT: I 321 LEU cc_start: 0.9506 (mp) cc_final: 0.9304 (mm) REVERT: I 481 LEU cc_start: 0.9001 (mp) cc_final: 0.8489 (pp) REVERT: I 545 PHE cc_start: 0.8177 (m-80) cc_final: 0.7900 (m-10) REVERT: I 546 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8180 (tp30) REVERT: I 642 SER cc_start: 0.9199 (p) cc_final: 0.8966 (t) REVERT: I 741 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8338 (mmm) REVERT: I 909 LYS cc_start: 0.8411 (pptt) cc_final: 0.8210 (pptt) REVERT: I 950 GLU cc_start: 0.9220 (tp30) cc_final: 0.8852 (tp30) REVERT: I 951 MET cc_start: 0.8984 (tmm) cc_final: 0.8711 (mtp) REVERT: K 43 ASN cc_start: 0.8537 (t0) cc_final: 0.7981 (t0) REVERT: K 58 LEU cc_start: 0.9120 (mt) cc_final: 0.8913 (mp) REVERT: K 69 ARG cc_start: 0.8406 (tpp-160) cc_final: 0.8145 (tpp-160) REVERT: K 72 GLN cc_start: 0.9319 (tp40) cc_final: 0.8579 (tm-30) REVERT: G 33 ARG cc_start: 0.8848 (tpt170) cc_final: 0.8596 (tpt170) REVERT: J 29 MET cc_start: 0.8651 (tpp) cc_final: 0.8257 (ttp) REVERT: J 133 ARG cc_start: 0.7840 (mtm110) cc_final: 0.7571 (mpt180) REVERT: J 169 LEU cc_start: 0.9299 (tm) cc_final: 0.9028 (pp) REVERT: J 213 LYS cc_start: 0.8334 (mtmt) cc_final: 0.8132 (mtmt) REVERT: J 216 LYS cc_start: 0.8445 (mtpt) cc_final: 0.8165 (tttm) REVERT: J 227 PHE cc_start: 0.9047 (OUTLIER) cc_final: 0.8452 (t80) REVERT: J 802 ASP cc_start: 0.8773 (OUTLIER) cc_final: 0.8502 (m-30) REVERT: J 1010 GLN cc_start: 0.7676 (OUTLIER) cc_final: 0.7109 (tp-100) REVERT: J 1040 MET cc_start: 0.5609 (OUTLIER) cc_final: 0.5409 (mpt) REVERT: J 1165 PHE cc_start: 0.7710 (OUTLIER) cc_final: 0.6398 (m-10) REVERT: J 1370 MET cc_start: 0.8754 (mtt) cc_final: 0.8483 (mtp) REVERT: L 54 GLN cc_start: 0.8572 (tp40) cc_final: 0.7915 (pp30) REVERT: L 55 VAL cc_start: 0.6469 (OUTLIER) cc_final: 0.5880 (t) REVERT: L 56 MET cc_start: 0.7389 (ptp) cc_final: 0.6858 (mpp) REVERT: L 146 GLU cc_start: 0.9388 (mt-10) cc_final: 0.9180 (tp30) REVERT: L 268 TYR cc_start: 0.9434 (t80) cc_final: 0.9040 (t80) REVERT: L 322 MET cc_start: 0.4521 (ptp) cc_final: 0.2872 (tmt) REVERT: L 538 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8372 (mp0) outliers start: 61 outliers final: 20 residues processed: 291 average time/residue: 0.8437 time to fit residues: 284.7477 Evaluate side-chains 258 residues out of total 3207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 230 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 320 ASP Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 741 MET Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain H residue 25 LYS Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 822 MET Chi-restraints excluded: chain J residue 1010 GLN Chi-restraints excluded: chain J residue 1016 THR Chi-restraints excluded: chain J residue 1028 ILE Chi-restraints excluded: chain J residue 1040 MET Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 256 PHE Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 538 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 38 optimal weight: 2.9990 chunk 300 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 198 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 chunk 304 optimal weight: 0.4980 chunk 284 optimal weight: 20.0000 chunk 330 optimal weight: 0.9990 chunk 341 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 922 ASN J 430 HIS J 777 HIS J1108 GLN L 283 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.106918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.063307 restraints weight = 71304.904| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.87 r_work: 0.2705 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 32476 Z= 0.156 Angle : 0.528 9.424 44339 Z= 0.279 Chirality : 0.041 0.157 5063 Planarity : 0.004 0.053 5391 Dihedral : 15.661 174.199 5397 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.94 % Allowed : 13.22 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.14), residues: 3725 helix: 2.12 (0.14), residues: 1509 sheet: 0.34 (0.24), residues: 478 loop : -0.40 (0.15), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 540 TYR 0.014 0.001 TYR J 631 PHE 0.021 0.001 PHE L 256 TRP 0.015 0.001 TRP J1020 HIS 0.004 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (32468) covalent geometry : angle 0.52736 / 0.28 (44327) hydrogen bonds : bond 0.04039 / 2.64 ( 1485) hydrogen bonds : angle 4.07844 / 2.89 ( 4085) metal coordination : bond 0.00826 / 0.42 ( 8) metal coordination : angle 1.56032 / 0.78 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 248 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 160 ASP cc_start: 0.8797 (t0) cc_final: 0.8202 (t0) REVERT: I 163 LYS cc_start: 0.8509 (mmmt) cc_final: 0.8274 (mmmt) REVERT: I 247 ARG cc_start: 0.9169 (ttp80) cc_final: 0.8841 (ttp80) REVERT: I 545 PHE cc_start: 0.8293 (m-80) cc_final: 0.8010 (m-10) REVERT: I 546 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8214 (tp30) REVERT: I 642 SER cc_start: 0.9232 (p) cc_final: 0.9007 (t) REVERT: I 741 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8308 (mmm) REVERT: I 909 LYS cc_start: 0.8491 (pptt) cc_final: 0.8282 (pptt) REVERT: I 950 GLU cc_start: 0.9216 (tp30) cc_final: 0.8844 (tp30) REVERT: I 965 GLN cc_start: 0.9165 (tp40) cc_final: 0.8883 (tm-30) REVERT: I 1138 VAL cc_start: 0.8854 (OUTLIER) cc_final: 0.8640 (p) REVERT: I 1243 MET cc_start: 0.9460 (ttp) cc_final: 0.9235 (ttp) REVERT: K 43 ASN cc_start: 0.8585 (t0) cc_final: 0.8053 (t0) REVERT: K 58 LEU cc_start: 0.9100 (mt) cc_final: 0.8886 (mp) REVERT: G 33 ARG cc_start: 0.8812 (tpt170) cc_final: 0.8550 (tpt170) REVERT: G 147 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8520 (pt0) REVERT: H 125 LYS cc_start: 0.9050 (tppt) cc_final: 0.8423 (tmtm) REVERT: J 29 MET cc_start: 0.8689 (tpp) cc_final: 0.8443 (ttm) REVERT: J 133 ARG cc_start: 0.7937 (mtm110) cc_final: 0.7563 (mpt180) REVERT: J 169 LEU cc_start: 0.9283 (tm) cc_final: 0.8998 (pp) REVERT: J 216 LYS cc_start: 0.8479 (mtpt) cc_final: 0.8255 (tttm) REVERT: J 227 PHE cc_start: 0.9058 (OUTLIER) cc_final: 0.8447 (t80) REVERT: J 414 GLU cc_start: 0.9163 (tp30) cc_final: 0.8930 (tp30) REVERT: J 658 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8486 (mm-30) REVERT: J 802 ASP cc_start: 0.8785 (OUTLIER) cc_final: 0.8535 (m-30) REVERT: J 995 TYR cc_start: 0.8228 (m-80) cc_final: 0.7861 (m-80) REVERT: J 1010 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7141 (tp40) REVERT: J 1025 MET cc_start: 0.8500 (tpp) cc_final: 0.7492 (tmt) REVERT: J 1040 MET cc_start: 0.5747 (OUTLIER) cc_final: 0.5276 (pmm) REVERT: J 1165 PHE cc_start: 0.7610 (OUTLIER) cc_final: 0.6384 (m-10) REVERT: J 1370 MET cc_start: 0.8757 (mtt) cc_final: 0.8486 (mtp) REVERT: L 54 GLN cc_start: 0.8646 (tp40) cc_final: 0.7928 (pp30) REVERT: L 55 VAL cc_start: 0.6564 (OUTLIER) cc_final: 0.5989 (t) REVERT: L 56 MET cc_start: 0.7315 (ptp) cc_final: 0.6860 (mpp) REVERT: L 136 GLU cc_start: 0.7450 (tm-30) cc_final: 0.6227 (mt-10) REVERT: L 268 TYR cc_start: 0.9451 (t80) cc_final: 0.9076 (t80) REVERT: L 322 MET cc_start: 0.4522 (ptp) cc_final: 0.2975 (tmt) REVERT: L 474 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.7515 (mtp) REVERT: L 538 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8428 (mp0) outliers start: 62 outliers final: 27 residues processed: 291 average time/residue: 0.8174 time to fit residues: 275.4784 Evaluate side-chains 266 residues out of total 3207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 228 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 320 ASP Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 741 MET Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 870 ILE Chi-restraints excluded: chain I residue 1025 PHE Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain K residue 16 ARG Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 1010 GLN Chi-restraints excluded: chain J residue 1016 THR Chi-restraints excluded: chain J residue 1028 ILE Chi-restraints excluded: chain J residue 1040 MET Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 358 VAL Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 474 MET Chi-restraints excluded: chain L residue 538 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 330 optimal weight: 5.9990 chunk 143 optimal weight: 8.9990 chunk 31 optimal weight: 0.5980 chunk 282 optimal weight: 10.0000 chunk 131 optimal weight: 0.8980 chunk 308 optimal weight: 8.9990 chunk 348 optimal weight: 40.0000 chunk 139 optimal weight: 0.4980 chunk 343 optimal weight: 7.9990 chunk 362 optimal weight: 4.9990 chunk 272 optimal weight: 4.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 65 ASN G 186 ASN J 430 HIS J 777 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.106161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.062568 restraints weight = 71519.399| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 2.85 r_work: 0.2686 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 32476 Z= 0.186 Angle : 0.543 9.953 44339 Z= 0.286 Chirality : 0.042 0.191 5063 Planarity : 0.004 0.057 5391 Dihedral : 15.711 174.157 5397 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.04 % Allowed : 14.10 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.14), residues: 3725 helix: 2.08 (0.14), residues: 1509 sheet: 0.37 (0.23), residues: 490 loop : -0.42 (0.15), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG I 540 TYR 0.015 0.001 TYR L 137 PHE 0.013 0.001 PHE I 405 TRP 0.019 0.001 TRP J1020 HIS 0.005 0.001 HIS L 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (32468) covalent geometry : angle 0.54234 / 0.29 (44327) hydrogen bonds : bond 0.04303 / 2.81 ( 1485) hydrogen bonds : angle 4.11892 / 2.91 ( 4085) metal coordination : bond 0.00954 / 0.49 ( 8) metal coordination : angle 1.61257 / 0.82 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 240 time to evaluate : 1.357 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: I 160 ASP cc_start: 0.8787 (t0) cc_final: 0.8188 (t0) REVERT: I 163 LYS cc_start: 0.8489 (mmmt) cc_final: 0.8264 (mmmt) REVERT: I 247 ARG cc_start: 0.9195 (ttp80) cc_final: 0.8880 (ttp80) REVERT: I 321 LEU cc_start: 0.9537 (mm) cc_final: 0.9328 (mp) REVERT: I 545 PHE cc_start: 0.8318 (m-80) cc_final: 0.8008 (m-10) REVERT: I 546 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8231 (tp30) REVERT: I 642 SER cc_start: 0.9246 (p) cc_final: 0.9017 (t) REVERT: I 909 LYS cc_start: 0.8471 (pptt) cc_final: 0.8262 (pptt) REVERT: I 950 GLU cc_start: 0.9214 (tp30) cc_final: 0.8862 (tp30) REVERT: I 1138 VAL cc_start: 0.8885 (OUTLIER) cc_final: 0.8636 (p) REVERT: I 1243 MET cc_start: 0.9484 (ttp) cc_final: 0.9277 (ttp) REVERT: K 43 ASN cc_start: 0.8640 (t0) cc_final: 0.8113 (t0) REVERT: K 58 LEU cc_start: 0.9068 (mt) cc_final: 0.8862 (mp) REVERT: K 69 ARG cc_start: 0.7997 (tpm170) cc_final: 0.7726 (tpm170) REVERT: K 72 GLN cc_start: 0.9007 (tp40) cc_final: 0.8774 (tm-30) REVERT: G 33 ARG cc_start: 0.8835 (tpt170) cc_final: 0.8574 (tpt170) REVERT: G 127 GLN cc_start: 0.9436 (mm-40) cc_final: 0.9151 (mp10) REVERT: G 147 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8524 (pt0) REVERT: H 51 MET cc_start: 0.9180 (OUTLIER) cc_final: 0.8924 (mmm) REVERT: J 29 MET cc_start: 0.8729 (tpp) cc_final: 0.8486 (ttm) REVERT: J 133 ARG cc_start: 0.7971 (mtm110) cc_final: 0.7556 (mpt180) REVERT: J 216 LYS cc_start: 0.8531 (mtpt) cc_final: 0.8319 (tttm) REVERT: J 227 PHE cc_start: 0.9033 (OUTLIER) cc_final: 0.8430 (t80) REVERT: J 414 GLU cc_start: 0.9190 (tp30) cc_final: 0.8964 (tp30) REVERT: J 802 ASP cc_start: 0.8809 (OUTLIER) cc_final: 0.8579 (m-30) REVERT: J 995 TYR cc_start: 0.8227 (m-80) cc_final: 0.7831 (m-80) REVERT: J 1010 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7198 (tp-100) REVERT: J 1040 MET cc_start: 0.5528 (OUTLIER) cc_final: 0.5019 (pmm) REVERT: J 1165 PHE cc_start: 0.7805 (OUTLIER) cc_final: 0.6486 (m-10) REVERT: J 1370 MET cc_start: 0.8731 (mtt) cc_final: 0.8495 (mtp) REVERT: L 54 GLN cc_start: 0.8726 (tp40) cc_final: 0.8059 (pp30) REVERT: L 55 VAL cc_start: 0.6624 (OUTLIER) cc_final: 0.6066 (t) REVERT: L 56 MET cc_start: 0.7256 (ptp) cc_final: 0.6776 (mpp) REVERT: L 134 VAL cc_start: 0.8067 (OUTLIER) cc_final: 0.7667 (p) REVERT: L 268 TYR cc_start: 0.9470 (t80) cc_final: 0.9108 (t80) REVERT: L 322 MET cc_start: 0.4616 (ptp) cc_final: 0.3109 (tmt) REVERT: L 474 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7548 (mtp) REVERT: L 538 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8460 (mp0) outliers start: 65 outliers final: 27 residues processed: 286 average time/residue: 0.8194 time to fit residues: 271.7280 Evaluate side-chains 269 residues out of total 3207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 230 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 65 ASN Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 1025 PHE Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain K residue 16 ARG Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 1010 GLN Chi-restraints excluded: chain J residue 1016 THR Chi-restraints excluded: chain J residue 1028 ILE Chi-restraints excluded: chain J residue 1040 MET Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1250 ASP Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 227 GLN Chi-restraints excluded: chain L residue 355 ILE Chi-restraints excluded: chain L residue 358 VAL Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 474 MET Chi-restraints excluded: chain L residue 538 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 155 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 150 optimal weight: 0.9980 chunk 214 optimal weight: 7.9990 chunk 256 optimal weight: 0.9980 chunk 165 optimal weight: 8.9990 chunk 290 optimal weight: 7.9990 chunk 157 optimal weight: 0.0170 chunk 325 optimal weight: 3.9990 chunk 316 optimal weight: 3.9990 chunk 319 optimal weight: 4.9990 overall best weight: 2.0022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 922 ASN ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 430 HIS J 777 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.105941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.063926 restraints weight = 70097.526| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.78 r_work: 0.2702 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 32476 Z= 0.163 Angle : 0.546 12.739 44339 Z= 0.285 Chirality : 0.041 0.298 5063 Planarity : 0.004 0.069 5391 Dihedral : 15.752 174.269 5397 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.97 % Allowed : 14.88 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.14), residues: 3725 helix: 2.12 (0.14), residues: 1509 sheet: 0.48 (0.24), residues: 475 loop : -0.40 (0.15), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG I 540 TYR 0.014 0.001 TYR J 631 PHE 0.012 0.001 PHE L 221 TRP 0.022 0.001 TRP J1020 HIS 0.004 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 (32468) covalent geometry : angle 0.54548 / 0.28 (44327) hydrogen bonds : bond 0.04063 / 2.66 ( 1485) hydrogen bonds : angle 4.09712 / 2.90 ( 4085) metal coordination : bond 0.00799 / 0.41 ( 8) metal coordination : angle 1.48969 / 0.77 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 236 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 160 ASP cc_start: 0.8781 (t0) cc_final: 0.8184 (t0) REVERT: I 163 LYS cc_start: 0.8427 (mmmt) cc_final: 0.8224 (mmmt) REVERT: I 247 ARG cc_start: 0.9192 (ttp80) cc_final: 0.8896 (ttp80) REVERT: I 321 LEU cc_start: 0.9531 (mm) cc_final: 0.9278 (mp) REVERT: I 545 PHE cc_start: 0.8321 (m-80) cc_final: 0.7995 (m-10) REVERT: I 546 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8222 (tp30) REVERT: I 909 LYS cc_start: 0.8497 (pptt) cc_final: 0.8269 (pptt) REVERT: I 950 GLU cc_start: 0.9199 (tp30) cc_final: 0.8835 (tp30) REVERT: I 965 GLN cc_start: 0.9132 (tp40) cc_final: 0.8870 (tm130) REVERT: I 1243 MET cc_start: 0.9480 (ttp) cc_final: 0.9273 (ttp) REVERT: K 43 ASN cc_start: 0.8681 (t0) cc_final: 0.8163 (t0) REVERT: G 147 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8545 (pt0) REVERT: H 51 MET cc_start: 0.9175 (mmm) cc_final: 0.8912 (mmm) REVERT: H 125 LYS cc_start: 0.9057 (tppt) cc_final: 0.8383 (tmtm) REVERT: J 133 ARG cc_start: 0.7996 (mtm110) cc_final: 0.7587 (mpt180) REVERT: J 169 LEU cc_start: 0.9284 (tm) cc_final: 0.8988 (pp) REVERT: J 227 PHE cc_start: 0.9015 (OUTLIER) cc_final: 0.8378 (t80) REVERT: J 414 GLU cc_start: 0.9192 (tp30) cc_final: 0.8970 (tp30) REVERT: J 802 ASP cc_start: 0.8790 (m-30) cc_final: 0.8590 (m-30) REVERT: J 995 TYR cc_start: 0.8204 (m-80) cc_final: 0.7824 (m-80) REVERT: J 1010 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7250 (tp-100) REVERT: J 1025 MET cc_start: 0.8499 (tpp) cc_final: 0.7491 (tmt) REVERT: J 1040 MET cc_start: 0.5549 (OUTLIER) cc_final: 0.5096 (pmm) REVERT: J 1165 PHE cc_start: 0.7626 (OUTLIER) cc_final: 0.6445 (m-10) REVERT: J 1370 MET cc_start: 0.8743 (mtt) cc_final: 0.8509 (mtp) REVERT: L 48 ILE cc_start: 0.9523 (OUTLIER) cc_final: 0.9220 (pp) REVERT: L 54 GLN cc_start: 0.8721 (tp40) cc_final: 0.8081 (pp30) REVERT: L 55 VAL cc_start: 0.6693 (OUTLIER) cc_final: 0.5940 (t) REVERT: L 56 MET cc_start: 0.7352 (ptp) cc_final: 0.6914 (mpp) REVERT: L 268 TYR cc_start: 0.9471 (t80) cc_final: 0.9153 (t80) REVERT: L 322 MET cc_start: 0.4587 (ptp) cc_final: 0.3107 (tmt) REVERT: L 538 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8465 (mp0) outliers start: 63 outliers final: 26 residues processed: 282 average time/residue: 0.8019 time to fit residues: 262.5779 Evaluate side-chains 259 residues out of total 3207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 225 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 870 ILE Chi-restraints excluded: chain I residue 1025 PHE Chi-restraints excluded: chain K residue 16 ARG Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 822 MET Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 1010 GLN Chi-restraints excluded: chain J residue 1016 THR Chi-restraints excluded: chain J residue 1028 ILE Chi-restraints excluded: chain J residue 1040 MET Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1250 ASP Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 355 ILE Chi-restraints excluded: chain L residue 358 VAL Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 538 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 9 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 290 optimal weight: 7.9990 chunk 139 optimal weight: 8.9990 chunk 294 optimal weight: 6.9990 chunk 170 optimal weight: 6.9990 chunk 302 optimal weight: 5.9990 chunk 205 optimal weight: 1.9990 chunk 305 optimal weight: 0.0270 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 65 ASN ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 430 HIS J 489 ASN J 777 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.107329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.063967 restraints weight = 71139.805| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.85 r_work: 0.2724 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32476 Z= 0.113 Angle : 0.529 12.040 44339 Z= 0.275 Chirality : 0.040 0.223 5063 Planarity : 0.003 0.073 5391 Dihedral : 15.656 174.197 5391 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.44 % Allowed : 15.70 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.14), residues: 3725 helix: 2.23 (0.14), residues: 1504 sheet: 0.58 (0.24), residues: 479 loop : -0.34 (0.15), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG I 540 TYR 0.012 0.001 TYR J 631 PHE 0.028 0.001 PHE I1025 TRP 0.024 0.001 TRP J1020 HIS 0.004 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (32468) covalent geometry : angle 0.52837 / 0.28 (44327) hydrogen bonds : bond 0.03468 / 2.29 ( 1485) hydrogen bonds : angle 3.98349 / 2.82 ( 4085) metal coordination : bond 0.00440 / 0.23 ( 8) metal coordination : angle 1.39217 / 0.72 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 239 time to evaluate : 1.173 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: I 160 ASP cc_start: 0.8800 (t0) cc_final: 0.8196 (t0) REVERT: I 177 ILE cc_start: 0.9444 (mt) cc_final: 0.9181 (mm) REVERT: I 247 ARG cc_start: 0.9200 (ttp80) cc_final: 0.8923 (ttp80) REVERT: I 741 MET cc_start: 0.8742 (mmt) cc_final: 0.8411 (mmm) REVERT: I 909 LYS cc_start: 0.8522 (pptt) cc_final: 0.8307 (pptt) REVERT: I 950 GLU cc_start: 0.9201 (tp30) cc_final: 0.8823 (tp30) REVERT: I 965 GLN cc_start: 0.9158 (tp40) cc_final: 0.8857 (tm-30) REVERT: K 43 ASN cc_start: 0.8662 (t0) cc_final: 0.8145 (t0) REVERT: K 69 ARG cc_start: 0.8336 (tpp-160) cc_final: 0.8129 (tpm170) REVERT: G 33 ARG cc_start: 0.8861 (tpt170) cc_final: 0.8600 (tpt170) REVERT: H 125 LYS cc_start: 0.9093 (tppt) cc_final: 0.8857 (tppt) REVERT: J 29 MET cc_start: 0.8691 (ttp) cc_final: 0.8329 (ttp) REVERT: J 133 ARG cc_start: 0.7985 (mtm110) cc_final: 0.7553 (mpt180) REVERT: J 169 LEU cc_start: 0.9275 (tm) cc_final: 0.8992 (pp) REVERT: J 227 PHE cc_start: 0.8984 (OUTLIER) cc_final: 0.8430 (t80) REVERT: J 802 ASP cc_start: 0.8754 (m-30) cc_final: 0.8510 (m-30) REVERT: J 995 TYR cc_start: 0.8201 (m-80) cc_final: 0.7815 (m-80) REVERT: J 1010 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7246 (tp40) REVERT: J 1040 MET cc_start: 0.5450 (OUTLIER) cc_final: 0.4985 (pmm) REVERT: J 1165 PHE cc_start: 0.7470 (OUTLIER) cc_final: 0.6410 (m-80) REVERT: J 1370 MET cc_start: 0.8675 (mtt) cc_final: 0.8469 (mtp) REVERT: L 48 ILE cc_start: 0.9485 (OUTLIER) cc_final: 0.9187 (pp) REVERT: L 54 GLN cc_start: 0.8741 (tp40) cc_final: 0.8065 (pp30) REVERT: L 55 VAL cc_start: 0.6661 (OUTLIER) cc_final: 0.5894 (t) REVERT: L 56 MET cc_start: 0.7427 (ptp) cc_final: 0.6963 (mpp) REVERT: L 268 TYR cc_start: 0.9509 (t80) cc_final: 0.9180 (t80) REVERT: L 277 MET cc_start: 0.7823 (tpt) cc_final: 0.7607 (tpt) REVERT: L 322 MET cc_start: 0.4690 (ptp) cc_final: 0.3150 (tmt) REVERT: L 538 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8466 (mp0) outliers start: 46 outliers final: 25 residues processed: 273 average time/residue: 0.8170 time to fit residues: 258.2843 Evaluate side-chains 257 residues out of total 3207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 225 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 477 GLU Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 870 ILE Chi-restraints excluded: chain I residue 1025 PHE Chi-restraints excluded: chain K residue 16 ARG Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 1010 GLN Chi-restraints excluded: chain J residue 1028 ILE Chi-restraints excluded: chain J residue 1040 MET Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 227 GLN Chi-restraints excluded: chain L residue 355 ILE Chi-restraints excluded: chain L residue 358 VAL Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 538 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 347 optimal weight: 5.9990 chunk 2 optimal weight: 0.5980 chunk 47 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 226 optimal weight: 3.9990 chunk 216 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 369 optimal weight: 0.6980 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 65 ASN I 922 ASN ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN G 186 ASN J 430 HIS J 777 HIS L 283 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.104890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.061789 restraints weight = 70989.813| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 2.84 r_work: 0.2685 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 32476 Z= 0.205 Angle : 0.585 12.432 44339 Z= 0.304 Chirality : 0.042 0.247 5063 Planarity : 0.004 0.078 5391 Dihedral : 15.725 174.094 5391 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.69 % Allowed : 15.91 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.14), residues: 3725 helix: 2.09 (0.14), residues: 1508 sheet: 0.50 (0.24), residues: 490 loop : -0.41 (0.15), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG I 540 TYR 0.015 0.001 TYR J 631 PHE 0.030 0.001 PHE I1025 TRP 0.025 0.001 TRP J1020 HIS 0.009 0.001 HIS I 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.20 (32468) covalent geometry : angle 0.58408 / 0.30 (44327) hydrogen bonds : bond 0.04439 / 2.89 ( 1485) hydrogen bonds : angle 4.13172 / 2.92 ( 4085) metal coordination : bond 0.01014 / 0.53 ( 8) metal coordination : angle 1.48893 / 0.78 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 222 time to evaluate : 1.359 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: I 160 ASP cc_start: 0.8773 (t0) cc_final: 0.8229 (t0) REVERT: I 247 ARG cc_start: 0.9193 (ttp80) cc_final: 0.8917 (ttp80) REVERT: I 321 LEU cc_start: 0.9545 (OUTLIER) cc_final: 0.9258 (mm) REVERT: I 741 MET cc_start: 0.8711 (mmt) cc_final: 0.8373 (mmm) REVERT: I 950 GLU cc_start: 0.9199 (tp30) cc_final: 0.8833 (tp30) REVERT: K 43 ASN cc_start: 0.8743 (t0) cc_final: 0.8213 (t0) REVERT: K 73 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8310 (tm-30) REVERT: H 51 MET cc_start: 0.9183 (OUTLIER) cc_final: 0.8944 (mmm) REVERT: J 29 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8389 (ttp) REVERT: J 133 ARG cc_start: 0.7988 (mtm110) cc_final: 0.7555 (mpt180) REVERT: J 169 LEU cc_start: 0.9281 (tm) cc_final: 0.9007 (pp) REVERT: J 227 PHE cc_start: 0.9000 (OUTLIER) cc_final: 0.8352 (t80) REVERT: J 802 ASP cc_start: 0.8820 (m-30) cc_final: 0.8609 (m-30) REVERT: J 995 TYR cc_start: 0.8168 (m-80) cc_final: 0.7750 (m-80) REVERT: J 1010 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7306 (tp-100) REVERT: J 1025 MET cc_start: 0.8454 (tpp) cc_final: 0.7433 (tmt) REVERT: J 1040 MET cc_start: 0.5619 (OUTLIER) cc_final: 0.5188 (pmm) REVERT: J 1165 PHE cc_start: 0.7500 (OUTLIER) cc_final: 0.6446 (m-80) REVERT: J 1370 MET cc_start: 0.8717 (mtt) cc_final: 0.8486 (mtp) REVERT: L 48 ILE cc_start: 0.9486 (OUTLIER) cc_final: 0.9163 (pp) REVERT: L 54 GLN cc_start: 0.8815 (tp40) cc_final: 0.8068 (pp30) REVERT: L 55 VAL cc_start: 0.6657 (OUTLIER) cc_final: 0.5919 (t) REVERT: L 56 MET cc_start: 0.7377 (ptp) cc_final: 0.6939 (mpp) REVERT: L 121 LYS cc_start: 0.9476 (mtmt) cc_final: 0.9238 (mtmm) REVERT: L 268 TYR cc_start: 0.9509 (t80) cc_final: 0.9192 (t80) REVERT: L 322 MET cc_start: 0.4742 (ptp) cc_final: 0.3217 (tmt) REVERT: L 538 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8475 (mp0) outliers start: 54 outliers final: 25 residues processed: 259 average time/residue: 0.8183 time to fit residues: 247.2208 Evaluate side-chains 248 residues out of total 3207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 212 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 65 ASN Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 320 ASP Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 870 ILE Chi-restraints excluded: chain I residue 1025 PHE Chi-restraints excluded: chain K residue 16 ARG Chi-restraints excluded: chain K residue 73 GLN Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 1010 GLN Chi-restraints excluded: chain J residue 1028 ILE Chi-restraints excluded: chain J residue 1040 MET Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1250 ASP Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 227 GLN Chi-restraints excluded: chain L residue 355 ILE Chi-restraints excluded: chain L residue 358 VAL Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 538 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 55 optimal weight: 0.6980 chunk 246 optimal weight: 0.9990 chunk 249 optimal weight: 2.9990 chunk 176 optimal weight: 0.0870 chunk 373 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 257 optimal weight: 5.9990 chunk 278 optimal weight: 1.9990 chunk 196 optimal weight: 8.9990 chunk 125 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 65 ASN J 430 HIS J 777 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.107329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.063657 restraints weight = 70638.858| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.88 r_work: 0.2730 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 32476 Z= 0.111 Angle : 0.560 13.452 44339 Z= 0.290 Chirality : 0.041 0.299 5063 Planarity : 0.004 0.082 5391 Dihedral : 15.653 174.116 5391 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.25 % Allowed : 16.51 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.14), residues: 3725 helix: 2.17 (0.14), residues: 1510 sheet: 0.62 (0.24), residues: 480 loop : -0.32 (0.15), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG I 540 TYR 0.011 0.001 TYR J 631 PHE 0.019 0.001 PHE L 221 TRP 0.023 0.001 TRP J1020 HIS 0.004 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (32468) covalent geometry : angle 0.55961 / 0.29 (44327) hydrogen bonds : bond 0.03442 / 2.28 ( 1485) hydrogen bonds : angle 3.99833 / 2.83 ( 4085) metal coordination : bond 0.00394 / 0.20 ( 8) metal coordination : angle 1.44018 / 0.73 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 223 time to evaluate : 1.204 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: I 160 ASP cc_start: 0.8816 (t0) cc_final: 0.8214 (t0) REVERT: I 177 ILE cc_start: 0.9438 (mt) cc_final: 0.9178 (mm) REVERT: I 247 ARG cc_start: 0.9217 (ttp80) cc_final: 0.8952 (ttp80) REVERT: I 321 LEU cc_start: 0.9545 (OUTLIER) cc_final: 0.9245 (mm) REVERT: I 741 MET cc_start: 0.8706 (mmt) cc_final: 0.8420 (mmm) REVERT: I 950 GLU cc_start: 0.9205 (tp30) cc_final: 0.8831 (tp30) REVERT: I 965 GLN cc_start: 0.9151 (tp40) cc_final: 0.8907 (tm-30) REVERT: I 1119 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.7843 (ttm) REVERT: K 43 ASN cc_start: 0.8714 (t0) cc_final: 0.8185 (t0) REVERT: K 73 GLN cc_start: 0.8539 (mt0) cc_final: 0.8335 (tm-30) REVERT: G 33 ARG cc_start: 0.8855 (tpt170) cc_final: 0.8613 (tpt170) REVERT: H 125 LYS cc_start: 0.9067 (tppt) cc_final: 0.8477 (tmtt) REVERT: J 29 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8332 (ttp) REVERT: J 133 ARG cc_start: 0.7976 (mtm110) cc_final: 0.7531 (mpt180) REVERT: J 151 MET cc_start: 0.8524 (ppp) cc_final: 0.8017 (mmt) REVERT: J 169 LEU cc_start: 0.9283 (tm) cc_final: 0.9002 (pp) REVERT: J 227 PHE cc_start: 0.8966 (OUTLIER) cc_final: 0.8434 (t80) REVERT: J 802 ASP cc_start: 0.8741 (m-30) cc_final: 0.8463 (m-30) REVERT: J 995 TYR cc_start: 0.8144 (m-80) cc_final: 0.7744 (m-80) REVERT: J 1010 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7337 (tp40) REVERT: J 1025 MET cc_start: 0.8549 (tpp) cc_final: 0.7541 (tmt) REVERT: J 1040 MET cc_start: 0.5587 (OUTLIER) cc_final: 0.5202 (pmm) REVERT: J 1165 PHE cc_start: 0.7404 (OUTLIER) cc_final: 0.6444 (m-80) REVERT: J 1370 MET cc_start: 0.8681 (mtt) cc_final: 0.8466 (mtp) REVERT: L 54 GLN cc_start: 0.8842 (tp40) cc_final: 0.8086 (pp30) REVERT: L 55 VAL cc_start: 0.6581 (OUTLIER) cc_final: 0.6027 (t) REVERT: L 56 MET cc_start: 0.7383 (ptp) cc_final: 0.6791 (mpp) REVERT: L 277 MET cc_start: 0.7737 (tpt) cc_final: 0.7529 (tpt) REVERT: L 322 MET cc_start: 0.4738 (ptp) cc_final: 0.3209 (tmt) REVERT: L 538 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8473 (mp0) outliers start: 40 outliers final: 26 residues processed: 250 average time/residue: 0.7923 time to fit residues: 231.1424 Evaluate side-chains 250 residues out of total 3207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 215 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 65 ASN Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 870 ILE Chi-restraints excluded: chain I residue 1025 PHE Chi-restraints excluded: chain I residue 1119 MET Chi-restraints excluded: chain K residue 16 ARG Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 1010 GLN Chi-restraints excluded: chain J residue 1028 ILE Chi-restraints excluded: chain J residue 1040 MET Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1250 ASP Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 227 GLN Chi-restraints excluded: chain L residue 355 ILE Chi-restraints excluded: chain L residue 358 VAL Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 538 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 375 optimal weight: 20.0000 chunk 303 optimal weight: 7.9990 chunk 380 optimal weight: 10.0000 chunk 150 optimal weight: 0.6980 chunk 167 optimal weight: 1.9990 chunk 89 optimal weight: 0.1980 chunk 362 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 218 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 65 ASN J 430 HIS J 777 HIS L 271 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.106557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.063111 restraints weight = 71419.971| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.85 r_work: 0.2711 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 32476 Z= 0.144 Angle : 0.568 12.235 44339 Z= 0.295 Chirality : 0.041 0.295 5063 Planarity : 0.004 0.085 5391 Dihedral : 15.636 173.974 5391 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.38 % Allowed : 16.70 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.14), residues: 3725 helix: 2.18 (0.14), residues: 1507 sheet: 0.61 (0.24), residues: 470 loop : -0.31 (0.15), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG I 540 TYR 0.014 0.001 TYR J 631 PHE 0.018 0.001 PHE L 221 TRP 0.019 0.001 TRP J1020 HIS 0.004 0.001 HIS L 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 (32468) covalent geometry : angle 0.56792 / 0.29 (44327) hydrogen bonds : bond 0.03777 / 2.48 ( 1485) hydrogen bonds : angle 4.03311 / 2.85 ( 4085) metal coordination : bond 0.00660 / 0.34 ( 8) metal coordination : angle 1.34515 / 0.69 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 222 time to evaluate : 1.272 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 160 ASP cc_start: 0.8818 (t0) cc_final: 0.8213 (t0) REVERT: I 177 ILE cc_start: 0.9442 (mt) cc_final: 0.9181 (mm) REVERT: I 247 ARG cc_start: 0.9202 (ttp80) cc_final: 0.8940 (ttp80) REVERT: I 321 LEU cc_start: 0.9541 (OUTLIER) cc_final: 0.9247 (mm) REVERT: I 741 MET cc_start: 0.8693 (mmt) cc_final: 0.8386 (mmm) REVERT: I 950 GLU cc_start: 0.9203 (tp30) cc_final: 0.8842 (tp30) REVERT: I 965 GLN cc_start: 0.9125 (tp40) cc_final: 0.8875 (tm-30) REVERT: K 43 ASN cc_start: 0.8724 (t0) cc_final: 0.8197 (t0) REVERT: K 71 GLU cc_start: 0.8665 (pp20) cc_final: 0.8363 (mp0) REVERT: K 72 GLN cc_start: 0.9072 (tp40) cc_final: 0.8769 (tm130) REVERT: G 33 ARG cc_start: 0.8832 (tpt170) cc_final: 0.8309 (mmt180) REVERT: H 95 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7819 (pttp) REVERT: H 125 LYS cc_start: 0.9081 (tppt) cc_final: 0.8458 (tmtt) REVERT: J 29 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8371 (ttp) REVERT: J 133 ARG cc_start: 0.8019 (mtm110) cc_final: 0.7575 (mpt180) REVERT: J 169 LEU cc_start: 0.9277 (tm) cc_final: 0.8995 (pp) REVERT: J 227 PHE cc_start: 0.8978 (OUTLIER) cc_final: 0.8415 (t80) REVERT: J 802 ASP cc_start: 0.8782 (m-30) cc_final: 0.8568 (m-30) REVERT: J 995 TYR cc_start: 0.8159 (m-80) cc_final: 0.7744 (m-80) REVERT: J 1010 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7350 (tp40) REVERT: J 1025 MET cc_start: 0.8574 (tpp) cc_final: 0.7586 (tmt) REVERT: J 1040 MET cc_start: 0.5663 (OUTLIER) cc_final: 0.5202 (pmm) REVERT: J 1165 PHE cc_start: 0.7466 (OUTLIER) cc_final: 0.6409 (m-80) REVERT: J 1370 MET cc_start: 0.8711 (mtt) cc_final: 0.8488 (mtp) REVERT: L 54 GLN cc_start: 0.8869 (tp40) cc_final: 0.8089 (pp30) REVERT: L 55 VAL cc_start: 0.6546 (OUTLIER) cc_final: 0.5989 (t) REVERT: L 56 MET cc_start: 0.7376 (ptp) cc_final: 0.6807 (mpp) REVERT: L 144 LEU cc_start: 0.9409 (mm) cc_final: 0.9205 (pp) REVERT: L 322 MET cc_start: 0.4760 (ptp) cc_final: 0.3233 (tmt) outliers start: 44 outliers final: 25 residues processed: 250 average time/residue: 0.8529 time to fit residues: 247.4588 Evaluate side-chains 247 residues out of total 3207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 214 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 870 ILE Chi-restraints excluded: chain K residue 16 ARG Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 1010 GLN Chi-restraints excluded: chain J residue 1028 ILE Chi-restraints excluded: chain J residue 1040 MET Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1250 ASP Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 227 GLN Chi-restraints excluded: chain L residue 355 ILE Chi-restraints excluded: chain L residue 358 VAL Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain L residue 442 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 85 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 90 optimal weight: 10.0000 chunk 210 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 104 optimal weight: 0.0770 chunk 153 optimal weight: 0.0970 chunk 102 optimal weight: 6.9990 chunk 233 optimal weight: 4.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 65 ASN I 761 GLN J 430 HIS J 777 HIS J1023 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.107685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.064519 restraints weight = 71109.991| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.87 r_work: 0.2753 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 32476 Z= 0.107 Angle : 0.564 13.016 44339 Z= 0.289 Chirality : 0.040 0.289 5063 Planarity : 0.004 0.084 5391 Dihedral : 15.559 173.637 5391 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.22 % Allowed : 16.85 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.14), residues: 3725 helix: 2.25 (0.14), residues: 1506 sheet: 0.76 (0.24), residues: 464 loop : -0.25 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG I 540 TYR 0.009 0.001 TYR J 631 PHE 0.018 0.001 PHE L 221 TRP 0.017 0.001 TRP J1020 HIS 0.004 0.000 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (32468) covalent geometry : angle 0.56313 / 0.29 (44327) hydrogen bonds : bond 0.03129 / 2.08 ( 1485) hydrogen bonds : angle 3.93086 / 2.77 ( 4085) metal coordination : bond 0.00346 / 0.18 ( 8) metal coordination : angle 1.37629 / 0.71 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11922.35 seconds wall clock time: 203 minutes 29.22 seconds (12209.22 seconds total)