Starting phenix.real_space_refine on Sat Aug 8 08:15:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ph9_17657/08_2026/8ph9_17657.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ph9_17657/08_2026/8ph9_17657.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ph9_17657/08_2026/8ph9_17657.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ph9_17657/08_2026/8ph9_17657.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ph9_17657/08_2026/8ph9_17657.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ph9_17657/08_2026/8ph9_17657.map" } resolution = 3.0 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= 0.008 sd= 0.053 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 86 5.49 5 Mg 1 5.21 5 S 107 5.16 5 C 16604 2.51 5 N 4773 2.21 5 O 5384 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26957 Number of models: 1 Model: "" Number of chains: 9 Chain: "G" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1799 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 222} Chain: "H" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1784 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 221} Chain: "I" Number of atoms: 10449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1325, 10449 Classifications: {'peptide': 1325} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1269} Chain breaks: 1 Chain: "J" Number of atoms: 10474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1347, 10474 Classifications: {'peptide': 1347} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1291} Chain breaks: 2 Chain: "K" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 655 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "R" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 318 Classifications: {'RNA': 15} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 7} Link IDs: {'rna2p': 3, 'rna3p': 11} Chain: "A" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 733 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "B" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 742 Classifications: {'DNA': 36} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 35} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14481 SG CYS J 70 23.865 71.908 82.014 1.00140.07 S ATOM 14495 SG CYS J 72 22.558 68.362 81.370 1.00130.51 S ATOM 14603 SG CYS J 85 21.118 70.398 84.197 1.00132.49 S ATOM 14627 SG CYS J 88 24.713 69.149 84.416 1.00133.10 S ATOM 20315 SG CYS J 814 57.267 125.816 93.527 1.00108.98 S ATOM 20880 SG CYS J 888 59.422 122.996 92.763 1.00113.36 S ATOM 20931 SG CYS J 895 58.617 125.771 90.052 1.00 99.51 S ATOM 20952 SG CYS J 898 61.133 126.328 92.749 1.00103.33 S Time building chain proxies: 4.89, per 1000 atoms: 0.18 Number of scatterers: 26957 At special positions: 0 Unit cell: (139.776, 170.56, 159.744, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 107 16.00 P 86 15.00 Mg 1 11.99 O 5384 8.00 N 4773 7.00 C 16604 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: 2.01 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1501 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 72 " pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 895 " Number of angles added : 12 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5942 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 47 sheets defined 38.5% alpha, 18.2% beta 37 base pairs and 64 stacking pairs defined. Time for finding SS restraints: 3.25 Creating SS restraints... Processing helix chain 'G' and resid 34 through 48 removed outlier: 3.662A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.624A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 154 through 159 removed outlier: 3.579A pdb=" N ARG G 158 " --> pdb=" O PRO G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 233 removed outlier: 4.179A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP G 233 " --> pdb=" O GLU G 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.581A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 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 154 through 163 removed outlier: 3.521A pdb=" N ARG H 158 " --> pdb=" O PRO H 154 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLU H 163 " --> pdb=" O ILE H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 229 Processing helix chain 'H' and resid 230 through 232 No H-bonds generated for 'chain 'H' and resid 230 through 232' Processing helix chain 'I' and resid 4 through 9 removed outlier: 3.813A pdb=" N LYS I 9 " --> pdb=" O TYR I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 37 removed outlier: 3.658A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE I 35 " --> pdb=" O GLN I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 57 removed outlier: 3.585A pdb=" N ALA I 52 " --> pdb=" O GLY I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.701A 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 removed outlier: 3.510A pdb=" N ARG I 247 " --> pdb=" O GLU I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 288 through 295 removed outlier: 3.644A pdb=" N GLY I 294 " --> pdb=" O TYR I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 328 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: 3.890A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 447 through 449 No H-bonds generated for 'chain 'I' and resid 447 through 449' Processing helix chain 'I' and resid 455 through 482 removed outlier: 3.760A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU I 481 " --> pdb=" O GLU I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 488 through 493 removed outlier: 3.841A pdb=" N MET I 492 " --> pdb=" O MET I 488 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE I 493 " --> pdb=" O PRO I 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 488 through 493' Processing helix chain 'I' and resid 494 through 508 removed outlier: 4.651A pdb=" N ILE I 498 " --> pdb=" O ASN I 494 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 551 through 555 Processing helix chain 'I' and resid 608 through 612 removed outlier: 3.962A 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 664 through 668 removed outlier: 3.674A pdb=" N ILE I 668 " --> pdb=" O ALA I 665 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 687 removed outlier: 3.991A pdb=" N ARG I 687 " --> pdb=" O ALA I 683 " (cutoff:3.500A) Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 942 through 983 removed outlier: 3.515A pdb=" N ALA I 981 " --> pdb=" O ALA I 977 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY I 982 " --> pdb=" O VAL I 978 " (cutoff:3.500A) Processing helix chain 'I' and resid 985 through 990 removed outlier: 4.005A pdb=" N ASP I 990 " --> pdb=" O ALA I 986 " (cutoff:3.500A) Processing helix chain 'I' and resid 994 through 1000 removed outlier: 3.977A pdb=" N LEU I 998 " --> pdb=" O ARG I 994 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU I 999 " --> pdb=" O ASP I 995 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1038 removed outlier: 3.656A pdb=" N ASN I1009 " --> pdb=" O GLU I1005 " (cutoff:3.500A) Processing helix chain 'I' and resid 1081 through 1085 Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 4.111A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.659A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1165 through 1177 Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1283 through 1292 Processing helix chain 'I' and resid 1297 through 1310 Processing helix chain 'I' and resid 1320 through 1333 removed outlier: 3.725A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU I1333 " --> pdb=" O GLU I1329 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 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 172 Processing helix chain 'J' and resid 181 through 192 removed outlier: 3.518A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 208 removed outlier: 3.644A pdb=" N GLU J 207 " --> pdb=" O GLU J 203 " (cutoff:3.500A) 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 263 through 285 Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 336 through 341 Processing helix chain 'J' and resid 370 through 377 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: 3.714A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 3.539A 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 450 through 452 No H-bonds generated for 'chain 'J' and resid 450 through 452' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 504 through 514 removed outlier: 3.702A pdb=" N LEU J 508 " --> pdb=" O GLN J 504 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 580 Processing helix chain 'J' and resid 588 through 592 removed outlier: 4.015A pdb=" N ILE J 591 " --> pdb=" O PRO J 588 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 612 Processing helix chain 'J' and resid 614 through 636 Processing helix chain 'J' and resid 649 through 671 Processing helix chain 'J' and resid 674 through 703 removed outlier: 3.864A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 729 Processing helix chain 'J' and resid 733 through 742 Processing helix chain 'J' and resid 768 through 804 removed outlier: 3.762A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THR J 790 " --> pdb=" O THR J 786 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 removed outlier: 3.598A pdb=" N ARG J 838 " --> pdb=" O PRO J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 884 through 888 Processing helix chain 'J' and resid 896 through 900 Processing helix chain 'J' and resid 914 through 925 Processing helix chain 'J' and resid 926 through 928 No H-bonds generated for 'chain 'J' and resid 926 through 928' Processing helix chain 'J' and resid 1136 through 1147 Processing helix chain 'J' and resid 1216 through 1225 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 3.963A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.251A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1318 through 1324 removed outlier: 3.592A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1354 removed outlier: 3.677A pdb=" N ASN J1350 " --> pdb=" O GLY J1346 " (cutoff:3.500A) Processing helix chain 'J' and resid 1360 through 1375 removed outlier: 4.198A pdb=" N ALA J1364 " --> pdb=" O GLY J1360 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA J1374 " --> pdb=" O MET J1370 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 17 through 32 removed outlier: 3.775A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 removed outlier: 3.796A pdb=" N GLU K 56 " --> pdb=" O ARG K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 84 Processing sheet with id=AA1, first strand: chain 'G' and resid 12 through 17 removed outlier: 5.176A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N HIS G 23 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N THR G 207 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.725A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLY G 149 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N CYS G 54 " --> pdb=" O GLY G 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 90 through 91 Processing sheet with id=AA4, first strand: chain 'G' and resid 108 through 111 removed outlier: 6.513A pdb=" N GLY G 108 " --> pdb=" O HIS G 132 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N HIS G 132 " --> pdb=" O GLY G 108 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL G 110 " --> pdb=" O ILE G 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'H' and resid 15 through 17 removed outlier: 6.578A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N THR H 196 " --> pdb=" O VAL H 192 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL H 192 " --> pdb=" O THR H 196 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 97 through 105 removed outlier: 7.559A pdb=" N SER H 141 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ILE H 61 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 90 through 92 Processing sheet with id=AA9, first strand: chain 'H' and resid 108 through 111 removed outlier: 4.054A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.427A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 66 through 75 removed outlier: 6.356A pdb=" N SER I 66 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N TYR I 105 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 136 through 138 Processing sheet with id=AB5, first strand: chain 'I' and resid 451 through 454 removed outlier: 6.346A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 154 through 159 removed outlier: 4.958A pdb=" N TYR I 172 " --> pdb=" O PHE I 188 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 238 through 239 Processing sheet with id=AB8, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.952A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 301 through 302 Processing sheet with id=AC1, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.667A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N THR I 595 " --> pdb=" O THR I 600 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N THR I 600 " --> pdb=" O THR I 595 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC3, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.544A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.174A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AC6, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC7, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.383A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.787A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 849 through 850 Processing sheet with id=AD1, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.919A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AD3, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AD4, first strand: chain 'I' and resid 1335 through 1340 Processing sheet with id=AD5, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.554A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 10.027A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.710A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 159 through 160 removed outlier: 7.236A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AD8, first strand: chain 'J' and resid 706 through 709 Processing sheet with id=AD9, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AE1, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE2, first strand: chain 'J' and resid 825 through 826 removed outlier: 4.228A pdb=" N GLU J 833 " --> pdb=" O VAL J 825 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 848 through 849 removed outlier: 6.797A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 949 through 951 removed outlier: 3.650A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 957 through 961 removed outlier: 3.974A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 1024 through 1028 removed outlier: 6.304A pdb=" N MET J1025 " --> pdb=" O ARG J1123 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ARG J1123 " --> pdb=" O MET J1025 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL J1027 " --> pdb=" O LEU J1121 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 1098 through 1100 Processing sheet with id=AE8, first strand: chain 'J' and resid 1046 through 1050 removed outlier: 3.648A pdb=" N ALA J1105 " --> pdb=" O VAL J1061 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 1155 through 1156 removed outlier: 6.375A pdb=" N ILE J1155 " --> pdb=" O ILE J1210 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 1187 through 1191 Processing sheet with id=AF2, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.484A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1094 hydrogen bonds defined for protein. 3084 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 95 hydrogen bonds 186 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 64 stacking parallelities Total time for adding SS restraints: 6.67 Time building geometry restraints manager: 2.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8832 1.34 - 1.46: 3954 1.46 - 1.58: 14398 1.58 - 1.70: 170 1.70 - 1.82: 186 Bond restraints: 27540 Sorted by residual: bond pdb=" C3' DC A 6 " pdb=" C2' DC A 6 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.16e+01 bond pdb=" C3' DA B 12 " pdb=" C2' DA B 12 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.59e+00 bond pdb=" C3' DC A 21 " pdb=" C2' DC A 21 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.49e+00 bond pdb=" C3' DA B 15 " pdb=" C2' DA B 15 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.54e+00 bond pdb=" C3' DT A 29 " pdb=" C2' DT A 29 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.29e+00 ... (remaining 27535 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 37204 2.25 - 4.50: 329 4.50 - 6.75: 29 6.75 - 9.00: 16 9.00 - 11.25: 2 Bond angle restraints: 37580 Sorted by residual: angle pdb=" O4' DC B 27 " pdb=" C4' DC B 27 " pdb=" C3' DC B 27 " ideal model delta sigma weight residual 106.00 103.36 2.64 6.00e-01 2.78e+00 1.94e+01 angle pdb=" N3 DT A 38 " pdb=" C4 DT A 38 " pdb=" O4 DT A 38 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT A 31 " pdb=" C4 DT A 31 " pdb=" O4 DT A 31 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" N3 DT B 33 " pdb=" C4 DT B 33 " pdb=" O4 DT B 33 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT B 24 " pdb=" C4 DT B 24 " pdb=" O4 DT B 24 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.77e+01 ... (remaining 37575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.12: 15893 35.12 - 70.24: 823 70.24 - 105.36: 41 105.36 - 140.49: 2 140.49 - 175.61: 2 Dihedral angle restraints: 16761 sinusoidal: 7524 harmonic: 9237 Sorted by residual: dihedral pdb=" CA ASN I 314 " pdb=" C ASN I 314 " pdb=" N MET I 315 " pdb=" CA MET I 315 " ideal model delta harmonic sigma weight residual 180.00 156.97 23.03 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA MET J 130 " pdb=" C MET J 130 " pdb=" N PRO J 131 " pdb=" CA PRO J 131 " ideal model delta harmonic sigma weight residual -180.00 -159.65 -20.35 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" C4' DG A 13 " pdb=" C3' DG A 13 " pdb=" O3' DG A 13 " pdb=" P DG A 14 " ideal model delta sinusoidal sigma weight residual -140.00 35.61 -175.61 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 16758 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2844 0.031 - 0.063: 923 0.063 - 0.094: 304 0.094 - 0.125: 207 0.125 - 0.156: 20 Chirality restraints: 4298 Sorted by residual: chirality pdb=" CA ASP I1154 " pdb=" N ASP I1154 " pdb=" C ASP I1154 " pdb=" CB ASP I1154 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.10e-01 chirality pdb=" C2' C R 13 " pdb=" C3' C R 13 " pdb=" O2' C R 13 " pdb=" C1' C R 13 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" C2' A R 4 " pdb=" C3' A R 4 " pdb=" O2' A R 4 " pdb=" C1' A R 4 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 4295 not shown) Planarity restraints: 4619 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP J1193 " -0.018 2.00e-02 2.50e+03 1.73e-02 7.51e+00 pdb=" CG TRP J1193 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP J1193 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP J1193 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP J1193 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP J1193 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP J1193 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP J1193 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP J1193 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP J1193 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU K 11 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.90e+00 pdb=" CD GLU K 11 " -0.034 2.00e-02 2.50e+03 pdb=" OE1 GLU K 11 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU K 11 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU K 68 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.43e+00 pdb=" CD GLU K 68 " -0.032 2.00e-02 2.50e+03 pdb=" OE1 GLU K 68 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU K 68 " 0.011 2.00e-02 2.50e+03 ... (remaining 4616 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 298 2.62 - 3.19: 22789 3.19 - 3.76: 42822 3.76 - 4.33: 57993 4.33 - 4.90: 96470 Nonbonded interactions: 220372 Sorted by model distance: nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1503 " model vdw 2.055 2.170 nonbonded pdb=" OD2 ASP J 462 " pdb="MG MG J1503 " model vdw 2.094 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1503 " model vdw 2.105 2.170 nonbonded pdb=" OD1 ASP J 464 " pdb="MG MG J1503 " model vdw 2.129 2.170 nonbonded pdb=" N GLN H 127 " pdb=" OE1 GLN H 127 " model vdw 2.200 3.120 ... (remaining 220367 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 4 through 233) selection = (chain 'H' and resid 4 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: 5.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 29.980 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 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:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 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 0.047 27548 Z= 0.194 Angle : 0.521 11.253 37592 Z= 0.332 Chirality : 0.041 0.156 4298 Planarity : 0.003 0.061 4619 Dihedral : 18.534 175.607 10819 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.57 % Allowed : 21.95 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.15), residues: 3202 helix: 2.36 (0.16), residues: 1118 sheet: 0.66 (0.25), residues: 456 loop : 0.03 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG K 69 TYR 0.011 0.001 TYR J 631 PHE 0.009 0.001 PHE J1325 TRP 0.046 0.001 TRP J1193 HIS 0.002 0.000 HIS J 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.19 (27540) covalent geometry : angle 0.51620 / 0.33 (37580) hydrogen bonds : bond 0.12384 / 8.17 ( 1187) hydrogen bonds : angle 4.90138 / 3.44 ( 3270) metal coordination : bond 0.00368 / 0.24 ( 8) metal coordination : angle 4.02795 / 2.27 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 193 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 145 LYS cc_start: 0.9093 (tttt) cc_final: 0.8800 (tttm) REVERT: K 3 ARG cc_start: 0.8770 (ttm-80) cc_final: 0.8262 (ttm-80) outliers start: 43 outliers final: 38 residues processed: 230 average time/residue: 0.6833 time to fit residues: 181.9787 Evaluate side-chains 224 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 186 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 125 LYS Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain G residue 229 GLU Chi-restraints excluded: chain G residue 235 ARG Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 320 ASP Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 937 ASP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1115 THR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 603 LYS Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1124 ILE Chi-restraints excluded: chain J residue 1164 SER Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 56 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 582 ASN I1111 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.077140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.053964 restraints weight = 64259.863| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 2.43 r_work: 0.2689 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2541 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9185 moved from start: 0.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 27548 Z= 0.265 Angle : 0.574 12.768 37592 Z= 0.300 Chirality : 0.043 0.242 4298 Planarity : 0.004 0.059 4619 Dihedral : 16.057 172.065 4605 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.81 % Allowed : 19.65 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.15), residues: 3202 helix: 2.14 (0.16), residues: 1133 sheet: 0.52 (0.24), residues: 463 loop : -0.03 (0.15), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 69 TYR 0.022 0.001 TYR J 631 PHE 0.020 0.001 PHE J1325 TRP 0.021 0.002 TRP J1193 HIS 0.005 0.001 HIS I 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00613 / 0.26 (27540) covalent geometry : angle 0.56449 / 0.30 (37580) hydrogen bonds : bond 0.04318 / 3.01 ( 1187) hydrogen bonds : angle 4.15498 / 2.90 ( 3270) metal coordination : bond 0.01403 / 0.90 ( 8) metal coordination : angle 5.86501 / 3.20 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 195 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 117 HIS cc_start: 0.8649 (t-90) cc_final: 0.8353 (t-90) REVERT: I 239 MET cc_start: 0.6729 (pp-130) cc_final: 0.6474 (pp-130) REVERT: I 510 GLN cc_start: 0.9167 (mt0) cc_final: 0.8902 (mt0) REVERT: J 133 ARG cc_start: 0.8613 (mtt180) cc_final: 0.8054 (mtm110) REVERT: J 479 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8358 (mt-10) REVERT: J 603 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8929 (tppp) REVERT: K 68 GLU cc_start: 0.8294 (tm-30) cc_final: 0.7904 (tm-30) outliers start: 77 outliers final: 28 residues processed: 251 average time/residue: 0.7531 time to fit residues: 217.3605 Evaluate side-chains 214 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 235 ARG Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 18 GLN Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 191 LYS Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 603 LYS Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1370 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 262 optimal weight: 0.5980 chunk 283 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 243 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 200 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.078248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.055066 restraints weight = 63554.351| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.43 r_work: 0.2725 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2578 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9159 moved from start: 0.0872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 27548 Z= 0.126 Angle : 0.489 9.072 37592 Z= 0.260 Chirality : 0.041 0.243 4298 Planarity : 0.003 0.046 4619 Dihedral : 15.926 173.396 4564 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.26 % Allowed : 20.60 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.15), residues: 3202 helix: 2.23 (0.16), residues: 1133 sheet: 0.57 (0.24), residues: 458 loop : -0.03 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 247 TYR 0.014 0.001 TYR J 631 PHE 0.011 0.001 PHE J1199 TRP 0.023 0.001 TRP J1193 HIS 0.004 0.001 HIS H 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (27540) covalent geometry : angle 0.47992 / 0.26 (37580) hydrogen bonds : bond 0.03712 / 2.58 ( 1187) hydrogen bonds : angle 3.98610 / 2.78 ( 3270) metal coordination : bond 0.00750 / 0.48 ( 8) metal coordination : angle 5.26363 / 2.88 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 195 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 117 HIS cc_start: 0.8629 (t-90) cc_final: 0.8340 (t-90) REVERT: H 145 LYS cc_start: 0.9155 (tttt) cc_final: 0.8929 (tttm) REVERT: I 239 MET cc_start: 0.6888 (pp-130) cc_final: 0.6658 (pp-130) REVERT: J 133 ARG cc_start: 0.8604 (mtt180) cc_final: 0.8096 (mtm110) REVERT: J 479 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8334 (mt-10) REVERT: J 603 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8919 (tppp) REVERT: J 901 ARG cc_start: 0.9276 (OUTLIER) cc_final: 0.8264 (ptm160) REVERT: J 1048 ARG cc_start: 0.8323 (mtp85) cc_final: 0.8101 (mmm160) REVERT: K 68 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7872 (tm-30) outliers start: 62 outliers final: 26 residues processed: 239 average time/residue: 0.7297 time to fit residues: 201.9304 Evaluate side-chains 215 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 187 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 235 ARG Chi-restraints excluded: chain H residue 18 GLN Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 603 LYS Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 901 ARG Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1370 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 62 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 326 optimal weight: 10.0000 chunk 215 optimal weight: 0.4980 chunk 277 optimal weight: 0.2980 chunk 33 optimal weight: 0.7980 chunk 243 optimal weight: 0.9980 chunk 145 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 294 optimal weight: 2.9990 chunk 242 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 618 GLN K 43 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.078844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.055725 restraints weight = 63120.485| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.42 r_work: 0.2745 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9126 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 27548 Z= 0.108 Angle : 0.477 9.750 37592 Z= 0.252 Chirality : 0.040 0.243 4298 Planarity : 0.003 0.056 4619 Dihedral : 15.875 173.676 4560 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.92 % Allowed : 20.12 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.15), residues: 3202 helix: 2.26 (0.16), residues: 1134 sheet: 0.62 (0.25), residues: 449 loop : -0.03 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 69 TYR 0.028 0.001 TYR H 185 PHE 0.010 0.001 PHE J1325 TRP 0.028 0.001 TRP J1193 HIS 0.003 0.000 HIS H 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (27540) covalent geometry : angle 0.46687 / 0.25 (37580) hydrogen bonds : bond 0.03363 / 2.35 ( 1187) hydrogen bonds : angle 3.86576 / 2.70 ( 3270) metal coordination : bond 0.00761 / 0.52 ( 8) metal coordination : angle 5.37322 / 2.96 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 198 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 117 HIS cc_start: 0.8654 (t-90) cc_final: 0.8355 (t-90) REVERT: H 145 LYS cc_start: 0.9115 (tttt) cc_final: 0.8881 (tttm) REVERT: H 212 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.8016 (t0) REVERT: I 239 MET cc_start: 0.6957 (pp-130) cc_final: 0.6694 (pp-130) REVERT: I 593 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.8816 (tttp) REVERT: I 1273 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8140 (mtt) REVERT: J 304 ASP cc_start: 0.8974 (t0) cc_final: 0.8527 (m-30) REVERT: J 479 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8319 (mt-10) REVERT: J 603 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8851 (tppp) REVERT: J 901 ARG cc_start: 0.9221 (OUTLIER) cc_final: 0.8238 (ptm160) REVERT: J 1048 ARG cc_start: 0.8386 (mtp85) cc_final: 0.8165 (mmm160) REVERT: K 68 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7937 (tm-30) outliers start: 80 outliers final: 30 residues processed: 259 average time/residue: 0.6657 time to fit residues: 201.5676 Evaluate side-chains 228 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 193 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 235 ARG Chi-restraints excluded: chain H residue 18 GLN Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 593 LYS Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 843 THR Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 285 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 603 LYS Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 901 ARG Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1309 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 212 optimal weight: 0.9980 chunk 224 optimal weight: 3.9990 chunk 302 optimal weight: 10.0000 chunk 144 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 299 optimal weight: 3.9990 chunk 61 optimal weight: 0.0270 chunk 160 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 overall best weight: 1.3842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 147 GLN ** I 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.077848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.054689 restraints weight = 63481.594| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 2.42 r_work: 0.2709 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9151 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27548 Z= 0.180 Angle : 0.518 11.475 37592 Z= 0.271 Chirality : 0.041 0.244 4298 Planarity : 0.004 0.049 4619 Dihedral : 15.940 173.136 4558 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.12 % Allowed : 20.78 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.15), residues: 3202 helix: 2.22 (0.16), residues: 1136 sheet: 0.58 (0.24), residues: 457 loop : -0.07 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 247 TYR 0.028 0.001 TYR H 185 PHE 0.016 0.001 PHE J1325 TRP 0.032 0.001 TRP J1193 HIS 0.004 0.001 HIS H 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (27540) covalent geometry : angle 0.50811 / 0.27 (37580) hydrogen bonds : bond 0.03702 / 2.60 ( 1187) hydrogen bonds : angle 3.88134 / 2.71 ( 3270) metal coordination : bond 0.01002 / 0.66 ( 8) metal coordination : angle 5.67081 / 3.10 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 193 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 117 HIS cc_start: 0.8714 (t-90) cc_final: 0.8428 (t-90) REVERT: H 66 HIS cc_start: 0.8737 (m-70) cc_final: 0.8498 (m-70) REVERT: I 510 GLN cc_start: 0.9171 (mt0) cc_final: 0.8931 (mt0) REVERT: I 593 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.8850 (tttp) REVERT: J 133 ARG cc_start: 0.8430 (mtt-85) cc_final: 0.7979 (mtm110) REVERT: J 166 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8965 (mm) REVERT: J 304 ASP cc_start: 0.9019 (t0) cc_final: 0.8559 (m-30) REVERT: J 479 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8331 (mt-10) REVERT: J 603 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8908 (tppp) REVERT: J 901 ARG cc_start: 0.9252 (OUTLIER) cc_final: 0.8176 (ptm160) REVERT: J 1048 ARG cc_start: 0.8443 (mtp85) cc_final: 0.8197 (mmm160) REVERT: K 68 GLU cc_start: 0.8288 (tm-30) cc_final: 0.8000 (tm-30) REVERT: K 69 ARG cc_start: 0.8087 (ttm-80) cc_final: 0.7872 (mtm110) outliers start: 58 outliers final: 33 residues processed: 235 average time/residue: 0.7118 time to fit residues: 193.8703 Evaluate side-chains 225 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 235 ARG Chi-restraints excluded: chain H residue 18 GLN Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 191 LYS Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 593 LYS Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 840 SER Chi-restraints excluded: chain I residue 843 THR Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 603 LYS Chi-restraints excluded: chain J residue 901 ARG Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain K residue 43 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 260 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 15 optimal weight: 0.3980 chunk 20 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 169 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 326 optimal weight: 10.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 147 GLN ** I 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 604 HIS K 43 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.078023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.054900 restraints weight = 63372.354| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.41 r_work: 0.2715 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9161 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27548 Z= 0.128 Angle : 0.495 10.505 37592 Z= 0.259 Chirality : 0.040 0.244 4298 Planarity : 0.003 0.055 4619 Dihedral : 15.932 173.554 4557 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.19 % Allowed : 21.18 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.15), residues: 3202 helix: 2.25 (0.16), residues: 1136 sheet: 0.59 (0.24), residues: 457 loop : -0.05 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 247 TYR 0.027 0.001 TYR H 185 PHE 0.012 0.001 PHE J1325 TRP 0.031 0.001 TRP J1193 HIS 0.003 0.000 HIS H 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (27540) covalent geometry : angle 0.48524 / 0.26 (37580) hydrogen bonds : bond 0.03458 / 2.42 ( 1187) hydrogen bonds : angle 3.81598 / 2.66 ( 3270) metal coordination : bond 0.00778 / 0.51 ( 8) metal coordination : angle 5.40335 / 2.96 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 190 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 117 HIS cc_start: 0.8694 (t-90) cc_final: 0.8408 (t-90) REVERT: H 66 HIS cc_start: 0.8715 (m-70) cc_final: 0.8493 (m-70) REVERT: H 212 ASP cc_start: 0.8329 (OUTLIER) cc_final: 0.8091 (t0) REVERT: I 593 LYS cc_start: 0.9302 (OUTLIER) cc_final: 0.8826 (tttp) REVERT: J 133 ARG cc_start: 0.8415 (mtt-85) cc_final: 0.7995 (mtm110) REVERT: J 166 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8974 (mm) REVERT: J 304 ASP cc_start: 0.9018 (t0) cc_final: 0.8563 (m-30) REVERT: J 479 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8354 (mt-10) REVERT: J 603 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8907 (tppp) REVERT: J 901 ARG cc_start: 0.9292 (OUTLIER) cc_final: 0.8276 (ptm160) REVERT: J 1048 ARG cc_start: 0.8485 (mtp85) cc_final: 0.8217 (mmm160) REVERT: K 68 GLU cc_start: 0.8401 (tm-30) cc_final: 0.7956 (tm-30) REVERT: K 69 ARG cc_start: 0.8142 (ttm-80) cc_final: 0.7913 (mtm110) outliers start: 60 outliers final: 31 residues processed: 236 average time/residue: 0.6640 time to fit residues: 182.5940 Evaluate side-chains 221 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 185 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 235 ARG Chi-restraints excluded: chain H residue 18 GLN Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 593 LYS Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 840 SER Chi-restraints excluded: chain I residue 843 THR Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 603 LYS Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 901 ARG Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1298 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 193 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 chunk 322 optimal weight: 30.0000 chunk 61 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 chunk 154 optimal weight: 0.3980 chunk 255 optimal weight: 3.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 762 ASN K 43 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.076814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.053614 restraints weight = 63516.039| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 2.41 r_work: 0.2688 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2542 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9189 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 27548 Z= 0.231 Angle : 0.545 11.897 37592 Z= 0.284 Chirality : 0.042 0.244 4298 Planarity : 0.004 0.050 4619 Dihedral : 16.007 173.241 4556 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.45 % Allowed : 21.18 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.15), residues: 3202 helix: 2.17 (0.16), residues: 1135 sheet: 0.51 (0.24), residues: 463 loop : -0.11 (0.15), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 247 TYR 0.028 0.001 TYR H 185 PHE 0.017 0.001 PHE J1325 TRP 0.036 0.001 TRP J1193 HIS 0.005 0.001 HIS H 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.23 (27540) covalent geometry : angle 0.53544 / 0.28 (37580) hydrogen bonds : bond 0.03875 / 2.71 ( 1187) hydrogen bonds : angle 3.89175 / 2.71 ( 3270) metal coordination : bond 0.01248 / 0.83 ( 8) metal coordination : angle 5.82223 / 3.19 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 185 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 117 HIS cc_start: 0.8683 (t-90) cc_final: 0.8411 (t-90) REVERT: H 66 HIS cc_start: 0.8722 (m-70) cc_final: 0.8511 (m-70) REVERT: H 122 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8209 (tm-30) REVERT: H 212 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.8146 (t0) REVERT: I 510 GLN cc_start: 0.9143 (mt0) cc_final: 0.8872 (mt0) REVERT: I 593 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.8863 (tttp) REVERT: J 133 ARG cc_start: 0.8425 (mtt-85) cc_final: 0.8041 (mtm110) REVERT: J 166 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8972 (mm) REVERT: J 256 ASP cc_start: 0.8000 (t0) cc_final: 0.7780 (t0) REVERT: J 603 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8967 (tppp) REVERT: J 846 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8112 (pm20) REVERT: J 901 ARG cc_start: 0.9305 (OUTLIER) cc_final: 0.8250 (ptm160) REVERT: K 68 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7718 (tm-30) outliers start: 67 outliers final: 39 residues processed: 239 average time/residue: 0.6653 time to fit residues: 184.9601 Evaluate side-chains 229 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 183 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 235 ARG Chi-restraints excluded: chain H residue 18 GLN Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 593 LYS Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 840 SER Chi-restraints excluded: chain I residue 843 THR Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 603 LYS Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 846 GLU Chi-restraints excluded: chain J residue 901 ARG Chi-restraints excluded: chain J residue 934 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain K residue 43 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 44 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 263 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 247 optimal weight: 0.2980 chunk 278 optimal weight: 0.9990 chunk 207 optimal weight: 5.9990 chunk 298 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 259 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 762 ASN K 43 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.077502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.054373 restraints weight = 63568.665| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.42 r_work: 0.2700 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2555 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9157 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27548 Z= 0.162 Angle : 0.527 10.967 37592 Z= 0.274 Chirality : 0.041 0.245 4298 Planarity : 0.004 0.069 4619 Dihedral : 16.014 173.409 4555 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.23 % Allowed : 21.48 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.15), residues: 3202 helix: 2.17 (0.16), residues: 1135 sheet: 0.53 (0.24), residues: 458 loop : -0.11 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG I 247 TYR 0.029 0.001 TYR H 185 PHE 0.014 0.001 PHE J1325 TRP 0.039 0.001 TRP J1193 HIS 0.005 0.001 HIS H 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (27540) covalent geometry : angle 0.51716 / 0.27 (37580) hydrogen bonds : bond 0.03700 / 2.59 ( 1187) hydrogen bonds : angle 3.86196 / 2.69 ( 3270) metal coordination : bond 0.00946 / 0.62 ( 8) metal coordination : angle 5.72060 / 3.14 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 190 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 117 HIS cc_start: 0.8748 (t-90) cc_final: 0.8463 (t-90) REVERT: H 122 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8109 (tm-30) REVERT: H 212 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.8123 (t0) REVERT: I 510 GLN cc_start: 0.9151 (mt0) cc_final: 0.8909 (mt0) REVERT: I 593 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8826 (tttp) REVERT: J 133 ARG cc_start: 0.8411 (mtt-85) cc_final: 0.8036 (mtm110) REVERT: J 166 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8984 (mm) REVERT: J 256 ASP cc_start: 0.8027 (t0) cc_final: 0.7796 (t0) REVERT: J 304 ASP cc_start: 0.9026 (t0) cc_final: 0.8569 (m-30) REVERT: J 603 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8898 (tppp) REVERT: J 846 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8083 (pm20) REVERT: J 901 ARG cc_start: 0.9269 (OUTLIER) cc_final: 0.8139 (ptm160) REVERT: J 1048 ARG cc_start: 0.8293 (mtp85) cc_final: 0.8063 (mtp85) REVERT: K 72 GLN cc_start: 0.8114 (tp40) cc_final: 0.7706 (tm-30) outliers start: 61 outliers final: 37 residues processed: 238 average time/residue: 0.6840 time to fit residues: 189.4267 Evaluate side-chains 229 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 185 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 235 ARG Chi-restraints excluded: chain H residue 18 GLN Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 488 MET Chi-restraints excluded: chain I residue 593 LYS Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 840 SER Chi-restraints excluded: chain I residue 843 THR Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 603 LYS Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 846 GLU Chi-restraints excluded: chain J residue 901 ARG Chi-restraints excluded: chain J residue 1059 LEU Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain K residue 43 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 26 optimal weight: 3.9990 chunk 123 optimal weight: 0.0020 chunk 120 optimal weight: 0.7980 chunk 296 optimal weight: 0.0770 chunk 64 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 165 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 295 optimal weight: 0.7980 chunk 314 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 overall best weight: 0.4946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 147 GLN H 66 HIS ** I 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 762 ASN K 43 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.078026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.054869 restraints weight = 63142.949| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.42 r_work: 0.2723 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2578 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9145 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 27548 Z= 0.112 Angle : 0.520 13.672 37592 Z= 0.271 Chirality : 0.040 0.245 4298 Planarity : 0.003 0.061 4619 Dihedral : 15.983 173.718 4555 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.94 % Allowed : 22.02 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.15), residues: 3202 helix: 2.22 (0.16), residues: 1135 sheet: 0.58 (0.24), residues: 452 loop : -0.10 (0.15), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG I 275 TYR 0.030 0.001 TYR H 185 PHE 0.011 0.001 PHE J1325 TRP 0.044 0.001 TRP J1193 HIS 0.004 0.000 HIS H 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (27540) covalent geometry : angle 0.51120 / 0.27 (37580) hydrogen bonds : bond 0.03459 / 2.42 ( 1187) hydrogen bonds : angle 3.80585 / 2.66 ( 3270) metal coordination : bond 0.00636 / 0.42 ( 8) metal coordination : angle 5.41072 / 2.97 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 190 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 117 HIS cc_start: 0.8730 (t-90) cc_final: 0.8451 (t-90) REVERT: H 122 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8165 (tm-30) REVERT: H 212 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.8120 (t0) REVERT: I 593 LYS cc_start: 0.9286 (OUTLIER) cc_final: 0.8810 (tttp) REVERT: J 133 ARG cc_start: 0.8398 (mtt-85) cc_final: 0.8032 (mtm110) REVERT: J 166 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8976 (mm) REVERT: J 304 ASP cc_start: 0.9000 (t0) cc_final: 0.8542 (m-30) REVERT: J 416 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.9075 (pp) REVERT: J 603 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8866 (tppp) REVERT: J 846 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8088 (pm20) REVERT: J 901 ARG cc_start: 0.9252 (OUTLIER) cc_final: 0.8251 (ptm160) REVERT: J 1048 ARG cc_start: 0.8304 (mtp85) cc_final: 0.8060 (mtp85) REVERT: K 46 THR cc_start: 0.9069 (OUTLIER) cc_final: 0.8802 (m) REVERT: K 69 ARG cc_start: 0.8168 (ttm-80) cc_final: 0.7842 (mtm110) REVERT: K 71 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7447 (tm-30) outliers start: 53 outliers final: 34 residues processed: 232 average time/residue: 0.6693 time to fit residues: 180.7064 Evaluate side-chains 231 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 188 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 235 ARG Chi-restraints excluded: chain H residue 18 GLN Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 593 LYS Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 840 SER Chi-restraints excluded: chain I residue 843 THR Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 603 LYS Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 846 GLU Chi-restraints excluded: chain J residue 901 ARG Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 46 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 291 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 295 optimal weight: 1.9990 chunk 223 optimal weight: 0.0770 chunk 130 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 168 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 overall best weight: 0.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 147 GLN ** I 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 834 GLN J 762 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.077725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.054650 restraints weight = 62932.698| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 2.40 r_work: 0.2713 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2567 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9167 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 27548 Z= 0.143 Angle : 0.527 11.251 37592 Z= 0.275 Chirality : 0.041 0.244 4298 Planarity : 0.003 0.064 4619 Dihedral : 15.984 173.689 4555 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.83 % Allowed : 22.10 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.15), residues: 3202 helix: 2.19 (0.16), residues: 1135 sheet: 0.61 (0.24), residues: 454 loop : -0.12 (0.15), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG I 275 TYR 0.030 0.001 TYR H 185 PHE 0.013 0.001 PHE J1325 TRP 0.048 0.001 TRP J1193 HIS 0.004 0.001 HIS H 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (27540) covalent geometry : angle 0.51863 / 0.27 (37580) hydrogen bonds : bond 0.03516 / 2.46 ( 1187) hydrogen bonds : angle 3.80160 / 2.65 ( 3270) metal coordination : bond 0.00795 / 0.53 ( 8) metal coordination : angle 5.33153 / 2.92 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6404 Ramachandran restraints generated. 3202 Oldfield, 0 Emsley, 3202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 188 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 117 HIS cc_start: 0.8705 (t-90) cc_final: 0.8433 (t-90) REVERT: H 122 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8150 (tm-30) REVERT: H 212 ASP cc_start: 0.8370 (OUTLIER) cc_final: 0.8141 (t0) REVERT: I 510 GLN cc_start: 0.9108 (mt0) cc_final: 0.8881 (mt0) REVERT: I 593 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.8859 (tttp) REVERT: J 130 MET cc_start: 0.8712 (ptm) cc_final: 0.8511 (ppp) REVERT: J 133 ARG cc_start: 0.8394 (mtt-85) cc_final: 0.8037 (mtm110) REVERT: J 166 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8993 (mm) REVERT: J 304 ASP cc_start: 0.9013 (t0) cc_final: 0.8566 (m-30) REVERT: J 416 ILE cc_start: 0.9322 (OUTLIER) cc_final: 0.9111 (pp) REVERT: J 603 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8905 (tppp) REVERT: J 846 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8125 (pm20) REVERT: J 901 ARG cc_start: 0.9292 (OUTLIER) cc_final: 0.8292 (ptm160) REVERT: J 1040 MET cc_start: 0.6421 (pmm) cc_final: 0.6107 (mpp) REVERT: J 1048 ARG cc_start: 0.8362 (mtp85) cc_final: 0.8117 (mtp85) REVERT: K 71 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7433 (tm-30) REVERT: K 74 GLU cc_start: 0.7162 (pp20) cc_final: 0.6959 (pp20) outliers start: 50 outliers final: 37 residues processed: 226 average time/residue: 0.7118 time to fit residues: 186.0887 Evaluate side-chains 226 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 181 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 235 ARG Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 18 GLN Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 488 MET Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 593 LYS Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 840 SER Chi-restraints excluded: chain I residue 843 THR Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 603 LYS Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 846 GLU Chi-restraints excluded: chain J residue 901 ARG Chi-restraints excluded: chain J residue 934 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1298 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 260 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 211 optimal weight: 1.9990 chunk 252 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 312 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 232 optimal weight: 2.9990 chunk 208 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 281 optimal weight: 30.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 66 HIS H 66 HIS I 513 GLN I1324 ASN J 762 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.075744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.052620 restraints weight = 63263.594| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 2.40 r_work: 0.2652 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2505 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9211 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 27548 Z= 0.310 Angle : 0.628 14.159 37592 Z= 0.323 Chirality : 0.044 0.245 4298 Planarity : 0.004 0.080 4619 Dihedral : 16.162 172.995 4555 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.86 % Allowed : 22.17 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.15), residues: 3202 helix: 2.01 (0.16), residues: 1130 sheet: 0.35 (0.23), residues: 475 loop : -0.20 (0.15), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG I 275 TYR 0.030 0.001 TYR H 185 PHE 0.021 0.002 PHE J1325 TRP 0.051 0.002 TRP J1193 HIS 0.007 0.001 HIS H 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00723 / 0.31 (27540) covalent geometry : angle 0.61744 / 0.32 (37580) hydrogen bonds : bond 0.04389 / 3.08 ( 1187) hydrogen bonds : angle 4.00385 / 2.79 ( 3270) metal coordination : bond 0.01671 / 1.12 ( 8) metal coordination : angle 6.34750 / 3.48 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8543.96 seconds wall clock time: 146 minutes 15.23 seconds (8775.23 seconds total)