Starting phenix.real_space_refine on Sat Aug 8 12:40:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8phk_17668/08_2026/8phk_17668.cif Found real_map, /net/cci-nas-00/data/ceres_data/8phk_17668/08_2026/8phk_17668.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8phk_17668/08_2026/8phk_17668.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8phk_17668/08_2026/8phk_17668.map" model { file = "/net/cci-nas-00/data/ceres_data/8phk_17668/08_2026/8phk_17668.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8phk_17668/08_2026/8phk_17668.cif" } resolution = 3.1 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= 0.009 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 87 5.49 5 Mg 1 5.21 5 S 112 5.16 5 C 17421 2.51 5 N 4998 2.21 5 O 5604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 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: 28225 Number of models: 1 Model: "" Number of chains: 10 Chain: "P" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1294 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 150} Chain: "I" Number of atoms: 10431 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1321, 10423 Classifications: {'peptide': 1321} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1265} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 1321, 10423 Classifications: {'peptide': 1321} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1265} Chain breaks: 1 bond proxies already assigned to first conformer: 10580 Chain: "J" Number of atoms: 10440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1342, 10440 Classifications: {'peptide': 1342} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1286} 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: "G" Number of atoms: 1807 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 232, 1799 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 222} Conformer: "B" Number of residues, atoms: 232, 1799 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 222} bond proxies already assigned to first conformer: 1812 Chain: "H" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1780 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Chain: "A" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 771 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "B" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 784 Classifications: {'DNA': 38} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 37} Chain: "R" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 260 Classifications: {'RNA': 12} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 5} Link IDs: {'rna3p': 11} 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 12174 SG CYS J 70 24.393 69.954 83.528 1.00119.04 S ATOM 12188 SG CYS J 72 23.310 66.311 83.232 1.00118.34 S ATOM 12296 SG CYS J 85 21.845 68.517 85.926 1.00117.72 S ATOM 12320 SG CYS J 88 25.534 67.472 86.117 1.00115.59 S ATOM 18008 SG CYS J 814 56.521 126.276 92.019 1.00108.47 S ATOM 18573 SG CYS J 888 58.636 123.461 91.132 1.00106.90 S ATOM 18624 SG CYS J 895 57.608 126.109 88.414 1.00 98.23 S ATOM 18645 SG CYS J 898 60.284 126.828 90.894 1.00 99.88 S Time building chain proxies: 8.11, per 1000 atoms: 0.29 Number of scatterers: 28225 At special positions: 0 Unit cell: (139.776, 169.728, 158.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 112 16.00 P 87 15.00 Mg 1 11.99 O 5604 8.00 N 4998 7.00 C 17421 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: 2.54 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1501 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 88 " pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 895 " Number of angles added : 12 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6238 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 51 sheets defined 38.5% alpha, 18.6% beta 38 base pairs and 60 stacking pairs defined. Time for finding SS restraints: 3.68 Creating SS restraints... Processing helix chain 'P' and resid 13 through 24 Processing helix chain 'P' and resid 38 through 42 Processing helix chain 'P' and resid 65 through 71 removed outlier: 3.620A pdb=" N ILE P 69 " --> pdb=" O HIS P 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 89 through 98 removed outlier: 3.525A pdb=" N ILE P 93 " --> pdb=" O PRO P 89 " (cutoff:3.500A) Processing helix chain 'P' and resid 120 through 124 removed outlier: 3.967A pdb=" N PHE P 123 " --> pdb=" O GLU P 120 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU P 124 " --> pdb=" O GLY P 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 120 through 124' Processing helix chain 'P' and resid 155 through 157 No H-bonds generated for 'chain 'P' and resid 155 through 157' Processing helix chain 'I' and resid 4 through 9 Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.646A pdb=" N LEU I 32 " --> pdb=" O LEU I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 57 removed outlier: 3.648A 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: 4.093A 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 270 through 281 Processing helix chain 'I' and resid 288 through 295 removed outlier: 3.829A pdb=" N ILE I 292 " --> pdb=" O PRO I 288 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA I 293 " --> pdb=" O VAL I 289 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY I 294 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS I 295 " --> pdb=" O TYR I 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 288 through 295' Processing helix chain 'I' and resid 318 through 329 removed outlier: 3.557A pdb=" N GLY I 329 " --> pdb=" O LEU I 325 " (cutoff:3.500A) Processing helix chain 'I' and resid 345 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 3.704A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 410 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 455 through 482 Processing helix chain 'I' and resid 488 through 493 removed outlier: 4.179A pdb=" N MET I 492 " --> pdb=" O MET I 488 " (cutoff:3.500A) removed outlier: 4.417A 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 495 through 509 removed outlier: 3.818A pdb=" N SER I 509 " --> pdb=" O PHE I 505 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 544 through 549 removed outlier: 4.058A pdb=" N ARG I 548 " --> pdb=" O GLY I 544 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP I 549 " --> pdb=" O PHE I 545 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 544 through 549' Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.529A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 608 through 614 removed outlier: 3.840A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR I 614 " --> pdb=" O GLU I 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 614' Processing helix chain 'I' and resid 624 through 628 removed outlier: 4.289A pdb=" N HIS I 628 " --> pdb=" O GLU I 625 " (cutoff:3.500A) Processing helix chain 'I' and resid 662 through 667 Processing helix chain 'I' and resid 675 through 687 removed outlier: 4.000A 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 826 Processing helix chain 'I' and resid 858 through 863 removed outlier: 3.660A pdb=" N LEU I 862 " --> pdb=" O GLY I 858 " (cutoff:3.500A) Processing helix chain 'I' and resid 942 through 983 Processing helix chain 'I' and resid 985 through 992 removed outlier: 3.573A pdb=" N LEU I 992 " --> pdb=" O LYS I 988 " (cutoff:3.500A) Processing helix chain 'I' and resid 993 through 997 removed outlier: 4.027A pdb=" N ARG I 996 " --> pdb=" O PRO I 993 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1038 removed outlier: 4.127A pdb=" N ASN I1009 " --> pdb=" O GLU I1005 " (cutoff:3.500A) Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 3.808A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.754A pdb=" N LEU I1113 " --> pdb=" O ILE I1109 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.518A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1177 removed outlier: 3.646A pdb=" N ARG I1171 " --> pdb=" O GLU I1167 " (cutoff:3.500A) Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1243 Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1284 through 1292 Processing helix chain 'I' and resid 1297 through 1311 Processing helix chain 'I' and resid 1320 through 1333 removed outlier: 3.812A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 34 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 Processing helix chain 'J' and resid 114 through 119 removed outlier: 3.656A pdb=" N SER J 119 " --> pdb=" O TRP J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 180 through 191 removed outlier: 3.664A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 208 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 Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 485 through 489 Processing helix chain 'J' and resid 504 through 514 removed outlier: 3.757A 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: 3.855A 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 removed outlier: 3.566A pdb=" N VAL J 618 " --> pdb=" O LEU J 614 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE J 619 " --> pdb=" O LYS J 615 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 703 removed outlier: 4.096A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 Processing helix chain 'J' and resid 768 through 804 removed outlier: 4.115A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA J 779 " --> pdb=" O SER J 775 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 removed outlier: 3.828A pdb=" N ARG J 838 " --> pdb=" O PRO J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 875 removed outlier: 3.688A pdb=" N ASN J 875 " --> pdb=" O LEU J 871 " (cutoff:3.500A) 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 1137 through 1146 Processing helix chain 'J' and resid 1216 through 1225 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 3.587A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.326A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1296 Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1318 through 1326 removed outlier: 3.714A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN J1326 " --> pdb=" O ALA J1322 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1354 removed outlier: 3.648A pdb=" N ASN J1350 " --> pdb=" O GLY J1346 " (cutoff:3.500A) Processing helix chain 'J' and resid 1360 through 1373 removed outlier: 3.768A pdb=" N ALA J1364 " --> pdb=" O GLY J1360 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 17 through 34 removed outlier: 3.661A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY K 34 " --> pdb=" O MET K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 removed outlier: 3.748A pdb=" N GLU K 56 " --> pdb=" O ARG K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 84 Processing helix chain 'G' and resid 34 through 48 removed outlier: 4.360A pdb=" N ALA G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.631A 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 162 removed outlier: 3.788A pdb=" N ARG G 158 " --> pdb=" O PRO G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 234 removed outlier: 4.212A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 Processing helix chain 'H' and resid 77 through 88 Processing helix chain 'H' and resid 154 through 160 removed outlier: 3.616A pdb=" N ARG H 158 " --> pdb=" O PRO H 154 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N HIS H 160 " --> pdb=" O SER H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 228 removed outlier: 3.772A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 229 through 232 removed outlier: 3.565A pdb=" N VAL H 232 " --> pdb=" O GLU H 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 229 through 232' Processing sheet with id=AA1, first strand: chain 'P' and resid 27 through 29 Processing sheet with id=AA2, first strand: chain 'P' and resid 32 through 37 Processing sheet with id=AA3, first strand: chain 'P' and resid 149 through 153 removed outlier: 7.490A pdb=" N MET P 140 " --> pdb=" O THR P 131 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE P 129 " --> pdb=" O LEU P 142 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ASN P 144 " --> pdb=" O GLN P 127 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLN P 127 " --> pdb=" O ASN P 144 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.586A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 59 through 60 removed outlier: 6.030A pdb=" N SER I 66 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TYR I 105 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ALA I 94 " --> pdb=" O GLY I 125 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLY I 125 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU I 96 " --> pdb=" O TYR I 123 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR I 123 " --> pdb=" O LEU I 96 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N VAL I 98 " --> pdb=" O GLU I 121 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLU I 121 " --> pdb=" O VAL I 98 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU I 100 " --> pdb=" O GLU I 119 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLU I 119 " --> pdb=" O LEU I 100 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU I 102 " --> pdb=" O ILE I 117 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE I 117 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE I 104 " --> pdb=" O LYS I 115 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 136 through 138 Processing sheet with id=AA7, first strand: chain 'I' and resid 148 through 151 Processing sheet with id=AA8, first strand: chain 'I' and resid 154 through 159 removed outlier: 4.872A pdb=" N TYR I 172 " --> pdb=" O PHE I 188 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 226 through 231 removed outlier: 4.790A pdb=" N GLU I 226 " --> pdb=" O PHE I 337 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 239 through 240 Processing sheet with id=AB2, first strand: chain 'I' and resid 296 through 297 removed outlier: 4.090A pdb=" N MET I 315 " --> pdb=" O VAL I 297 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 301 through 303 removed outlier: 6.613A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 529 through 531 Processing sheet with id=AB5, first strand: chain 'I' and resid 580 through 581 removed outlier: 3.681A pdb=" N LYS I 593 " --> pdb=" O GLU I 602 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR I 595 " --> pdb=" O THR I 600 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N THR I 600 " --> pdb=" O THR I 595 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AB7, first strand: chain 'I' and resid 716 through 717 removed outlier: 4.122A pdb=" N ALA I 784 " --> pdb=" O ALA I 716 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.123A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AC1, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC2, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.524A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 9.697A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.724A pdb=" N LYS I1048 " --> pdb=" O SER I 840 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 849 through 850 removed outlier: 3.551A pdb=" N GLU I 849 " --> pdb=" O VAL I 887 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 882 through 884 removed outlier: 3.972A pdb=" N VAL I 884 " --> pdb=" O LEU I 918 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AC7, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AC8, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AC9, first strand: chain 'I' and resid 1335 through 1340 Processing sheet with id=AD1, first strand: chain 'J' and resid 103 through 112 removed outlier: 10.029A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.816A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 159 through 160 removed outlier: 6.682A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 253 through 254 removed outlier: 4.081A pdb=" N VAL J 253 " --> pdb=" O ALA J 261 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AD5, first strand: chain 'J' and resid 705 through 709 removed outlier: 3.687A pdb=" N THR J 705 " --> pdb=" O GLN J 716 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AD7, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AD8, first strand: chain 'J' and resid 825 through 827 removed outlier: 3.911A pdb=" N GLU J 833 " --> pdb=" O VAL J 825 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLU J 827 " --> pdb=" O VAL J 831 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N VAL J 831 " --> pdb=" O GLU J 827 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 842 through 843 removed outlier: 4.096A pdb=" N ARG J 842 " --> pdb=" O LEU J 864 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 848 through 849 removed outlier: 6.396A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 949 through 951 removed outlier: 4.635A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 957 through 961 removed outlier: 4.265A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 1024 through 1028 removed outlier: 6.379A pdb=" N MET J1025 " --> pdb=" O ARG J1123 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ARG J1123 " --> pdb=" O MET J1025 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N VAL J1027 " --> pdb=" O LEU J1121 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 1098 through 1100 Processing sheet with id=AE6, first strand: chain 'J' and resid 1186 through 1191 removed outlier: 4.512A pdb=" N TYR J1186 " --> pdb=" O ILE J1177 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.474A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 12 through 17 removed outlier: 5.001A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N HIS G 23 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N THR G 207 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.571A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLY G 149 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N CYS G 54 " --> pdb=" O GLY G 149 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 90 through 91 Processing sheet with id=AF2, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.948A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 152 through 153 Processing sheet with id=AF4, first strand: chain 'H' and resid 15 through 20 removed outlier: 6.732A pdb=" N HIS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU H 206 " --> pdb=" O ARG H 182 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ARG H 182 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 97 through 105 removed outlier: 7.938A pdb=" N SER H 141 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ILE H 61 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 108 through 111 removed outlier: 6.592A pdb=" N GLY H 108 " --> pdb=" O HIS H 132 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS H 132 " --> pdb=" O GLY H 108 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL H 110 " --> pdb=" O ILE H 130 " (cutoff:3.500A) 1143 hydrogen bonds defined for protein. 3212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 98 hydrogen bonds 192 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 60 stacking parallelities Total time for adding SS restraints: 7.78 Time building geometry restraints manager: 3.30 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: 9269 1.34 - 1.46: 4631 1.46 - 1.58: 14577 1.58 - 1.70: 172 1.70 - 1.82: 194 Bond restraints: 28843 Sorted by residual: bond pdb=" C3' DC A 39 " pdb=" C2' DC A 39 " 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 10 " pdb=" C2' DA B 10 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DG A 22 " pdb=" C2' DG A 22 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.88e+00 bond pdb=" C3' DA A 34 " pdb=" C2' DA A 34 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.41e+00 bond pdb=" C3' DT B 33 " pdb=" C2' DT B 33 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.06e+00 ... (remaining 28838 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 39152 2.89 - 5.78: 177 5.78 - 8.68: 20 8.68 - 11.57: 5 11.57 - 14.46: 1 Bond angle restraints: 39355 Sorted by residual: angle pdb=" CB MET I 488 " pdb=" CG MET I 488 " pdb=" SD MET I 488 " ideal model delta sigma weight residual 112.70 127.16 -14.46 3.00e+00 1.11e-01 2.32e+01 angle pdb=" CG ARG I1034 " pdb=" CD ARG I1034 " pdb=" NE ARG I1034 " ideal model delta sigma weight residual 112.00 122.32 -10.32 2.20e+00 2.07e-01 2.20e+01 angle pdb=" O4' DC B 21 " pdb=" C4' DC B 21 " pdb=" C3' DC B 21 " ideal model delta sigma weight residual 106.00 103.23 2.77 6.00e-01 2.78e+00 2.13e+01 angle pdb=" C PHE H 8 " pdb=" CA PHE H 8 " pdb=" CB PHE H 8 " ideal model delta sigma weight residual 115.79 110.33 5.46 1.19e+00 7.06e-01 2.10e+01 angle pdb=" N3 DT A 30 " pdb=" C4 DT A 30 " pdb=" O4 DT A 30 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 ... (remaining 39350 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.24: 16170 29.24 - 58.47: 1248 58.47 - 87.71: 122 87.71 - 116.95: 6 116.95 - 146.19: 3 Dihedral angle restraints: 17549 sinusoidal: 7856 harmonic: 9693 Sorted by residual: dihedral pdb=" CA ARG I 994 " pdb=" C ARG I 994 " pdb=" N ASP I 995 " pdb=" CA ASP I 995 " ideal model delta harmonic sigma weight residual -180.00 -160.59 -19.41 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA PRO I 993 " pdb=" C PRO I 993 " pdb=" N ARG I 994 " pdb=" CA ARG I 994 " ideal model delta harmonic sigma weight residual -180.00 -161.00 -19.00 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" C4' DC A 39 " pdb=" C3' DC A 39 " pdb=" O3' DC A 39 " pdb=" P DC A 40 " ideal model delta sinusoidal sigma weight residual 220.00 73.81 146.19 1 3.50e+01 8.16e-04 1.43e+01 ... (remaining 17546 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3183 0.036 - 0.072: 864 0.072 - 0.109: 350 0.109 - 0.145: 93 0.145 - 0.181: 5 Chirality restraints: 4495 Sorted by residual: chirality pdb=" CB ILE P 117 " pdb=" CA ILE P 117 " pdb=" CG1 ILE P 117 " pdb=" CG2 ILE P 117 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.19e-01 chirality pdb=" CA MET I 488 " pdb=" N MET I 488 " pdb=" C MET I 488 " pdb=" CB MET I 488 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.26e-01 chirality pdb=" CA ILE H 107 " pdb=" N ILE H 107 " pdb=" C ILE H 107 " pdb=" CB ILE H 107 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.63e-01 ... (remaining 4492 not shown) Planarity restraints: 4843 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP P 106 " -0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO P 107 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO P 107 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO P 107 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN G 137 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.91e+00 pdb=" C ASN G 137 " 0.034 2.00e-02 2.50e+03 pdb=" O ASN G 137 " -0.013 2.00e-02 2.50e+03 pdb=" N ALA G 138 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU J 925 " 0.009 2.00e-02 2.50e+03 1.91e-02 3.63e+00 pdb=" CD GLU J 925 " -0.033 2.00e-02 2.50e+03 pdb=" OE1 GLU J 925 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU J 925 " 0.012 2.00e-02 2.50e+03 ... (remaining 4840 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 274 2.60 - 3.18: 23617 3.18 - 3.75: 46241 3.75 - 4.33: 60553 4.33 - 4.90: 99606 Nonbonded interactions: 230291 Sorted by model distance: nonbonded pdb=" OP1 U R 17 " pdb="MG MG J1503 " model vdw 2.027 2.170 nonbonded pdb=" P U R 17 " pdb="MG MG J1503 " model vdw 2.031 2.530 nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1503 " model vdw 2.072 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1503 " model vdw 2.087 2.170 nonbonded pdb=" OD2 ASP J 460 " pdb="MG MG J1503 " model vdw 2.091 2.170 ... (remaining 230286 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 218 or resid 220 through 233)) selection = (chain 'H' and (resid 4 through 218 or resid 220 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 37.360 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 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 0.043 28851 Z= 0.192 Angle : 0.562 14.462 39367 Z= 0.346 Chirality : 0.041 0.181 4495 Planarity : 0.004 0.054 4843 Dihedral : 18.805 146.185 11311 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.54 % Favored : 97.43 % Rotamer: Outliers : 0.10 % Allowed : 24.54 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 1.00 (0.15), residues: 3354 helix: 2.08 (0.16), residues: 1161 sheet: 0.24 (0.23), residues: 518 loop : -0.16 (0.15), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG I 473 TYR 0.006 0.001 TYR J 140 PHE 0.012 0.001 PHE G 231 TRP 0.028 0.001 TRP I 183 HIS 0.007 0.000 HIS I1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.19 (28843) covalent geometry : angle 0.55865 / 0.35 (39355) hydrogen bonds : bond 0.13107 / 8.99 ( 1235) hydrogen bonds : angle 5.27760 / 3.60 ( 3404) metal coordination : bond 0.00406 / 0.20 ( 8) metal coordination : angle 3.66457 / 1.74 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 476 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 127 GLN cc_start: 0.7905 (pm20) cc_final: 0.7643 (pm20) REVERT: I 515 MET cc_start: 0.7628 (ttm) cc_final: 0.7058 (ttp) REVERT: I 516 ASP cc_start: 0.7910 (p0) cc_final: 0.7415 (p0) REVERT: I 1188 ASP cc_start: 0.7901 (t0) cc_final: 0.7618 (t0) REVERT: I 1273 MET cc_start: 0.8710 (mtt) cc_final: 0.8353 (mtt) REVERT: J 329 ASP cc_start: 0.8162 (m-30) cc_final: 0.7729 (m-30) REVERT: J 485 MET cc_start: 0.8770 (tpp) cc_final: 0.8322 (tpt) REVERT: J 724 MET cc_start: 0.8329 (ttm) cc_final: 0.8039 (ttp) REVERT: J 878 ASP cc_start: 0.7725 (p0) cc_final: 0.7241 (t70) REVERT: K 61 ASN cc_start: 0.9346 (t0) cc_final: 0.9131 (t0) REVERT: K 79 GLU cc_start: 0.8548 (pt0) cc_final: 0.8287 (pt0) REVERT: H 65 LEU cc_start: 0.9409 (tp) cc_final: 0.9145 (tt) REVERT: H 66 HIS cc_start: 0.8096 (m170) cc_final: 0.7669 (m170) REVERT: H 182 ARG cc_start: 0.8169 (mmm-85) cc_final: 0.7611 (tpt-90) outliers start: 1 outliers final: 0 residues processed: 476 average time/residue: 0.2328 time to fit residues: 166.6888 Evaluate side-chains 246 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 1.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 53 ASN I 193 ASN I 273 HIS J 206 ASN J 266 ASN J 341 ASN J 792 ASN ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1279 GLN K 43 ASN K 73 GLN ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.075290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.053882 restraints weight = 110352.938| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 3.39 r_work: 0.2823 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2819 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2819 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 28851 Z= 0.202 Angle : 0.625 9.973 39367 Z= 0.331 Chirality : 0.043 0.185 4495 Planarity : 0.005 0.061 4843 Dihedral : 15.717 150.896 4706 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.74 % Favored : 97.23 % Rotamer: Outliers : 2.54 % Allowed : 22.91 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 0.89 (0.15), residues: 3354 helix: 2.01 (0.16), residues: 1161 sheet: 0.26 (0.23), residues: 509 loop : -0.27 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 247 TYR 0.020 0.001 TYR J 631 PHE 0.017 0.001 PHE I1144 TRP 0.024 0.002 TRP I 183 HIS 0.005 0.001 HIS P 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.20 (28843) covalent geometry : angle 0.62029 / 0.33 (39355) hydrogen bonds : bond 0.04211 / 2.84 ( 1235) hydrogen bonds : angle 4.43276 / 3.02 ( 3404) metal coordination : bond 0.01313 / 0.71 ( 8) metal coordination : angle 4.43920 / 2.28 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 258 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 15 GLN cc_start: 0.9254 (tp40) cc_final: 0.8809 (tm-30) REVERT: P 37 LYS cc_start: 0.7898 (mppt) cc_final: 0.7566 (mptt) REVERT: P 127 GLN cc_start: 0.8072 (pm20) cc_final: 0.7722 (pm20) REVERT: P 151 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8517 (tptt) REVERT: I 142 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8250 (mt-10) REVERT: I 516 ASP cc_start: 0.8562 (p0) cc_final: 0.8177 (p0) REVERT: I 1188 ASP cc_start: 0.8711 (t0) cc_final: 0.8196 (t0) REVERT: I 1290 MET cc_start: 0.9261 (ttm) cc_final: 0.8851 (ttm) REVERT: J 42 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8536 (mp0) REVERT: J 47 ARG cc_start: 0.8446 (mmp80) cc_final: 0.8187 (mpt180) REVERT: J 114 ILE cc_start: 0.9317 (tp) cc_final: 0.9090 (tp) REVERT: J 301 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8695 (mt-10) REVERT: J 329 ASP cc_start: 0.8746 (m-30) cc_final: 0.8366 (m-30) REVERT: K 8 ASP cc_start: 0.8278 (p0) cc_final: 0.7856 (p0) REVERT: K 43 ASN cc_start: 0.8868 (t0) cc_final: 0.8332 (t0) REVERT: K 70 GLN cc_start: 0.9104 (tt0) cc_final: 0.8575 (tm-30) REVERT: H 65 LEU cc_start: 0.9539 (tp) cc_final: 0.9336 (tp) REVERT: H 93 GLN cc_start: 0.8310 (pm20) cc_final: 0.7853 (pm20) REVERT: H 182 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8455 (tmt-80) REVERT: H 204 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8292 (pp20) outliers start: 70 outliers final: 33 residues processed: 312 average time/residue: 0.1981 time to fit residues: 97.4231 Evaluate side-chains 262 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 225 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 151 LYS Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain I residue 1034 ARG Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 413 ASP Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 932 MET Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1144 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 25 LYS Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 182 ARG Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 204 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 319 optimal weight: 8.9990 chunk 271 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 268 optimal weight: 2.9990 chunk 257 optimal weight: 10.0000 chunk 152 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 134 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 165 HIS I1108 ASN I1111 GLN J 424 ASN J 488 ASN J 921 GLN ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.071010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.049174 restraints weight = 99413.070| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 3.19 r_work: 0.2698 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2698 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2698 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 28851 Z= 0.270 Angle : 0.642 14.962 39367 Z= 0.335 Chirality : 0.044 0.244 4495 Planarity : 0.005 0.059 4843 Dihedral : 15.865 147.835 4706 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.07 % Favored : 96.90 % Rotamer: Outliers : 3.44 % Allowed : 21.79 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 0.72 (0.15), residues: 3354 helix: 1.93 (0.15), residues: 1158 sheet: 0.26 (0.23), residues: 503 loop : -0.45 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P 40 TYR 0.028 0.002 TYR J 631 PHE 0.023 0.002 PHE J 172 TRP 0.039 0.002 TRP I 183 HIS 0.007 0.001 HIS I 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00610 / 0.27 (28843) covalent geometry : angle 0.63342 / 0.33 (39355) hydrogen bonds : bond 0.04514 / 3.05 ( 1235) hydrogen bonds : angle 4.42722 / 3.02 ( 3404) metal coordination : bond 0.01515 / 0.74 ( 8) metal coordination : angle 6.12547 / 3.22 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 221 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 15 GLN cc_start: 0.9232 (tp40) cc_final: 0.8860 (tm-30) REVERT: P 127 GLN cc_start: 0.7991 (pm20) cc_final: 0.7760 (pm20) REVERT: I 315 MET cc_start: 0.8513 (ptp) cc_final: 0.8093 (ptp) REVERT: I 503 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8736 (ptpp) REVERT: I 1188 ASP cc_start: 0.8829 (t0) cc_final: 0.8233 (t0) REVERT: J 503 SER cc_start: 0.8800 (m) cc_final: 0.8533 (t) REVERT: J 811 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8603 (mt-10) REVERT: J 1278 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8237 (mt-10) REVERT: K 43 ASN cc_start: 0.8955 (t0) cc_final: 0.8327 (t0) REVERT: H 65 LEU cc_start: 0.9473 (tp) cc_final: 0.9270 (tp) REVERT: H 165 GLU cc_start: 0.4703 (OUTLIER) cc_final: 0.3878 (tm-30) outliers start: 97 outliers final: 50 residues processed: 300 average time/residue: 0.1886 time to fit residues: 90.5358 Evaluate side-chains 256 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 204 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 42 LYS Chi-restraints excluded: chain P residue 76 SER Chi-restraints excluded: chain P residue 124 GLU Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 151 LYS Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 342 ASP Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 503 LYS Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain I residue 1034 ARG Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1040 MET Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1144 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 165 GLU Chi-restraints excluded: chain H residue 192 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 196 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 94 HIS J1259 GLN ** K 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.072542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.050670 restraints weight = 104677.083| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 3.34 r_work: 0.2736 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2736 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2736 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28851 Z= 0.121 Angle : 0.557 13.141 39367 Z= 0.291 Chirality : 0.042 0.234 4495 Planarity : 0.004 0.038 4843 Dihedral : 15.815 148.921 4706 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.68 % Favored : 97.29 % Rotamer: Outliers : 2.33 % Allowed : 22.80 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 0.76 (0.15), residues: 3354 helix: 1.95 (0.15), residues: 1166 sheet: 0.31 (0.23), residues: 488 loop : -0.44 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 182 TYR 0.016 0.001 TYR J1186 PHE 0.014 0.001 PHE I 385 TRP 0.033 0.002 TRP I 183 HIS 0.004 0.001 HIS P 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (28843) covalent geometry : angle 0.54701 / 0.29 (39355) hydrogen bonds : bond 0.03684 / 2.46 ( 1235) hydrogen bonds : angle 4.21518 / 2.88 ( 3404) metal coordination : bond 0.00695 / 0.34 ( 8) metal coordination : angle 6.11608 / 3.22 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 226 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 15 GLN cc_start: 0.9184 (tp40) cc_final: 0.8826 (tm-30) REVERT: P 127 GLN cc_start: 0.7966 (pm20) cc_final: 0.7734 (pm20) REVERT: P 134 ASP cc_start: 0.9015 (t0) cc_final: 0.7839 (t0) REVERT: P 138 ARG cc_start: 0.9359 (mtp-110) cc_final: 0.8888 (ttp-110) REVERT: I 1134 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.8667 (mp10) REVERT: I 1188 ASP cc_start: 0.8844 (t0) cc_final: 0.8211 (t0) REVERT: J 180 MET cc_start: 0.8238 (mmt) cc_final: 0.7707 (mtp) REVERT: J 443 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8399 (mm-30) REVERT: J 811 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8553 (mt-10) REVERT: J 1278 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8256 (mt-10) REVERT: K 43 ASN cc_start: 0.8898 (t0) cc_final: 0.8241 (t0) REVERT: H 65 LEU cc_start: 0.9467 (tp) cc_final: 0.9212 (tp) REVERT: H 76 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7862 (mp0) REVERT: H 93 GLN cc_start: 0.8193 (pm20) cc_final: 0.7794 (pm20) REVERT: H 165 GLU cc_start: 0.4628 (OUTLIER) cc_final: 0.4420 (tp30) outliers start: 65 outliers final: 40 residues processed: 282 average time/residue: 0.1805 time to fit residues: 81.1298 Evaluate side-chains 256 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 213 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 42 LYS Chi-restraints excluded: chain P residue 76 SER Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain I residue 1034 ARG Chi-restraints excluded: chain I residue 1134 GLN Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 432 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 932 MET Chi-restraints excluded: chain J residue 1054 THR Chi-restraints excluded: chain J residue 1144 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 165 GLU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 192 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 296 optimal weight: 7.9990 chunk 214 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 105 optimal weight: 0.0970 chunk 94 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 20 HIS P 95 GLN J 465 GLN ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.072658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.050751 restraints weight = 116495.796| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 3.48 r_work: 0.2722 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28851 Z= 0.124 Angle : 0.537 13.317 39367 Z= 0.280 Chirality : 0.041 0.187 4495 Planarity : 0.004 0.041 4843 Dihedral : 15.792 149.001 4706 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.74 % Favored : 97.23 % Rotamer: Outliers : 2.57 % Allowed : 22.59 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 0.82 (0.15), residues: 3354 helix: 2.04 (0.15), residues: 1160 sheet: 0.34 (0.23), residues: 488 loop : -0.42 (0.15), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 77 TYR 0.016 0.001 TYR J1186 PHE 0.013 0.001 PHE P 130 TRP 0.029 0.001 TRP I 183 HIS 0.004 0.001 HIS P 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (28843) covalent geometry : angle 0.52672 / 0.28 (39355) hydrogen bonds : bond 0.03551 / 2.37 ( 1235) hydrogen bonds : angle 4.11358 / 2.81 ( 3404) metal coordination : bond 0.00710 / 0.36 ( 8) metal coordination : angle 5.91289 / 3.10 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 221 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 15 GLN cc_start: 0.9198 (tp40) cc_final: 0.8849 (tm-30) REVERT: P 127 GLN cc_start: 0.7978 (pm20) cc_final: 0.7304 (pp30) REVERT: P 134 ASP cc_start: 0.9083 (t0) cc_final: 0.8230 (t0) REVERT: P 138 ARG cc_start: 0.9382 (mtp-110) cc_final: 0.8908 (ttp-110) REVERT: I 465 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7798 (tpt170) REVERT: I 1188 ASP cc_start: 0.8848 (t0) cc_final: 0.8178 (t0) REVERT: J 180 MET cc_start: 0.8159 (mmt) cc_final: 0.7840 (mtp) REVERT: J 811 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8560 (mt-10) REVERT: J 1189 MET cc_start: 0.8704 (mmp) cc_final: 0.8205 (tpp) REVERT: J 1278 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8212 (mt-10) REVERT: K 43 ASN cc_start: 0.8902 (t0) cc_final: 0.8223 (t0) REVERT: H 65 LEU cc_start: 0.9473 (tp) cc_final: 0.9220 (tp) REVERT: H 76 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7840 (mp0) REVERT: H 93 GLN cc_start: 0.8196 (pm20) cc_final: 0.7818 (pm20) REVERT: H 125 LYS cc_start: 0.8777 (mtpp) cc_final: 0.8351 (mmmm) outliers start: 72 outliers final: 48 residues processed: 283 average time/residue: 0.1985 time to fit residues: 89.3404 Evaluate side-chains 258 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 208 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 42 LYS Chi-restraints excluded: chain P residue 76 SER Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 342 ASP Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 465 ARG Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 503 LYS Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain I residue 1034 ARG Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1134 GLN Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 432 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 932 MET Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1144 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 166 ARG Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 192 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 174 optimal weight: 4.9990 chunk 196 optimal weight: 0.0020 chunk 70 optimal weight: 6.9990 chunk 193 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 218 optimal weight: 0.6980 chunk 306 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 238 optimal weight: 0.9980 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 95 GLN J 762 ASN ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.072298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.050163 restraints weight = 116896.700| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 3.45 r_work: 0.2721 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9011 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28851 Z= 0.127 Angle : 0.537 11.297 39367 Z= 0.280 Chirality : 0.041 0.166 4495 Planarity : 0.004 0.039 4843 Dihedral : 15.792 148.899 4706 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.66 % Favored : 97.32 % Rotamer: Outliers : 2.50 % Allowed : 22.73 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 0.83 (0.15), residues: 3354 helix: 2.05 (0.15), residues: 1160 sheet: 0.31 (0.23), residues: 484 loop : -0.41 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 69 TYR 0.012 0.001 TYR J 140 PHE 0.013 0.001 PHE I 385 TRP 0.026 0.001 TRP I 183 HIS 0.004 0.001 HIS P 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (28843) covalent geometry : angle 0.52683 / 0.28 (39355) hydrogen bonds : bond 0.03503 / 2.34 ( 1235) hydrogen bonds : angle 4.06422 / 2.78 ( 3404) metal coordination : bond 0.00786 / 0.40 ( 8) metal coordination : angle 5.89023 / 3.10 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 215 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 15 GLN cc_start: 0.9131 (tp40) cc_final: 0.8851 (tm-30) REVERT: P 127 GLN cc_start: 0.7871 (pm20) cc_final: 0.7193 (pp30) REVERT: I 465 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7826 (tpt170) REVERT: I 1188 ASP cc_start: 0.8851 (t0) cc_final: 0.8217 (t0) REVERT: J 180 MET cc_start: 0.8170 (mmt) cc_final: 0.7939 (mtp) REVERT: J 811 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8649 (mt-10) REVERT: J 1278 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8223 (mt-10) REVERT: K 43 ASN cc_start: 0.8865 (t0) cc_final: 0.8199 (t0) REVERT: K 73 GLN cc_start: 0.8679 (mm-40) cc_final: 0.8183 (mt0) REVERT: H 10 LYS cc_start: 0.8667 (mmmm) cc_final: 0.8363 (mmtm) REVERT: H 65 LEU cc_start: 0.9446 (tp) cc_final: 0.9204 (tp) REVERT: H 76 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7877 (mp0) REVERT: H 93 GLN cc_start: 0.8238 (pm20) cc_final: 0.7892 (pm20) REVERT: H 95 LYS cc_start: 0.8537 (pttm) cc_final: 0.8261 (pttp) REVERT: H 125 LYS cc_start: 0.8771 (mtpp) cc_final: 0.8480 (mmmm) REVERT: H 137 ASN cc_start: 0.9128 (OUTLIER) cc_final: 0.8784 (p0) outliers start: 70 outliers final: 52 residues processed: 276 average time/residue: 0.1881 time to fit residues: 82.8877 Evaluate side-chains 261 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 206 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 42 LYS Chi-restraints excluded: chain P residue 76 SER Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 342 ASP Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 465 ARG Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 503 LYS Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain I residue 1034 ARG Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1134 GLN Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 432 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 932 MET Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1144 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 166 ARG Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 192 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 102 optimal weight: 8.9990 chunk 130 optimal weight: 6.9990 chunk 293 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 238 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 294 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 41 ASN ** 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 = 0.3445 r_free = 0.3445 target = 0.072231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.050693 restraints weight = 95296.107| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 3.11 r_work: 0.2738 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28851 Z= 0.137 Angle : 0.535 11.027 39367 Z= 0.280 Chirality : 0.041 0.161 4495 Planarity : 0.004 0.040 4843 Dihedral : 15.794 148.803 4706 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.71 % Favored : 97.26 % Rotamer: Outliers : 2.47 % Allowed : 22.63 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 0.83 (0.15), residues: 3354 helix: 2.08 (0.15), residues: 1160 sheet: 0.27 (0.23), residues: 490 loop : -0.42 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 69 TYR 0.012 0.001 TYR J 631 PHE 0.013 0.001 PHE I 385 TRP 0.026 0.001 TRP I 183 HIS 0.004 0.001 HIS P 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (28843) covalent geometry : angle 0.52557 / 0.28 (39355) hydrogen bonds : bond 0.03512 / 2.34 ( 1235) hydrogen bonds : angle 4.04831 / 2.77 ( 3404) metal coordination : bond 0.00839 / 0.42 ( 8) metal coordination : angle 5.87116 / 3.07 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 207 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 15 GLN cc_start: 0.9169 (tp40) cc_final: 0.8841 (tm-30) REVERT: P 127 GLN cc_start: 0.7897 (pm20) cc_final: 0.7206 (pp30) REVERT: I 465 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7750 (tpt170) REVERT: I 1188 ASP cc_start: 0.8822 (t0) cc_final: 0.8141 (t0) REVERT: J 443 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8253 (mm-30) REVERT: J 811 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8597 (mt-10) REVERT: J 1189 MET cc_start: 0.8698 (mmp) cc_final: 0.8236 (tpp) REVERT: K 43 ASN cc_start: 0.8872 (t0) cc_final: 0.8201 (t0) REVERT: K 73 GLN cc_start: 0.8695 (mm-40) cc_final: 0.8189 (mt0) REVERT: H 10 LYS cc_start: 0.8679 (mmmm) cc_final: 0.8369 (mmtm) REVERT: H 65 LEU cc_start: 0.9451 (tp) cc_final: 0.9211 (tp) REVERT: H 76 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7841 (mp0) REVERT: H 93 GLN cc_start: 0.8174 (pm20) cc_final: 0.7854 (pm20) REVERT: H 95 LYS cc_start: 0.8523 (pttm) cc_final: 0.8268 (pttp) REVERT: H 137 ASN cc_start: 0.9170 (OUTLIER) cc_final: 0.8800 (p0) outliers start: 69 outliers final: 54 residues processed: 268 average time/residue: 0.2018 time to fit residues: 86.2519 Evaluate side-chains 259 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 202 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 42 LYS Chi-restraints excluded: chain P residue 76 SER Chi-restraints excluded: chain P residue 78 PHE Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 342 ASP Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 465 ARG Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 503 LYS Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1134 GLN Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 432 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 932 MET Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1144 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 159 ILE Chi-restraints excluded: chain H residue 166 ARG Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 192 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 167 optimal weight: 10.0000 chunk 127 optimal weight: 0.7980 chunk 3 optimal weight: 7.9990 chunk 242 optimal weight: 9.9990 chunk 187 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 240 optimal weight: 5.9990 chunk 65 optimal weight: 0.0010 chunk 147 optimal weight: 0.0980 chunk 279 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 overall best weight: 1.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 41 ASN ** 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 = 0.3434 r_free = 0.3434 target = 0.071887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.049873 restraints weight = 110081.989| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 3.36 r_work: 0.2717 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2716 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2716 r_free = 0.2716 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2716 r_free = 0.2716 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2716 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9003 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28851 Z= 0.140 Angle : 0.538 11.875 39367 Z= 0.281 Chirality : 0.041 0.170 4495 Planarity : 0.004 0.040 4843 Dihedral : 15.797 148.731 4706 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.66 % Favored : 97.32 % Rotamer: Outliers : 2.40 % Allowed : 22.73 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 0.84 (0.15), residues: 3354 helix: 2.11 (0.15), residues: 1161 sheet: 0.27 (0.23), residues: 487 loop : -0.42 (0.15), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG P 160 TYR 0.013 0.001 TYR J1186 PHE 0.013 0.001 PHE I 385 TRP 0.027 0.001 TRP I 183 HIS 0.003 0.001 HIS P 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (28843) covalent geometry : angle 0.52913 / 0.28 (39355) hydrogen bonds : bond 0.03517 / 2.34 ( 1235) hydrogen bonds : angle 4.03421 / 2.76 ( 3404) metal coordination : bond 0.00847 / 0.43 ( 8) metal coordination : angle 5.75110 / 2.94 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 206 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 15 GLN cc_start: 0.9165 (tp40) cc_final: 0.8846 (tm-30) REVERT: P 127 GLN cc_start: 0.7876 (pm20) cc_final: 0.7219 (pp30) REVERT: I 465 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7774 (tpt170) REVERT: I 1188 ASP cc_start: 0.8851 (t0) cc_final: 0.8192 (t0) REVERT: J 443 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8283 (mm-30) REVERT: J 811 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8641 (mt-10) REVERT: J 1189 MET cc_start: 0.8704 (mmp) cc_final: 0.8234 (tpp) REVERT: K 43 ASN cc_start: 0.8880 (t0) cc_final: 0.8210 (t0) REVERT: K 73 GLN cc_start: 0.8697 (mm-40) cc_final: 0.8213 (mt0) REVERT: H 10 LYS cc_start: 0.8709 (mmmm) cc_final: 0.8424 (mmtm) REVERT: H 65 LEU cc_start: 0.9431 (tp) cc_final: 0.9203 (tp) REVERT: H 76 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7879 (mp0) REVERT: H 93 GLN cc_start: 0.8186 (pm20) cc_final: 0.7875 (pm20) REVERT: H 95 LYS cc_start: 0.8513 (pttm) cc_final: 0.8268 (pttp) REVERT: H 137 ASN cc_start: 0.9142 (m-40) cc_final: 0.8775 (p0) outliers start: 67 outliers final: 56 residues processed: 265 average time/residue: 0.1801 time to fit residues: 76.7360 Evaluate side-chains 256 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 198 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 76 SER Chi-restraints excluded: chain P residue 78 PHE Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 183 TRP Chi-restraints excluded: chain I residue 342 ASP Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 465 ARG Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 503 LYS Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 432 LEU 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 553 THR Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 932 MET Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1144 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1321 SER Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 159 ILE Chi-restraints excluded: chain H residue 166 ARG Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 192 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 71 optimal weight: 1.9990 chunk 302 optimal weight: 5.9990 chunk 339 optimal weight: 50.0000 chunk 279 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 242 optimal weight: 10.0000 chunk 320 optimal weight: 0.6980 chunk 186 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 chunk 315 optimal weight: 3.9990 chunk 321 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 95 GLN ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.071586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.049722 restraints weight = 112921.040| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 3.40 r_work: 0.2696 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 28851 Z= 0.157 Angle : 0.548 12.922 39367 Z= 0.286 Chirality : 0.041 0.163 4495 Planarity : 0.004 0.041 4843 Dihedral : 15.812 148.582 4706 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.74 % Favored : 97.23 % Rotamer: Outliers : 2.36 % Allowed : 22.52 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.15), residues: 3354 helix: 2.14 (0.15), residues: 1155 sheet: 0.24 (0.23), residues: 487 loop : -0.42 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 69 TYR 0.018 0.001 TYR J 631 PHE 0.015 0.001 PHE I 385 TRP 0.028 0.001 TRP I 183 HIS 0.004 0.001 HIS P 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (28843) covalent geometry : angle 0.53846 / 0.29 (39355) hydrogen bonds : bond 0.03598 / 2.40 ( 1235) hydrogen bonds : angle 4.03802 / 2.76 ( 3404) metal coordination : bond 0.00969 / 0.50 ( 8) metal coordination : angle 5.81985 / 2.98 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 202 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 15 GLN cc_start: 0.9189 (tp40) cc_final: 0.8847 (tm-30) REVERT: P 95 GLN cc_start: 0.8894 (mp-120) cc_final: 0.8618 (mm-40) REVERT: P 127 GLN cc_start: 0.7916 (pm20) cc_final: 0.7250 (pp30) REVERT: I 142 GLU cc_start: 0.8841 (tt0) cc_final: 0.8540 (mt-10) REVERT: I 465 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7763 (tpt170) REVERT: I 1188 ASP cc_start: 0.8863 (t0) cc_final: 0.8198 (t0) REVERT: J 443 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8069 (mm-30) REVERT: J 811 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8647 (mt-10) REVERT: J 1189 MET cc_start: 0.8682 (mmp) cc_final: 0.8215 (tpp) REVERT: J 1193 TRP cc_start: 0.8978 (p90) cc_final: 0.8689 (p90) REVERT: K 43 ASN cc_start: 0.8902 (t0) cc_final: 0.8249 (t0) REVERT: K 73 GLN cc_start: 0.8687 (mm-40) cc_final: 0.8194 (mt0) REVERT: H 65 LEU cc_start: 0.9445 (tp) cc_final: 0.9174 (tp) REVERT: H 76 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7919 (mp0) REVERT: H 93 GLN cc_start: 0.8125 (pm20) cc_final: 0.7827 (pm20) REVERT: H 95 LYS cc_start: 0.8521 (pttm) cc_final: 0.8286 (pttp) outliers start: 66 outliers final: 58 residues processed: 261 average time/residue: 0.1789 time to fit residues: 75.4508 Evaluate side-chains 257 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 197 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 76 SER Chi-restraints excluded: chain P residue 78 PHE Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 183 TRP Chi-restraints excluded: chain I residue 342 ASP Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 465 ARG Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 503 LYS Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1134 GLN Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 432 LEU 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 553 THR Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 932 MET Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1144 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1321 SER Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 159 ILE Chi-restraints excluded: chain H residue 166 ARG Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 192 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 235 optimal weight: 4.9990 chunk 113 optimal weight: 0.0970 chunk 143 optimal weight: 1.9990 chunk 315 optimal weight: 2.9990 chunk 246 optimal weight: 0.4980 chunk 58 optimal weight: 0.0980 chunk 112 optimal weight: 0.0770 chunk 14 optimal weight: 20.0000 chunk 29 optimal weight: 0.4980 chunk 60 optimal weight: 4.9990 chunk 269 optimal weight: 0.0010 overall best weight: 0.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 673 HIS J 921 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.073567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.051770 restraints weight = 121582.018| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 3.58 r_work: 0.2746 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 28851 Z= 0.103 Angle : 0.539 13.287 39367 Z= 0.280 Chirality : 0.041 0.169 4495 Planarity : 0.004 0.047 4843 Dihedral : 15.748 148.652 4706 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.36 % Favored : 97.61 % Rotamer: Outliers : 1.63 % Allowed : 23.36 % Favored : 75.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.15), residues: 3354 helix: 2.10 (0.15), residues: 1163 sheet: 0.40 (0.24), residues: 481 loop : -0.41 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 69 TYR 0.010 0.001 TYR J 631 PHE 0.012 0.001 PHE P 130 TRP 0.026 0.001 TRP I 183 HIS 0.002 0.000 HIS P 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (28843) covalent geometry : angle 0.53048 / 0.28 (39355) hydrogen bonds : bond 0.03196 / 2.13 ( 1235) hydrogen bonds : angle 3.93809 / 2.69 ( 3404) metal coordination : bond 0.00255 / 0.14 ( 8) metal coordination : angle 5.34243 / 2.64 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 214 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1 MET cc_start: 0.8300 (tpp) cc_final: 0.8068 (tpp) REVERT: P 15 GLN cc_start: 0.9154 (tp40) cc_final: 0.8837 (tm-30) REVERT: P 127 GLN cc_start: 0.7936 (pm20) cc_final: 0.7318 (pp30) REVERT: P 138 ARG cc_start: 0.9374 (mtp-110) cc_final: 0.8772 (ttp-110) REVERT: I 1188 ASP cc_start: 0.8781 (t0) cc_final: 0.8060 (t0) REVERT: J 443 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8289 (mm-30) REVERT: J 811 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8616 (mt-10) REVERT: J 1189 MET cc_start: 0.8705 (mmp) cc_final: 0.8228 (tpp) REVERT: J 1193 TRP cc_start: 0.8940 (p90) cc_final: 0.8645 (p90) REVERT: J 1370 MET cc_start: 0.8990 (tpp) cc_final: 0.8663 (ttm) REVERT: K 43 ASN cc_start: 0.8845 (t0) cc_final: 0.8090 (t0) REVERT: K 73 GLN cc_start: 0.8694 (mm-40) cc_final: 0.8206 (mt0) REVERT: H 65 LEU cc_start: 0.9431 (tp) cc_final: 0.9211 (tp) REVERT: H 76 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7943 (mp0) REVERT: H 93 GLN cc_start: 0.8131 (pm20) cc_final: 0.7835 (pm20) REVERT: H 95 LYS cc_start: 0.8450 (pttm) cc_final: 0.8229 (pttp) REVERT: H 137 ASN cc_start: 0.9157 (m-40) cc_final: 0.8782 (p0) outliers start: 45 outliers final: 36 residues processed: 253 average time/residue: 0.1779 time to fit residues: 72.2215 Evaluate side-chains 240 residues out of total 2873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 203 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 78 PHE Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 183 TRP Chi-restraints excluded: chain I residue 255 ILE Chi-restraints excluded: chain I residue 342 ASP Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1023 HIS Chi-restraints excluded: chain I residue 1134 GLN Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 432 LEU Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 932 MET Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 166 ARG Chi-restraints excluded: chain H residue 183 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 201 optimal weight: 0.0980 chunk 256 optimal weight: 8.9990 chunk 236 optimal weight: 4.9990 chunk 29 optimal weight: 0.0770 chunk 151 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 chunk 163 optimal weight: 10.0000 chunk 11 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 overall best weight: 1.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 921 GLN G 194 GLN ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.071590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.049909 restraints weight = 108914.627| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 3.33 r_work: 0.2706 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2700 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 28851 Z= 0.181 Angle : 0.560 12.695 39367 Z= 0.292 Chirality : 0.042 0.192 4495 Planarity : 0.004 0.053 4843 Dihedral : 15.784 148.645 4706 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.86 % Favored : 97.11 % Rotamer: Outliers : 1.56 % Allowed : 23.57 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 0.91 (0.15), residues: 3354 helix: 2.21 (0.15), residues: 1157 sheet: 0.30 (0.23), residues: 493 loop : -0.41 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 182 TYR 0.013 0.001 TYR I 172 PHE 0.014 0.001 PHE I 385 TRP 0.024 0.001 TRP I 183 HIS 0.004 0.001 HIS P 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (28843) covalent geometry : angle 0.55196 / 0.29 (39355) hydrogen bonds : bond 0.03606 / 2.40 ( 1235) hydrogen bonds : angle 3.97994 / 2.72 ( 3404) metal coordination : bond 0.01122 / 0.58 ( 8) metal coordination : angle 5.60751 / 2.86 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7699.87 seconds wall clock time: 132 minutes 21.23 seconds (7941.23 seconds total)