Starting phenix.real_space_refine on Fri Mar 6 12:00:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mke_23893/03_2026/7mke_23893.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mke_23893/03_2026/7mke_23893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mke_23893/03_2026/7mke_23893.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mke_23893/03_2026/7mke_23893.map" model { file = "/net/cci-nas-00/data/ceres_data/7mke_23893/03_2026/7mke_23893.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mke_23893/03_2026/7mke_23893.cif" } resolution = 3.7 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= 0.014 sd= 0.070 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 79 5.49 5 Mg 1 5.21 5 S 128 5.16 5 C 18989 2.51 5 N 5413 2.21 5 O 6029 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30641 Number of models: 1 Model: "" Number of chains: 11 Chain: "G" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1808 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 9, 'TRANS': 223} Chain: "H" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1714 Classifications: {'peptide': 223} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 212} Chain breaks: 1 Chain: "I" Number of atoms: 10567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10567 Classifications: {'peptide': 1340} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1281} Chain: "J" Number of atoms: 10377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10377 Classifications: {'peptide': 1335} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1278} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "L" Number of atoms: 3781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3781 Classifications: {'peptide': 465} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 451} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "P" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 907 Classifications: {'DNA': 44} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 43} Chain breaks: 1 Chain: "Q" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 749 Classifications: {'DNA': 37} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 36} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'1N7': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'1N7:plan-1': 2} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'1N7': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'1N7:plan-1': 2} Unresolved non-hydrogen planarities: 6 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14538 SG CYS J 70 100.691 52.642 74.134 1.00 96.23 S ATOM 14552 SG CYS J 72 99.702 50.812 72.593 1.00 96.96 S ATOM 14660 SG CYS J 85 102.572 51.997 70.782 1.00103.27 S ATOM 14684 SG CYS J 88 101.419 54.865 72.505 1.00104.22 S ATOM 20367 SG CYS J 814 124.499 107.404 109.180 1.00 80.68 S ATOM 20932 SG CYS J 888 121.489 105.813 107.397 1.00 74.16 S ATOM 20983 SG CYS J 895 122.663 104.491 110.686 1.00 68.11 S ATOM 21004 SG CYS J 898 121.210 107.972 110.653 1.00 69.90 S Time building chain proxies: 6.36, per 1000 atoms: 0.21 Number of scatterers: 30641 At special positions: 0 Unit cell: (152.64, 182.32, 193.98, 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 128 16.00 P 79 15.00 Mg 1 11.99 O 6029 8.00 N 5413 7.00 C 18989 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: 2.41 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " Number of angles added : 12 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6818 Finding SS restraints... Secondary structure from input PDB file: 133 helices and 51 sheets defined 42.6% alpha, 14.1% beta 37 base pairs and 60 stacking pairs defined. Time for finding SS restraints: 3.65 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 removed outlier: 4.094A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.941A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 154 through 159 removed outlier: 3.871A pdb=" N ILE G 159 " --> pdb=" O ALA G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 228 Processing helix chain 'G' and resid 228 through 233 removed outlier: 3.849A pdb=" N ASP G 233 " --> pdb=" O GLU G 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 49 Processing helix chain 'H' and resid 77 through 87 removed outlier: 3.729A pdb=" N GLY H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 154 through 158 Processing helix chain 'H' and resid 212 through 227 Processing helix chain 'I' and resid 28 through 39 Processing helix chain 'I' and resid 48 through 57 removed outlier: 3.513A pdb=" N ALA I 52 " --> pdb=" O GLY I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.888A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 removed outlier: 3.558A pdb=" N LEU I 246 " --> pdb=" O PRO I 243 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 280 Processing helix chain 'I' and resid 288 through 293 removed outlier: 4.342A pdb=" N ILE I 292 " --> pdb=" O PRO I 288 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA I 293 " --> pdb=" O VAL I 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 288 through 293' Processing helix chain 'I' and resid 318 through 328 Processing helix chain 'I' and resid 345 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 389 removed outlier: 3.880A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 removed outlier: 3.837A pdb=" N ILE I 425 " --> pdb=" O SER I 421 " (cutoff:3.500A) Processing helix chain 'I' and resid 455 through 481 removed outlier: 3.690A pdb=" N ARG I 470 " --> pdb=" O VAL I 466 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 508 removed outlier: 4.878A pdb=" N ALA I 501 " --> pdb=" O PRO I 497 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER I 508 " --> pdb=" O GLU I 504 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 539 through 543 removed outlier: 4.045A pdb=" N ALA I 543 " --> pdb=" O ARG I 540 " (cutoff:3.500A) Processing helix chain 'I' and resid 544 through 549 removed outlier: 3.811A pdb=" N ARG I 548 " --> pdb=" O GLY I 544 " (cutoff:3.500A) Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.823A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 609 through 614 removed outlier: 4.362A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR I 614 " --> pdb=" O GLU I 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 609 through 614' Processing helix chain 'I' and resid 663 through 668 removed outlier: 3.802A pdb=" N LEU I 667 " --> pdb=" O GLY I 664 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE I 668 " --> pdb=" O ALA I 665 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 removed outlier: 3.645A pdb=" N HIS I 673 " --> pdb=" O PHE I 670 " (cutoff:3.500A) Processing helix chain 'I' and resid 675 through 686 Processing helix chain 'I' and resid 687 through 689 No H-bonds generated for 'chain 'I' and resid 687 through 689' Processing helix chain 'I' and resid 704 through 712 removed outlier: 4.028A pdb=" N VAL I 708 " --> pdb=" O MET I 704 " (cutoff:3.500A) Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 860 through 865 removed outlier: 3.744A pdb=" N SER I 863 " --> pdb=" O ALA I 860 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS I 864 " --> pdb=" O ALA I 861 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU I 865 " --> pdb=" O LEU I 862 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 860 through 865' Processing helix chain 'I' and resid 898 through 907 Processing helix chain 'I' and resid 942 through 981 removed outlier: 3.650A pdb=" N VAL I 980 " --> pdb=" O ARG I 976 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA I 981 " --> pdb=" O ALA I 977 " (cutoff:3.500A) Processing helix chain 'I' and resid 996 through 1000 removed outlier: 3.672A pdb=" N LEU I1000 " --> pdb=" O TRP I 997 " (cutoff:3.500A) Processing helix chain 'I' and resid 1007 through 1038 removed outlier: 3.927A pdb=" N GLU I1012 " --> pdb=" O GLN I1008 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N GLN I1013 " --> pdb=" O ASN I1009 " (cutoff:3.500A) Processing helix chain 'I' and resid 1099 through 1101 No H-bonds generated for 'chain 'I' and resid 1099 through 1101' Processing helix chain 'I' and resid 1102 through 1107 removed outlier: 3.593A pdb=" N ARG I1106 " --> pdb=" O GLY I1102 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.622A pdb=" N LEU I1113 " --> pdb=" O ILE I1109 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN I1134 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1149 removed outlier: 3.671A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1177 Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1284 through 1292 Processing helix chain 'I' and resid 1299 through 1310 Processing helix chain 'I' and resid 1320 through 1333 removed outlier: 3.939A pdb=" N LEU I1333 " --> pdb=" O GLU I1329 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 95 through 100 removed outlier: 3.652A pdb=" N ARG J 98 " --> pdb=" O THR J 95 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG J 99 " --> pdb=" O LYS J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 118 Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 181 through 192 Processing helix chain 'J' and resid 193 through 208 removed outlier: 4.125A pdb=" N GLU J 197 " --> pdb=" O ASP J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 230 Processing helix chain 'J' and resid 234 through 236 No H-bonds generated for 'chain 'J' and resid 234 through 236' Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 286 removed outlier: 4.355A pdb=" N ASP J 267 " --> pdb=" O SER J 263 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 301 Processing helix chain 'J' and resid 304 through 309 Processing helix chain 'J' and resid 326 through 332 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 removed outlier: 3.785A pdb=" N ALA J 397 " --> pdb=" O THR J 393 " (cutoff:3.500A) Processing helix chain 'J' and resid 407 through 416 removed outlier: 3.651A pdb=" N ILE J 411 " --> pdb=" O VAL J 407 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 450 through 452 No H-bonds generated for 'chain 'J' and resid 450 through 452' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 485 through 489 Processing helix chain 'J' and resid 504 through 514 removed outlier: 3.586A 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 593 removed outlier: 3.714A pdb=" N ASN J 593 " --> pdb=" O SER J 590 " (cutoff:3.500A) Processing helix chain 'J' and resid 598 through 613 Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.718A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 644 removed outlier: 3.981A pdb=" N MET J 644 " --> pdb=" O ILE J 641 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 702 Processing helix chain 'J' and resid 720 through 728 removed outlier: 3.578A pdb=" N MET J 724 " --> pdb=" O ASN J 720 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 804 removed outlier: 4.313A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA J 779 " --> pdb=" O SER J 775 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N THR J 790 " --> pdb=" O THR J 786 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 838 Processing helix chain 'J' and resid 865 through 874 Processing helix chain 'J' and resid 884 through 888 removed outlier: 3.831A pdb=" N CYS J 888 " --> pdb=" O VAL J 885 " (cutoff:3.500A) Processing helix chain 'J' and resid 914 through 925 removed outlier: 3.558A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 930 Processing helix chain 'J' and resid 1137 through 1147 Processing helix chain 'J' and resid 1216 through 1225 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 4.251A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.290A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 Processing helix chain 'J' and resid 1308 through 1313 Processing helix chain 'J' and resid 1319 through 1324 Processing helix chain 'J' and resid 1327 through 1339 removed outlier: 3.928A pdb=" N VAL J1331 " --> pdb=" O GLU J1327 " (cutoff:3.500A) Processing helix chain 'J' and resid 1347 through 1353 Processing helix chain 'J' and resid 1362 through 1373 Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 17 through 32 removed outlier: 3.572A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 Processing helix chain 'K' and resid 60 through 78 Processing helix chain 'L' and resid 96 through 106 Processing helix chain 'L' and resid 112 through 135 Processing helix chain 'L' and resid 137 through 153 removed outlier: 3.564A pdb=" N ILE L 141 " --> pdb=" O TYR L 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 157 through 162 removed outlier: 3.826A pdb=" N LEU L 161 " --> pdb=" O ARG L 157 " (cutoff:3.500A) Processing helix chain 'L' and resid 216 through 234 Processing helix chain 'L' and resid 245 through 258 removed outlier: 3.600A pdb=" N GLN L 258 " --> pdb=" O GLU L 254 " (cutoff:3.500A) Processing helix chain 'L' and resid 262 through 292 removed outlier: 4.138A pdb=" N LEU L 290 " --> pdb=" O LEU L 286 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS L 291 " --> pdb=" O ILE L 287 " (cutoff:3.500A) Processing helix chain 'L' and resid 299 through 307 removed outlier: 3.783A pdb=" N THR L 304 " --> pdb=" O LYS L 300 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU L 305 " --> pdb=" O ASN L 301 " (cutoff:3.500A) Processing helix chain 'L' and resid 319 through 323 Processing helix chain 'L' and resid 324 through 330 removed outlier: 3.671A pdb=" N GLU L 328 " --> pdb=" O LYS L 324 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS L 329 " --> pdb=" O PRO L 325 " (cutoff:3.500A) Processing helix chain 'L' and resid 333 through 352 removed outlier: 3.535A pdb=" N THR L 351 " --> pdb=" O ILE L 347 " (cutoff:3.500A) Processing helix chain 'L' and resid 354 through 394 removed outlier: 5.729A pdb=" N ARG L 385 " --> pdb=" O GLU L 381 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N LEU L 386 " --> pdb=" O ALA L 382 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL L 387 " --> pdb=" O ASN L 383 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR L 394 " --> pdb=" O ILE L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 418 Processing helix chain 'L' and resid 420 through 424 removed outlier: 4.369A pdb=" N ARG L 423 " --> pdb=" O GLU L 420 " (cutoff:3.500A) Processing helix chain 'L' and resid 426 through 446 removed outlier: 4.118A pdb=" N TYR L 430 " --> pdb=" O LYS L 426 " (cutoff:3.500A) Processing helix chain 'L' and resid 453 through 475 removed outlier: 3.806A pdb=" N GLN L 472 " --> pdb=" O ARG L 468 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU L 473 " --> pdb=" O GLN L 469 " (cutoff:3.500A) Processing helix chain 'L' and resid 479 through 487 Processing helix chain 'L' and resid 492 through 501 Processing helix chain 'L' and resid 518 through 523 removed outlier: 3.923A pdb=" N PHE L 522 " --> pdb=" O HIS L 518 " (cutoff:3.500A) Processing helix chain 'L' and resid 530 through 550 Processing helix chain 'L' and resid 552 through 563 Processing helix chain 'L' and resid 572 through 581 Processing helix chain 'L' and resid 583 through 599 Processing helix chain 'L' and resid 603 through 609 removed outlier: 4.279A pdb=" N LEU L 607 " --> pdb=" O ARG L 603 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 13 through 17 removed outlier: 8.683A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR G 27 " --> pdb=" O ASP G 15 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG G 182 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 13 through 17 removed outlier: 8.683A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR G 27 " --> pdb=" O ASP G 15 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU G 198 " --> pdb=" O ALA G 190 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 98 through 105 Processing sheet with id=AA4, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AA5, first strand: chain 'G' and resid 108 through 111 removed outlier: 6.486A pdb=" N GLY G 108 " --> pdb=" O HIS G 132 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N HIS G 132 " --> pdb=" O GLY G 108 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL G 110 " --> pdb=" O ILE G 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 24 through 31 removed outlier: 6.395A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLU H 204 " --> pdb=" O ILE H 183 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE H 183 " --> pdb=" O GLU H 204 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLU H 206 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 24 through 31 removed outlier: 6.395A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 97 through 101 removed outlier: 3.789A pdb=" N VAL H 98 " --> pdb=" O VAL H 146 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU H 58 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 90 through 91 removed outlier: 3.714A pdb=" N ARG H 91 " --> pdb=" O GLU H 122 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 109 through 111 Processing sheet with id=AB2, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB3, first strand: chain 'I' and resid 59 through 60 removed outlier: 7.043A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ILE I 104 " --> pdb=" O LYS I 115 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 59 through 60 removed outlier: 7.043A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB6, first strand: chain 'I' and resid 451 through 454 removed outlier: 3.593A pdb=" N HIS I 150 " --> pdb=" O ARG I 452 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 154 through 156 removed outlier: 3.533A pdb=" N ILE I 176 " --> pdb=" O LEU I 184 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU I 187 " --> pdb=" O PHE I 195 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 284 through 285 removed outlier: 3.755A pdb=" N GLU I 240 " --> pdb=" O ILE I 229 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE I 229 " --> pdb=" O GLU I 240 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.607A pdb=" N ILE I 255 " --> pdb=" O TYR I 262 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 296 through 297 removed outlier: 3.594A pdb=" N MET I 315 " --> pdb=" O VAL I 297 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 301 through 303 removed outlier: 6.954A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.637A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC5, first strand: chain 'I' and resid 633 through 635 Processing sheet with id=AC6, first strand: chain 'I' and resid 700 through 701 Processing sheet with id=AC7, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.611A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 722 through 727 removed outlier: 6.854A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AD1, first strand: chain 'I' and resid 1079 through 1080 removed outlier: 6.864A pdb=" N VAL I 818 " --> pdb=" O ASN I1080 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL I1225 " --> pdb=" O ILE I1210 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 830 through 838 removed outlier: 3.946A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 842 through 843 Processing sheet with id=AD4, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.998A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 887 through 889 Processing sheet with id=AD6, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AD7, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AD8, first strand: chain 'I' and resid 1268 through 1269 removed outlier: 3.758A pdb=" N GLN I1268 " --> pdb=" O VAL J 347 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 1335 through 1340 Processing sheet with id=AE1, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.110A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY J 103 " --> pdb=" O VAL J 244 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU J 107 " --> pdb=" O THR J 240 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 10.435A pdb=" N SER J 109 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 10.124A pdb=" N ILE J 238 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 252 through 255 removed outlier: 3.642A pdb=" N ARG J 259 " --> pdb=" O LEU J 255 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N PHE J 260 " --> pdb=" O ILE L 505 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AE4, first strand: chain 'J' and resid 552 through 556 Processing sheet with id=AE5, first strand: chain 'J' and resid 706 through 707 Processing sheet with id=AE6, first strand: chain 'J' and resid 820 through 822 removed outlier: 3.630A pdb=" N VAL J 880 " --> pdb=" O MET J 822 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 848 through 849 removed outlier: 6.498A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 949 through 951 removed outlier: 3.735A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 991 through 997 removed outlier: 4.185A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU J1009 " --> pdb=" O ILE J 958 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 965 through 967 Processing sheet with id=AF2, first strand: chain 'J' and resid 1025 through 1028 removed outlier: 4.711A pdb=" N ALA J1122 " --> pdb=" O VAL J1027 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 1080 through 1081 Processing sheet with id=AF4, first strand: chain 'J' and resid 1049 through 1050 removed outlier: 3.666A pdb=" N VAL J1107 " --> pdb=" O LEU J1059 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 1162 through 1165 Processing sheet with id=AF6, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 6.512A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1257 hydrogen bonds defined for protein. 3555 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 91 hydrogen bonds 182 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 60 stacking parallelities Total time for adding SS restraints: 7.72 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9847 1.34 - 1.46: 5954 1.46 - 1.58: 15063 1.58 - 1.70: 171 1.70 - 1.82: 234 Bond restraints: 31269 Sorted by residual: bond pdb=" C19 1N7 L 701 " pdb=" C3 1N7 L 701 " ideal model delta sigma weight residual 1.532 1.824 -0.292 2.00e-02 2.50e+03 2.13e+02 bond pdb=" C19 1N7 I1402 " pdb=" C3 1N7 I1402 " ideal model delta sigma weight residual 1.532 1.821 -0.289 2.00e-02 2.50e+03 2.08e+02 bond pdb=" C19 1N7 L 702 " pdb=" C3 1N7 L 702 " ideal model delta sigma weight residual 1.532 1.820 -0.288 2.00e-02 2.50e+03 2.08e+02 bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.818 -0.286 2.00e-02 2.50e+03 2.05e+02 bond pdb=" C3 1N7 L 701 " pdb=" C4 1N7 L 701 " ideal model delta sigma weight residual 1.532 1.729 -0.197 2.00e-02 2.50e+03 9.68e+01 ... (remaining 31264 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.66: 42296 3.66 - 7.32: 261 7.32 - 10.98: 25 10.98 - 14.64: 0 14.64 - 18.31: 1 Bond angle restraints: 42583 Sorted by residual: angle pdb=" C LEU I 487 " pdb=" N MET I 488 " pdb=" CA MET I 488 " ideal model delta sigma weight residual 120.67 138.98 -18.31 1.34e+00 5.57e-01 1.87e+02 angle pdb=" C ILE H 168 " pdb=" N GLY H 169 " pdb=" CA GLY H 169 " ideal model delta sigma weight residual 121.70 132.49 -10.79 1.80e+00 3.09e-01 3.59e+01 angle pdb=" C LEU I 484 " pdb=" N ASP I 485 " pdb=" CA ASP I 485 " ideal model delta sigma weight residual 121.70 131.01 -9.31 1.80e+00 3.09e-01 2.68e+01 angle pdb=" N ASP I 516 " pdb=" CA ASP I 516 " pdb=" C ASP I 516 " ideal model delta sigma weight residual 109.96 102.78 7.18 1.49e+00 4.50e-01 2.32e+01 angle pdb=" C LEU I 397 " pdb=" N SER I 398 " pdb=" CA SER I 398 " ideal model delta sigma weight residual 121.54 130.25 -8.71 1.91e+00 2.74e-01 2.08e+01 ... (remaining 42578 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.44: 18412 34.44 - 68.88: 830 68.88 - 103.31: 37 103.31 - 137.75: 1 137.75 - 172.19: 3 Dihedral angle restraints: 19283 sinusoidal: 8706 harmonic: 10577 Sorted by residual: dihedral pdb=" CA PRO I 897 " pdb=" C PRO I 897 " pdb=" N GLU I 898 " pdb=" CA GLU I 898 " ideal model delta harmonic sigma weight residual -180.00 -138.69 -41.31 0 5.00e+00 4.00e-02 6.83e+01 dihedral pdb=" CA ASP J1184 " pdb=" C ASP J1184 " pdb=" N PRO J1185 " pdb=" CA PRO J1185 " ideal model delta harmonic sigma weight residual -180.00 -140.53 -39.47 0 5.00e+00 4.00e-02 6.23e+01 dihedral pdb=" CA ARG G 235 " pdb=" C ARG G 235 " pdb=" N ASP G 236 " pdb=" CA ASP G 236 " ideal model delta harmonic sigma weight residual 180.00 -143.98 -36.02 0 5.00e+00 4.00e-02 5.19e+01 ... (remaining 19280 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 4507 0.094 - 0.188: 354 0.188 - 0.282: 13 0.282 - 0.376: 1 0.376 - 0.469: 4 Chirality restraints: 4879 Sorted by residual: chirality pdb=" C19 1N7 L 701 " pdb=" C18 1N7 L 701 " pdb=" C2 1N7 L 701 " pdb=" C3 1N7 L 701 " both_signs ideal model delta sigma weight residual False -2.53 -3.00 0.47 2.00e-01 2.50e+01 5.51e+00 chirality pdb=" C19 1N7 I1402 " pdb=" C18 1N7 I1402 " pdb=" C2 1N7 I1402 " pdb=" C3 1N7 I1402 " both_signs ideal model delta sigma weight residual False -2.53 -2.99 0.46 2.00e-01 2.50e+01 5.20e+00 chirality pdb=" C19 1N7 I1401 " pdb=" C18 1N7 I1401 " pdb=" C2 1N7 I1401 " pdb=" C3 1N7 I1401 " both_signs ideal model delta sigma weight residual False -2.53 -2.98 0.45 2.00e-01 2.50e+01 5.08e+00 ... (remaining 4876 not shown) Planarity restraints: 5259 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP I 485 " 0.015 2.00e-02 2.50e+03 3.05e-02 9.32e+00 pdb=" C ASP I 485 " -0.053 2.00e-02 2.50e+03 pdb=" O ASP I 485 " 0.020 2.00e-02 2.50e+03 pdb=" N THR I 486 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR I 896 " -0.050 5.00e-02 4.00e+02 7.56e-02 9.15e+00 pdb=" N PRO I 897 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO I 897 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO I 897 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE J1325 " 0.015 2.00e-02 2.50e+03 2.98e-02 8.87e+00 pdb=" C PHE J1325 " -0.051 2.00e-02 2.50e+03 pdb=" O PHE J1325 " 0.020 2.00e-02 2.50e+03 pdb=" N GLN J1326 " 0.017 2.00e-02 2.50e+03 ... (remaining 5256 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 618 2.64 - 3.21: 27434 3.21 - 3.77: 49210 3.77 - 4.34: 62382 4.34 - 4.90: 101290 Nonbonded interactions: 240934 Sorted by model distance: nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1501 " model vdw 2.077 2.170 nonbonded pdb=" OE1 GLU J 811 " pdb=" OG1 THR J 890 " model vdw 2.229 3.040 nonbonded pdb=" O THR J 528 " pdb=" OG1 THR J 528 " model vdw 2.247 3.040 nonbonded pdb=" O ASP L 514 " pdb=" OG SER L 517 " model vdw 2.251 3.040 nonbonded pdb=" N ASP H 15 " pdb=" OD1 ASP H 15 " model vdw 2.258 3.120 ... (remaining 240929 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 5 through 158 or resid 167 through 233)) selection = (chain 'H' and resid 5 through 233) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 33.580 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 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 : 0.009 0.292 31277 Z= 0.439 Angle : 0.920 41.773 42595 Z= 0.488 Chirality : 0.052 0.469 4879 Planarity : 0.006 0.076 5259 Dihedral : 17.406 172.190 12465 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.85 % Favored : 91.10 % Rotamer: Outliers : 7.42 % Allowed : 13.21 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.11 % Twisted Proline : 0.70 % Twisted General : 0.17 % 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: -2.11 (0.13), residues: 3651 helix: -0.21 (0.13), residues: 1377 sheet: -1.69 (0.24), residues: 435 loop : -2.30 (0.13), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 974 TYR 0.022 0.002 TYR G 177 PHE 0.016 0.002 PHE J 620 TRP 0.007 0.001 TRP I1276 HIS 0.007 0.001 HIS J 777 Details of bonding type rmsd covalent geometry : bond 0.00939 (31269) covalent geometry : angle 0.86368 (42583) hydrogen bonds : bond 0.17181 ( 1321) hydrogen bonds : angle 6.91948 ( 3737) metal coordination : bond 0.01314 ( 8) metal coordination : angle 18.81852 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 233 poor density : 148 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 194 GLN cc_start: 0.8190 (tp40) cc_final: 0.7984 (tp40) REVERT: I 213 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8791 (tt) REVERT: I 240 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7887 (pm20) REVERT: I 315 MET cc_start: 0.8341 (mmm) cc_final: 0.8127 (mmm) REVERT: I 369 MET cc_start: 0.8467 (tmm) cc_final: 0.8051 (tmm) REVERT: I 492 MET cc_start: 0.8533 (pmm) cc_final: 0.7918 (pmm) REVERT: I 515 MET cc_start: 0.8572 (ttp) cc_final: 0.8354 (ttp) REVERT: I 658 GLN cc_start: 0.9265 (OUTLIER) cc_final: 0.7965 (pp30) REVERT: I 697 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8211 (mtmm) REVERT: I 1287 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8836 (tp) REVERT: J 56 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.9176 (tt) REVERT: J 126 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.8981 (pp) REVERT: J 255 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8563 (mm) REVERT: J 596 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9186 (mm) REVERT: J 697 MET cc_start: 0.8806 (ttp) cc_final: 0.8590 (ttp) REVERT: J 706 VAL cc_start: 0.8739 (OUTLIER) cc_final: 0.8392 (m) REVERT: J 746 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8807 (mt) REVERT: J 1034 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.7941 (m-80) REVERT: L 365 MET cc_start: 0.9155 (mmt) cc_final: 0.8869 (mmt) REVERT: L 379 MET cc_start: 0.8757 (ppp) cc_final: 0.8517 (ppp) REVERT: L 487 MET cc_start: 0.8510 (mmt) cc_final: 0.8232 (mmt) outliers start: 233 outliers final: 110 residues processed: 370 average time/residue: 0.1654 time to fit residues: 105.1969 Evaluate side-chains 253 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 131 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 32 GLU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 240 GLU Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 572 ILE Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 643 SER Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 658 GLN Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 819 SER Chi-restraints excluded: chain I residue 830 THR Chi-restraints excluded: chain I residue 851 THR Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 990 ASP Chi-restraints excluded: chain I residue 1038 GLN Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1287 LEU Chi-restraints excluded: chain I residue 1337 ILE Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 115 TRP Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 353 SER Chi-restraints excluded: chain J residue 394 ILE Chi-restraints excluded: chain J residue 410 ASP Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 536 LEU Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 654 ILE Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 684 ASP Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 806 ASP Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 890 THR Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 962 ASN Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1034 PHE Chi-restraints excluded: chain J residue 1058 SER Chi-restraints excluded: chain J residue 1176 VAL Chi-restraints excluded: chain J residue 1229 VAL Chi-restraints excluded: chain J residue 1250 ASP Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 331 HIS Chi-restraints excluded: chain L residue 354 THR Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 558 VAL Chi-restraints excluded: chain L residue 567 MET Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 580 PHE Chi-restraints excluded: chain L residue 606 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 132 HIS I 808 ASN I1268 GLN J 206 ASN J 335 GLN J 365 GLN J 465 GLN J 861 ASN ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.079702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.051242 restraints weight = 116065.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.053104 restraints weight = 62397.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.053735 restraints weight = 39844.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.054002 restraints weight = 30838.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.054180 restraints weight = 30185.139| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31277 Z= 0.122 Angle : 0.647 34.432 42595 Z= 0.320 Chirality : 0.042 0.151 4879 Planarity : 0.005 0.068 5259 Dihedral : 15.617 171.634 5398 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.81 % Favored : 94.14 % Rotamer: Outliers : 3.98 % Allowed : 15.47 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.11 % Twisted Proline : 0.70 % Twisted General : 0.09 % 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: -1.29 (0.13), residues: 3651 helix: 0.74 (0.14), residues: 1399 sheet: -1.50 (0.24), residues: 450 loop : -2.03 (0.13), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 363 TYR 0.016 0.001 TYR L 430 PHE 0.011 0.001 PHE I 514 TRP 0.024 0.001 TRP L 326 HIS 0.005 0.001 HIS H 132 Details of bonding type rmsd covalent geometry : bond 0.00261 (31269) covalent geometry : angle 0.59782 (42583) hydrogen bonds : bond 0.04147 ( 1321) hydrogen bonds : angle 4.97720 ( 3737) metal coordination : bond 0.01114 ( 8) metal coordination : angle 14.82345 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 157 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 118 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8021 (ptmt) REVERT: I 240 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7564 (pm20) REVERT: I 315 MET cc_start: 0.8190 (mmm) cc_final: 0.7843 (mmm) REVERT: I 369 MET cc_start: 0.8739 (tmm) cc_final: 0.8206 (tmm) REVERT: I 492 MET cc_start: 0.8454 (pmm) cc_final: 0.7629 (pmm) REVERT: I 515 MET cc_start: 0.8607 (ttp) cc_final: 0.8323 (ttp) REVERT: I 653 MET cc_start: 0.8551 (ttt) cc_final: 0.8281 (ttt) REVERT: I 658 GLN cc_start: 0.9254 (OUTLIER) cc_final: 0.7254 (pp30) REVERT: I 800 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7549 (mtm) REVERT: I 1244 HIS cc_start: 0.8604 (OUTLIER) cc_final: 0.8212 (p-80) REVERT: I 1274 GLU cc_start: 0.8204 (mp0) cc_final: 0.7938 (mm-30) REVERT: I 1287 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8454 (tp) REVERT: J 706 VAL cc_start: 0.8672 (OUTLIER) cc_final: 0.8433 (m) REVERT: J 746 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8919 (mp) REVERT: L 291 CYS cc_start: 0.0874 (OUTLIER) cc_final: 0.0394 (m) REVERT: L 365 MET cc_start: 0.9188 (mmt) cc_final: 0.8870 (mmt) REVERT: L 379 MET cc_start: 0.8694 (ppp) cc_final: 0.8339 (ppp) outliers start: 125 outliers final: 71 residues processed: 271 average time/residue: 0.1562 time to fit residues: 73.6364 Evaluate side-chains 220 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 140 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 118 LYS Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 240 GLU Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 396 ASP Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 643 SER Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 658 GLN Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 808 ASN Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1038 GLN Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1287 LEU Chi-restraints excluded: chain I residue 1337 ILE Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 115 TRP Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 394 ILE Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 684 ASP Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 767 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 886 VAL Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 291 CYS Chi-restraints excluded: chain L residue 331 HIS Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 561 MET Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 606 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 348 optimal weight: 5.9990 chunk 366 optimal weight: 30.0000 chunk 34 optimal weight: 3.9990 chunk 359 optimal weight: 10.0000 chunk 213 optimal weight: 1.9990 chunk 190 optimal weight: 9.9990 chunk 238 optimal weight: 4.9990 chunk 38 optimal weight: 20.0000 chunk 28 optimal weight: 6.9990 chunk 275 optimal weight: 30.0000 chunk 225 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 832 HIS I1038 GLN ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN J 861 ASN K 75 GLN ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.076819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.048176 restraints weight = 116581.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.049690 restraints weight = 60923.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.050630 restraints weight = 40959.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.051230 restraints weight = 32524.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.051520 restraints weight = 28497.022| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 31277 Z= 0.229 Angle : 0.661 20.437 42595 Z= 0.334 Chirality : 0.043 0.149 4879 Planarity : 0.004 0.064 5259 Dihedral : 15.391 171.289 5290 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.61 % Favored : 92.30 % Rotamer: Outliers : 4.58 % Allowed : 16.55 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.11 % Twisted Proline : 0.70 % Twisted General : 0.03 % 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: -0.97 (0.14), residues: 3651 helix: 1.10 (0.14), residues: 1401 sheet: -1.40 (0.24), residues: 461 loop : -1.92 (0.14), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 352 TYR 0.013 0.001 TYR L 430 PHE 0.015 0.001 PHE I1144 TRP 0.011 0.001 TRP L 326 HIS 0.005 0.001 HIS I1313 Details of bonding type rmsd covalent geometry : bond 0.00518 (31269) covalent geometry : angle 0.63647 (42583) hydrogen bonds : bond 0.04134 ( 1321) hydrogen bonds : angle 4.83743 ( 3737) metal coordination : bond 0.01581 ( 8) metal coordination : angle 10.59939 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 138 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 240 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7927 (pm20) REVERT: I 369 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8120 (tmm) REVERT: I 492 MET cc_start: 0.8489 (pmm) cc_final: 0.7605 (pmm) REVERT: I 658 GLN cc_start: 0.9404 (OUTLIER) cc_final: 0.7391 (pp30) REVERT: I 800 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7466 (mtm) REVERT: I 1119 MET cc_start: 0.8981 (tpt) cc_final: 0.8773 (tpp) REVERT: I 1244 HIS cc_start: 0.8751 (OUTLIER) cc_final: 0.8344 (p-80) REVERT: I 1274 GLU cc_start: 0.8123 (mp0) cc_final: 0.7887 (mm-30) REVERT: I 1287 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8722 (tp) REVERT: J 130 MET cc_start: 0.8255 (mmm) cc_final: 0.8011 (mmm) REVERT: J 157 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8721 (mm110) REVERT: J 534 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8545 (tm-30) REVERT: J 706 VAL cc_start: 0.8781 (OUTLIER) cc_final: 0.8536 (m) REVERT: J 746 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8943 (mp) REVERT: J 898 CYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7640 (m) REVERT: J 1215 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7894 (mp0) REVERT: L 291 CYS cc_start: 0.0635 (OUTLIER) cc_final: 0.0120 (m) REVERT: L 567 MET cc_start: 0.8161 (ppp) cc_final: 0.7442 (ppp) outliers start: 144 outliers final: 81 residues processed: 269 average time/residue: 0.1606 time to fit residues: 75.1519 Evaluate side-chains 229 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 135 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 PHE Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 240 GLU Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 396 ASP Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 643 SER Chi-restraints excluded: chain I residue 658 GLN Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 822 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 851 THR Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1287 LEU Chi-restraints excluded: chain I residue 1337 ILE Chi-restraints excluded: chain J residue 20 ILE Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 115 TRP Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 157 GLN Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 394 ILE Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 534 GLU Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 684 ASP Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 767 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 886 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 898 CYS Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1215 GLU Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 291 CYS Chi-restraints excluded: chain L residue 331 HIS Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 561 MET Chi-restraints excluded: chain L residue 573 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 161 optimal weight: 0.9980 chunk 92 optimal weight: 20.0000 chunk 150 optimal weight: 5.9990 chunk 226 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 249 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 370 optimal weight: 30.0000 chunk 252 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 chunk 163 optimal weight: 7.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 808 ASN I1136 GLN I1336 ASN ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN J 861 ASN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.077810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.049454 restraints weight = 115129.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.050984 restraints weight = 59502.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.051971 restraints weight = 39801.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.052570 restraints weight = 31408.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.052941 restraints weight = 27419.576| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31277 Z= 0.143 Angle : 0.579 14.628 42595 Z= 0.299 Chirality : 0.041 0.143 4879 Planarity : 0.004 0.062 5259 Dihedral : 15.191 170.506 5279 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.22 % Favored : 93.73 % Rotamer: Outliers : 4.04 % Allowed : 17.95 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.11 % Twisted Proline : 0.70 % Twisted General : 0.03 % 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: -0.70 (0.14), residues: 3651 helix: 1.33 (0.14), residues: 1403 sheet: -1.25 (0.24), residues: 458 loop : -1.77 (0.14), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 352 TYR 0.013 0.001 TYR G 177 PHE 0.015 0.001 PHE J1199 TRP 0.009 0.001 TRP L 326 HIS 0.003 0.001 HIS I1313 Details of bonding type rmsd covalent geometry : bond 0.00318 (31269) covalent geometry : angle 0.56768 (42583) hydrogen bonds : bond 0.03596 ( 1321) hydrogen bonds : angle 4.53605 ( 3737) metal coordination : bond 0.01227 ( 8) metal coordination : angle 6.92165 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 144 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 27 THR cc_start: 0.9142 (OUTLIER) cc_final: 0.8927 (p) REVERT: I 240 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7332 (pm20) REVERT: I 369 MET cc_start: 0.8638 (tmm) cc_final: 0.8150 (tmm) REVERT: I 492 MET cc_start: 0.8450 (pmm) cc_final: 0.7542 (pmm) REVERT: I 513 GLN cc_start: 0.9218 (OUTLIER) cc_final: 0.8992 (pm20) REVERT: I 658 GLN cc_start: 0.9361 (OUTLIER) cc_final: 0.7339 (pp30) REVERT: I 800 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7431 (mtm) REVERT: I 1244 HIS cc_start: 0.8647 (OUTLIER) cc_final: 0.8286 (p-80) REVERT: I 1274 GLU cc_start: 0.8131 (mp0) cc_final: 0.7853 (mm-30) REVERT: I 1287 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8554 (tp) REVERT: J 130 MET cc_start: 0.8189 (mmm) cc_final: 0.7897 (mmm) REVERT: J 534 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8546 (tm-30) REVERT: J 746 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8960 (mp) REVERT: J 898 CYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7601 (m) REVERT: K 43 ASN cc_start: 0.8451 (t0) cc_final: 0.8226 (t0) REVERT: L 291 CYS cc_start: 0.0425 (OUTLIER) cc_final: -0.0121 (m) REVERT: L 365 MET cc_start: 0.8865 (mmt) cc_final: 0.8553 (mmm) REVERT: L 470 MET cc_start: 0.8954 (mtp) cc_final: 0.8721 (tpp) REVERT: L 567 MET cc_start: 0.8319 (ppp) cc_final: 0.7773 (ppp) outliers start: 127 outliers final: 73 residues processed: 262 average time/residue: 0.1578 time to fit residues: 72.3085 Evaluate side-chains 221 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 137 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 PHE Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 240 GLU Chi-restraints excluded: chain I residue 396 ASP Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 643 SER Chi-restraints excluded: chain I residue 658 GLN Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 741 MET Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 822 VAL Chi-restraints excluded: chain I residue 851 THR Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1047 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1287 LEU Chi-restraints excluded: chain I residue 1337 ILE Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 115 TRP Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 534 GLU Chi-restraints excluded: chain J residue 536 LEU Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 684 ASP Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 767 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 886 VAL Chi-restraints excluded: chain J residue 898 CYS Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1046 ILE Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 291 CYS Chi-restraints excluded: chain L residue 331 HIS Chi-restraints excluded: chain L residue 511 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 310 optimal weight: 2.9990 chunk 370 optimal weight: 30.0000 chunk 238 optimal weight: 4.9990 chunk 358 optimal weight: 6.9990 chunk 192 optimal weight: 4.9990 chunk 317 optimal weight: 5.9990 chunk 273 optimal weight: 8.9990 chunk 114 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 34 optimal weight: 20.0000 chunk 326 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 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 = 0.3601 r_free = 0.3601 target = 0.077570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.048980 restraints weight = 116132.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.050517 restraints weight = 60286.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.051497 restraints weight = 40328.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.052092 restraints weight = 31817.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.052404 restraints weight = 27916.013| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 31277 Z= 0.172 Angle : 0.588 12.301 42595 Z= 0.302 Chirality : 0.041 0.142 4879 Planarity : 0.004 0.062 5259 Dihedral : 15.076 170.215 5262 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.98 % Favored : 92.96 % Rotamer: Outliers : 4.30 % Allowed : 18.33 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.11 % Twisted Proline : 0.70 % Twisted General : 0.03 % 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: -0.60 (0.14), residues: 3651 helix: 1.42 (0.14), residues: 1402 sheet: -1.19 (0.24), residues: 458 loop : -1.72 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 352 TYR 0.012 0.001 TYR L 430 PHE 0.014 0.001 PHE J1199 TRP 0.029 0.001 TRP I 997 HIS 0.003 0.001 HIS I1313 Details of bonding type rmsd covalent geometry : bond 0.00388 (31269) covalent geometry : angle 0.57923 (42583) hydrogen bonds : bond 0.03610 ( 1321) hydrogen bonds : angle 4.47725 ( 3737) metal coordination : bond 0.01367 ( 8) metal coordination : angle 5.90116 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 141 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 27 THR cc_start: 0.9189 (OUTLIER) cc_final: 0.8983 (p) REVERT: I 240 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7303 (pm20) REVERT: I 369 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8170 (tmm) REVERT: I 492 MET cc_start: 0.8590 (pmm) cc_final: 0.7649 (pmm) REVERT: I 513 GLN cc_start: 0.9270 (OUTLIER) cc_final: 0.9068 (pm20) REVERT: I 658 GLN cc_start: 0.9376 (OUTLIER) cc_final: 0.7318 (pp30) REVERT: I 697 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7520 (ttmm) REVERT: I 800 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7471 (mtm) REVERT: I 1244 HIS cc_start: 0.8663 (OUTLIER) cc_final: 0.8299 (p-80) REVERT: I 1274 GLU cc_start: 0.8129 (mp0) cc_final: 0.7845 (mm-30) REVERT: I 1287 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8644 (tp) REVERT: J 130 MET cc_start: 0.8182 (mmm) cc_final: 0.7850 (mmm) REVERT: J 180 MET cc_start: 0.6662 (ttt) cc_final: 0.6418 (tpt) REVERT: J 534 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8546 (tm-30) REVERT: J 706 VAL cc_start: 0.8770 (OUTLIER) cc_final: 0.8537 (m) REVERT: J 746 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8950 (mp) REVERT: J 898 CYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7615 (m) REVERT: K 43 ASN cc_start: 0.8494 (t0) cc_final: 0.8243 (t0) REVERT: K 69 ARG cc_start: 0.9211 (tpp80) cc_final: 0.8715 (tpp80) REVERT: L 277 MET cc_start: 0.8850 (mpt) cc_final: 0.8307 (mmt) REVERT: L 291 CYS cc_start: 0.0456 (OUTLIER) cc_final: -0.0070 (m) REVERT: L 470 MET cc_start: 0.8978 (mtp) cc_final: 0.8693 (tpp) REVERT: L 561 MET cc_start: 0.8838 (tpt) cc_final: 0.8596 (tpt) REVERT: L 567 MET cc_start: 0.8297 (ppp) cc_final: 0.7780 (ppp) REVERT: L 580 PHE cc_start: 0.6014 (OUTLIER) cc_final: 0.4887 (m-80) outliers start: 135 outliers final: 90 residues processed: 266 average time/residue: 0.1590 time to fit residues: 74.3418 Evaluate side-chains 244 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 139 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 PHE Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 240 GLU Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 396 ASP Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 658 GLN Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 741 MET Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 822 VAL Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1036 ILE Chi-restraints excluded: chain I residue 1047 LEU Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1287 LEU Chi-restraints excluded: chain I residue 1337 ILE Chi-restraints excluded: chain J residue 20 ILE Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 115 TRP Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 534 GLU Chi-restraints excluded: chain J residue 536 LEU Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 684 ASP Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 767 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 886 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 898 CYS Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1046 ILE Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1326 GLN Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 291 CYS Chi-restraints excluded: chain L residue 331 HIS Chi-restraints excluded: chain L residue 344 LEU Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 580 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 249 optimal weight: 8.9990 chunk 358 optimal weight: 3.9990 chunk 158 optimal weight: 0.4980 chunk 88 optimal weight: 9.9990 chunk 350 optimal weight: 10.0000 chunk 256 optimal weight: 20.0000 chunk 192 optimal weight: 9.9990 chunk 349 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 334 optimal weight: 50.0000 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 193 ASN I1136 GLN ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 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 = 0.3581 r_free = 0.3581 target = 0.076730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.048142 restraints weight = 116044.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.049637 restraints weight = 60776.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.050596 restraints weight = 40982.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.051134 restraints weight = 32494.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.051369 restraints weight = 28574.201| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 31277 Z= 0.235 Angle : 0.644 13.385 42595 Z= 0.327 Chirality : 0.042 0.145 4879 Planarity : 0.004 0.061 5259 Dihedral : 15.079 170.751 5259 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.70 % Favored : 92.25 % Rotamer: Outliers : 4.81 % Allowed : 18.46 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.11 % Twisted Proline : 0.70 % Twisted General : 0.03 % 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: -0.67 (0.14), residues: 3651 helix: 1.31 (0.14), residues: 1415 sheet: -1.23 (0.24), residues: 452 loop : -1.74 (0.14), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 637 TYR 0.016 0.001 TYR I1229 PHE 0.014 0.001 PHE I1144 TRP 0.021 0.001 TRP I 997 HIS 0.004 0.001 HIS I1313 Details of bonding type rmsd covalent geometry : bond 0.00534 (31269) covalent geometry : angle 0.63690 (42583) hydrogen bonds : bond 0.03871 ( 1321) hydrogen bonds : angle 4.57153 ( 3737) metal coordination : bond 0.01658 ( 8) metal coordination : angle 5.77608 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 140 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 27 THR cc_start: 0.9190 (OUTLIER) cc_final: 0.8966 (p) REVERT: G 41 ASN cc_start: 0.8703 (t0) cc_final: 0.8404 (t0) REVERT: I 118 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8342 (ptmt) REVERT: I 240 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7270 (tm-30) REVERT: I 369 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8182 (tmm) REVERT: I 492 MET cc_start: 0.8572 (pmm) cc_final: 0.7751 (pmm) REVERT: I 658 GLN cc_start: 0.9376 (OUTLIER) cc_final: 0.7645 (pp30) REVERT: I 697 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7537 (ttmm) REVERT: I 800 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7505 (mtm) REVERT: I 1085 MET cc_start: 0.8907 (mmt) cc_final: 0.8661 (mmt) REVERT: I 1274 GLU cc_start: 0.8124 (mp0) cc_final: 0.7850 (mm-30) REVERT: I 1287 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8741 (tp) REVERT: J 130 MET cc_start: 0.8160 (mmm) cc_final: 0.7795 (mmm) REVERT: J 180 MET cc_start: 0.6631 (ttt) cc_final: 0.6410 (tpt) REVERT: J 534 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8621 (tm-30) REVERT: J 706 VAL cc_start: 0.8821 (OUTLIER) cc_final: 0.8591 (m) REVERT: J 746 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8793 (mp) REVERT: J 898 CYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7687 (m) REVERT: K 25 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.8137 (ttp80) REVERT: K 69 ARG cc_start: 0.9226 (tpp80) cc_final: 0.8736 (tpp80) REVERT: L 291 CYS cc_start: 0.0669 (OUTLIER) cc_final: 0.0069 (m) REVERT: L 365 MET cc_start: 0.9009 (mmt) cc_final: 0.8695 (mmm) REVERT: L 561 MET cc_start: 0.8777 (tpt) cc_final: 0.8485 (tpt) REVERT: L 567 MET cc_start: 0.8322 (ppp) cc_final: 0.7811 (ppp) REVERT: L 580 PHE cc_start: 0.6108 (OUTLIER) cc_final: 0.4975 (m-80) outliers start: 151 outliers final: 103 residues processed: 281 average time/residue: 0.1617 time to fit residues: 78.4691 Evaluate side-chains 254 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 136 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 PHE Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 222 THR Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 81 ILE Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 118 LYS Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 240 GLU Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 396 ASP Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 512 SER Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 658 GLN Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 741 MET Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 822 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 851 THR Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1036 ILE Chi-restraints excluded: chain I residue 1047 LEU Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1287 LEU Chi-restraints excluded: chain I residue 1337 ILE Chi-restraints excluded: chain J residue 20 ILE Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 115 TRP Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 534 GLU Chi-restraints excluded: chain J residue 536 LEU Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 554 GLU Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 684 ASP Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 767 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 886 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 898 CYS Chi-restraints excluded: chain J residue 913 GLU Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1046 ILE Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1326 GLN Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 25 ARG Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 291 CYS Chi-restraints excluded: chain L residue 331 HIS Chi-restraints excluded: chain L residue 344 LEU Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 580 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 14 optimal weight: 4.9990 chunk 319 optimal weight: 0.0000 chunk 44 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 370 optimal weight: 30.0000 chunk 9 optimal weight: 4.9990 chunk 181 optimal weight: 7.9990 chunk 172 optimal weight: 0.6980 chunk 266 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 340 optimal weight: 40.0000 overall best weight: 2.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 206 ASN J 365 GLN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 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 = 0.3601 r_free = 0.3601 target = 0.077588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.049030 restraints weight = 115701.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.050572 restraints weight = 60085.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.051545 restraints weight = 40249.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.052148 restraints weight = 31851.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.052470 restraints weight = 27872.227| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31277 Z= 0.154 Angle : 0.588 12.438 42595 Z= 0.301 Chirality : 0.041 0.154 4879 Planarity : 0.004 0.062 5259 Dihedral : 14.968 170.546 5257 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.52 % Favored : 93.43 % Rotamer: Outliers : 4.20 % Allowed : 19.22 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.11 % Twisted Proline : 0.70 % Twisted General : 0.03 % 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: -0.54 (0.14), residues: 3651 helix: 1.39 (0.14), residues: 1418 sheet: -1.12 (0.24), residues: 448 loop : -1.65 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 678 TYR 0.015 0.001 TYR I1229 PHE 0.013 0.001 PHE J1037 TRP 0.016 0.001 TRP I 997 HIS 0.004 0.001 HIS I1244 Details of bonding type rmsd covalent geometry : bond 0.00349 (31269) covalent geometry : angle 0.58201 (42583) hydrogen bonds : bond 0.03548 ( 1321) hydrogen bonds : angle 4.39911 ( 3737) metal coordination : bond 0.01211 ( 8) metal coordination : angle 4.98296 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 140 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 27 THR cc_start: 0.9202 (OUTLIER) cc_final: 0.8989 (p) REVERT: I 240 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7086 (tm-30) REVERT: I 369 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8172 (tmm) REVERT: I 488 MET cc_start: 0.7521 (tpp) cc_final: 0.7306 (tpp) REVERT: I 492 MET cc_start: 0.8545 (pmm) cc_final: 0.7758 (pmm) REVERT: I 658 GLN cc_start: 0.9358 (OUTLIER) cc_final: 0.7271 (pp30) REVERT: I 697 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7782 (mtmm) REVERT: I 800 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7465 (mtm) REVERT: I 1274 GLU cc_start: 0.8119 (mp0) cc_final: 0.7824 (mm-30) REVERT: I 1287 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8652 (tp) REVERT: J 130 MET cc_start: 0.8209 (mmm) cc_final: 0.7895 (mmm) REVERT: J 534 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8544 (tm-30) REVERT: J 706 VAL cc_start: 0.8795 (OUTLIER) cc_final: 0.8565 (m) REVERT: J 746 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8782 (mp) REVERT: J 898 CYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7620 (m) REVERT: J 1199 PHE cc_start: 0.7034 (m-80) cc_final: 0.6592 (m-80) REVERT: K 25 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.8112 (ttp80) REVERT: K 43 ASN cc_start: 0.8443 (t0) cc_final: 0.8182 (t0) REVERT: K 69 ARG cc_start: 0.9201 (tpp80) cc_final: 0.8700 (tpp80) REVERT: L 291 CYS cc_start: 0.0758 (OUTLIER) cc_final: 0.0184 (m) REVERT: L 470 MET cc_start: 0.8993 (mtp) cc_final: 0.8791 (tpp) REVERT: L 487 MET cc_start: 0.8789 (mmm) cc_final: 0.8589 (mmt) REVERT: L 561 MET cc_start: 0.8767 (tpt) cc_final: 0.8476 (tpt) REVERT: L 567 MET cc_start: 0.8374 (ppp) cc_final: 0.7878 (ppp) REVERT: L 580 PHE cc_start: 0.5856 (OUTLIER) cc_final: 0.4704 (m-80) outliers start: 132 outliers final: 100 residues processed: 261 average time/residue: 0.1588 time to fit residues: 71.6562 Evaluate side-chains 252 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 138 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 PHE Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 81 ILE Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 240 GLU Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 512 SER Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 658 GLN Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 741 MET Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 822 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 851 THR Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1036 ILE Chi-restraints excluded: chain I residue 1047 LEU Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1287 LEU Chi-restraints excluded: chain I residue 1337 ILE Chi-restraints excluded: chain J residue 20 ILE Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 115 TRP Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 534 GLU Chi-restraints excluded: chain J residue 536 LEU Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 554 GLU Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 684 ASP Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 767 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 886 VAL Chi-restraints excluded: chain J residue 898 CYS Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1037 PHE Chi-restraints excluded: chain J residue 1046 ILE Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1326 GLN Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 25 ARG Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 291 CYS Chi-restraints excluded: chain L residue 331 HIS Chi-restraints excluded: chain L residue 344 LEU Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 580 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 339 optimal weight: 5.9990 chunk 308 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 chunk 260 optimal weight: 0.0970 chunk 30 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 352 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 223 optimal weight: 4.9990 chunk 266 optimal weight: 6.9990 chunk 131 optimal weight: 10.0000 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 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 = 0.3598 r_free = 0.3598 target = 0.077455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.048899 restraints weight = 116148.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.050425 restraints weight = 60470.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.051399 restraints weight = 40630.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.051995 restraints weight = 32134.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.052307 restraints weight = 28147.079| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 31277 Z= 0.172 Angle : 0.594 11.855 42595 Z= 0.304 Chirality : 0.041 0.142 4879 Planarity : 0.004 0.062 5259 Dihedral : 14.915 170.551 5257 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.09 % Favored : 92.85 % Rotamer: Outliers : 4.42 % Allowed : 19.22 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.11 % Twisted Proline : 0.70 % Twisted General : 0.03 % 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: -0.51 (0.14), residues: 3651 helix: 1.42 (0.14), residues: 1418 sheet: -1.14 (0.24), residues: 448 loop : -1.63 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 678 TYR 0.015 0.001 TYR I1229 PHE 0.011 0.001 PHE I1144 TRP 0.014 0.001 TRP I 997 HIS 0.004 0.001 HIS I1244 Details of bonding type rmsd covalent geometry : bond 0.00389 (31269) covalent geometry : angle 0.58861 (42583) hydrogen bonds : bond 0.03540 ( 1321) hydrogen bonds : angle 4.37611 ( 3737) metal coordination : bond 0.01318 ( 8) metal coordination : angle 4.90501 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 141 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 27 THR cc_start: 0.9215 (OUTLIER) cc_final: 0.9002 (p) REVERT: I 240 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7091 (tm-30) REVERT: I 256 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8676 (mp0) REVERT: I 369 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8179 (tmm) REVERT: I 492 MET cc_start: 0.8492 (pmm) cc_final: 0.7706 (pmm) REVERT: I 658 GLN cc_start: 0.9360 (OUTLIER) cc_final: 0.7590 (pp30) REVERT: I 697 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7784 (mtmm) REVERT: I 800 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7469 (mtm) REVERT: I 1274 GLU cc_start: 0.8105 (mp0) cc_final: 0.7810 (mm-30) REVERT: I 1287 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8679 (tp) REVERT: I 1331 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8115 (ttm170) REVERT: J 130 MET cc_start: 0.8224 (mmm) cc_final: 0.7906 (mmm) REVERT: J 534 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8601 (tm-30) REVERT: J 706 VAL cc_start: 0.8811 (OUTLIER) cc_final: 0.8580 (m) REVERT: J 746 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8783 (mp) REVERT: K 25 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.8124 (ttp80) REVERT: K 43 ASN cc_start: 0.8442 (t0) cc_final: 0.8182 (t0) REVERT: K 69 ARG cc_start: 0.9199 (tpp80) cc_final: 0.8699 (tpp80) REVERT: L 277 MET cc_start: 0.8818 (mpt) cc_final: 0.8577 (mmt) REVERT: L 291 CYS cc_start: 0.0747 (OUTLIER) cc_final: 0.0181 (m) REVERT: L 365 MET cc_start: 0.8976 (mmt) cc_final: 0.8657 (mmm) REVERT: L 470 MET cc_start: 0.8960 (mtp) cc_final: 0.8630 (tpp) REVERT: L 561 MET cc_start: 0.8688 (tpt) cc_final: 0.8375 (tpt) REVERT: L 567 MET cc_start: 0.8394 (ppp) cc_final: 0.7917 (ppp) REVERT: L 580 PHE cc_start: 0.5820 (OUTLIER) cc_final: 0.4716 (m-80) outliers start: 139 outliers final: 105 residues processed: 269 average time/residue: 0.1663 time to fit residues: 76.6578 Evaluate side-chains 258 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 138 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 PHE Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 81 ILE Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 240 GLU Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 256 GLU Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 512 SER Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 658 GLN Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 741 MET Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 822 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 851 THR Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1036 ILE Chi-restraints excluded: chain I residue 1047 LEU Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1287 LEU Chi-restraints excluded: chain I residue 1331 ARG Chi-restraints excluded: chain I residue 1337 ILE Chi-restraints excluded: chain J residue 20 ILE Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 115 TRP Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 534 GLU Chi-restraints excluded: chain J residue 536 LEU Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 554 GLU Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 684 ASP Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 767 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 886 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1037 PHE Chi-restraints excluded: chain J residue 1046 ILE Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1326 GLN Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 25 ARG Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 291 CYS Chi-restraints excluded: chain L residue 331 HIS Chi-restraints excluded: chain L residue 344 LEU Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 580 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 98 optimal weight: 7.9990 chunk 298 optimal weight: 5.9990 chunk 271 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 340 optimal weight: 40.0000 chunk 277 optimal weight: 20.0000 chunk 48 optimal weight: 7.9990 chunk 182 optimal weight: 5.9990 chunk 120 optimal weight: 8.9990 chunk 156 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 365 GLN J 907 HIS ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 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 = 0.3568 r_free = 0.3568 target = 0.076115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.047785 restraints weight = 116352.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.049254 restraints weight = 61083.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.050193 restraints weight = 41123.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.050719 restraints weight = 32551.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.051080 restraints weight = 28595.591| |-----------------------------------------------------------------------------| r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 31277 Z= 0.287 Angle : 0.695 12.047 42595 Z= 0.352 Chirality : 0.043 0.149 4879 Planarity : 0.004 0.061 5259 Dihedral : 15.007 171.316 5257 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.19 % Favored : 91.76 % Rotamer: Outliers : 4.14 % Allowed : 19.73 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.11 % Twisted Proline : 0.70 % Twisted General : 0.03 % 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: -0.71 (0.14), residues: 3651 helix: 1.25 (0.14), residues: 1417 sheet: -1.35 (0.24), residues: 442 loop : -1.70 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 678 TYR 0.013 0.001 TYR I 578 PHE 0.016 0.001 PHE I1144 TRP 0.015 0.001 TRP I 997 HIS 0.005 0.001 HIS J 545 Details of bonding type rmsd covalent geometry : bond 0.00650 (31269) covalent geometry : angle 0.68858 (42583) hydrogen bonds : bond 0.04049 ( 1321) hydrogen bonds : angle 4.60435 ( 3737) metal coordination : bond 0.01852 ( 8) metal coordination : angle 5.78053 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 136 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 27 THR cc_start: 0.9188 (OUTLIER) cc_final: 0.8959 (p) REVERT: G 41 ASN cc_start: 0.8673 (t0) cc_final: 0.8376 (t0) REVERT: I 240 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7271 (tm-30) REVERT: I 256 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8673 (mp0) REVERT: I 369 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8193 (tmm) REVERT: I 492 MET cc_start: 0.8520 (pmm) cc_final: 0.7727 (pmm) REVERT: I 538 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8855 (pp) REVERT: I 658 GLN cc_start: 0.9368 (OUTLIER) cc_final: 0.7693 (pp30) REVERT: I 697 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7645 (ttmm) REVERT: I 800 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7507 (mtm) REVERT: I 1274 GLU cc_start: 0.8146 (mp0) cc_final: 0.7878 (mm-30) REVERT: I 1287 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8844 (tp) REVERT: I 1331 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8220 (ttm170) REVERT: J 130 MET cc_start: 0.8191 (mmm) cc_final: 0.7796 (mmm) REVERT: J 205 LEU cc_start: 0.6157 (OUTLIER) cc_final: 0.5954 (mp) REVERT: J 534 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8627 (tm-30) REVERT: J 706 VAL cc_start: 0.8884 (OUTLIER) cc_final: 0.8654 (m) REVERT: J 746 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8800 (mp) REVERT: J 898 CYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7683 (m) REVERT: J 1258 ARG cc_start: 0.9210 (OUTLIER) cc_final: 0.8744 (tmt90) REVERT: K 25 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8166 (ttp80) REVERT: K 69 ARG cc_start: 0.9206 (tpp80) cc_final: 0.8717 (tpp80) REVERT: L 277 MET cc_start: 0.8813 (mpt) cc_final: 0.8568 (mmt) REVERT: L 291 CYS cc_start: 0.0688 (OUTLIER) cc_final: 0.0103 (m) REVERT: L 365 MET cc_start: 0.8987 (mmt) cc_final: 0.8658 (mmm) REVERT: L 470 MET cc_start: 0.8987 (mtp) cc_final: 0.8610 (tpp) REVERT: L 561 MET cc_start: 0.8775 (tpt) cc_final: 0.8459 (tpt) REVERT: L 567 MET cc_start: 0.8385 (ppp) cc_final: 0.7915 (ppp) REVERT: L 580 PHE cc_start: 0.5839 (OUTLIER) cc_final: 0.4722 (m-80) outliers start: 130 outliers final: 101 residues processed: 256 average time/residue: 0.1703 time to fit residues: 74.2932 Evaluate side-chains 255 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 135 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 PHE Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 81 ILE Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 240 GLU Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 256 GLU Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 512 SER Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 658 GLN Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 741 MET Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 822 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 851 THR Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1036 ILE Chi-restraints excluded: chain I residue 1047 LEU Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1287 LEU Chi-restraints excluded: chain I residue 1331 ARG Chi-restraints excluded: chain I residue 1337 ILE Chi-restraints excluded: chain J residue 20 ILE Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 115 TRP Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 534 GLU Chi-restraints excluded: chain J residue 536 LEU Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 554 GLU Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 767 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 886 VAL Chi-restraints excluded: chain J residue 898 CYS Chi-restraints excluded: chain J residue 907 HIS Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1037 PHE Chi-restraints excluded: chain J residue 1046 ILE Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1258 ARG Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1326 GLN Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 25 ARG Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 291 CYS Chi-restraints excluded: chain L residue 331 HIS Chi-restraints excluded: chain L residue 344 LEU Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 580 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 157 optimal weight: 0.9980 chunk 285 optimal weight: 30.0000 chunk 274 optimal weight: 9.9990 chunk 61 optimal weight: 20.0000 chunk 237 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 117 optimal weight: 0.9980 chunk 154 optimal weight: 0.9980 chunk 265 optimal weight: 3.9990 chunk 269 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN J 861 ASN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 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 = 0.3619 r_free = 0.3619 target = 0.078365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.050121 restraints weight = 114732.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.051690 restraints weight = 59094.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.052679 restraints weight = 39236.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.053248 restraints weight = 30897.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.053626 restraints weight = 27020.317| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 31277 Z= 0.111 Angle : 0.582 11.629 42595 Z= 0.297 Chirality : 0.041 0.168 4879 Planarity : 0.004 0.063 5259 Dihedral : 14.807 170.527 5255 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.75 % Favored : 94.19 % Rotamer: Outliers : 2.99 % Allowed : 20.94 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.11 % Twisted Proline : 0.70 % Twisted General : 0.03 % 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: -0.43 (0.14), residues: 3651 helix: 1.46 (0.14), residues: 1421 sheet: -1.17 (0.24), residues: 448 loop : -1.54 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG J 905 TYR 0.013 0.001 TYR J 512 PHE 0.016 0.001 PHE I 337 TRP 0.013 0.001 TRP I 997 HIS 0.009 0.001 HIS I1244 Details of bonding type rmsd covalent geometry : bond 0.00241 (31269) covalent geometry : angle 0.57709 (42583) hydrogen bonds : bond 0.03339 ( 1321) hydrogen bonds : angle 4.27255 ( 3737) metal coordination : bond 0.00907 ( 8) metal coordination : angle 4.33812 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 143 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 27 THR cc_start: 0.9215 (OUTLIER) cc_final: 0.8998 (p) REVERT: G 194 GLN cc_start: 0.8086 (tp40) cc_final: 0.7811 (tp-100) REVERT: I 240 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7396 (tm-30) REVERT: I 369 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8211 (tmm) REVERT: I 492 MET cc_start: 0.8403 (pmm) cc_final: 0.7561 (pmm) REVERT: I 658 GLN cc_start: 0.9307 (OUTLIER) cc_final: 0.7253 (pp30) REVERT: I 697 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7728 (mtmm) REVERT: I 800 MET cc_start: 0.7716 (OUTLIER) cc_final: 0.7396 (mtm) REVERT: I 1274 GLU cc_start: 0.8088 (mp0) cc_final: 0.7782 (mm-30) REVERT: I 1287 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8562 (tp) REVERT: J 130 MET cc_start: 0.8270 (mmm) cc_final: 0.7995 (mmm) REVERT: J 180 MET cc_start: 0.7055 (tpt) cc_final: 0.6648 (tpt) REVERT: J 534 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8613 (tm-30) REVERT: J 706 VAL cc_start: 0.8741 (OUTLIER) cc_final: 0.8509 (m) REVERT: J 746 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8771 (mp) REVERT: J 898 CYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7583 (m) REVERT: J 1025 MET cc_start: 0.6899 (mmt) cc_final: 0.6110 (tpt) REVERT: K 25 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.8036 (tmm-80) REVERT: K 43 ASN cc_start: 0.8404 (t0) cc_final: 0.8150 (t0) REVERT: L 277 MET cc_start: 0.8806 (mpt) cc_final: 0.8560 (mmt) REVERT: L 291 CYS cc_start: 0.0555 (OUTLIER) cc_final: 0.0010 (m) REVERT: L 365 MET cc_start: 0.8985 (mmt) cc_final: 0.8668 (mmm) REVERT: L 470 MET cc_start: 0.8932 (mtp) cc_final: 0.8615 (tpp) REVERT: L 487 MET cc_start: 0.8954 (mmm) cc_final: 0.8753 (mmt) REVERT: L 561 MET cc_start: 0.8622 (tpt) cc_final: 0.8289 (tpt) REVERT: L 567 MET cc_start: 0.8432 (ppp) cc_final: 0.7959 (ppp) REVERT: L 580 PHE cc_start: 0.5745 (OUTLIER) cc_final: 0.4604 (m-80) outliers start: 94 outliers final: 72 residues processed: 227 average time/residue: 0.1656 time to fit residues: 64.5491 Evaluate side-chains 224 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 138 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 PHE Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 81 ILE Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 240 GLU Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 512 SER Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 658 GLN Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 741 MET Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 851 THR Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1287 LEU Chi-restraints excluded: chain I residue 1337 ILE Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 115 TRP Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 534 GLU Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 554 GLU Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 767 LEU Chi-restraints excluded: chain J residue 783 LEU Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 886 VAL Chi-restraints excluded: chain J residue 898 CYS Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1037 PHE Chi-restraints excluded: chain J residue 1046 ILE Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1326 GLN Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 25 ARG Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 291 CYS Chi-restraints excluded: chain L residue 331 HIS Chi-restraints excluded: chain L residue 344 LEU Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 580 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 12 optimal weight: 6.9990 chunk 223 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 325 optimal weight: 4.9990 chunk 228 optimal weight: 5.9990 chunk 280 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 248 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 92 optimal weight: 20.0000 chunk 79 optimal weight: 20.0000 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN J 907 HIS ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 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 = 0.3593 r_free = 0.3593 target = 0.077208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.048854 restraints weight = 115965.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.050362 restraints weight = 60413.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.051280 restraints weight = 40475.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.051891 restraints weight = 32085.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.052249 restraints weight = 28039.237| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 31277 Z= 0.198 Angle : 0.624 11.255 42595 Z= 0.316 Chirality : 0.042 0.181 4879 Planarity : 0.004 0.062 5259 Dihedral : 14.792 170.519 5252 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.26 % Favored : 92.69 % Rotamer: Outliers : 3.15 % Allowed : 20.75 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.11 % Twisted Proline : 0.70 % Twisted General : 0.03 % 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: -0.46 (0.14), residues: 3651 helix: 1.45 (0.14), residues: 1421 sheet: -1.21 (0.25), residues: 428 loop : -1.56 (0.14), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 678 TYR 0.014 0.001 TYR I1229 PHE 0.013 0.001 PHE I1144 TRP 0.011 0.001 TRP I 997 HIS 0.010 0.001 HIS I1244 Details of bonding type rmsd covalent geometry : bond 0.00449 (31269) covalent geometry : angle 0.61909 (42583) hydrogen bonds : bond 0.03554 ( 1321) hydrogen bonds : angle 4.36655 ( 3737) metal coordination : bond 0.01407 ( 8) metal coordination : angle 4.51506 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5534.99 seconds wall clock time: 96 minutes 3.42 seconds (5763.42 seconds total)