Starting phenix.real_space_refine on Sun Jul 5 22:27:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mke_23893/07_2026/7mke_23893.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mke_23893/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7mke_23893/07_2026/7mke_23893.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mke_23893/07_2026/7mke_23893.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mke_23893/07_2026/7mke_23893.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mke_23893/07_2026/7mke_23893.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7mke_23893/07_2026/7mke_23893.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mke_23893/07_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-6108/lib/python3.11/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: 18 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: 18 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: 5.14, per 1000 atoms: 0.17 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: 2.42 Conformation dependent library (CDL) restraints added in 1.3 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: 3.32 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: 7.37 Time building geometry restraints manager: 3.31 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: 42293 3.66 - 7.32: 264 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=" O4' DG P 43 " pdb=" C4' DG P 43 " pdb=" C3' DG P 43 " ideal model delta sigma weight residual 106.00 103.10 2.90 6.00e-01 2.78e+00 2.34e+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 ... (remaining 42578 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.44: 18150 34.44 - 68.88: 818 68.88 - 103.31: 35 103.31 - 137.75: 1 137.75 - 172.19: 3 Dihedral angle restraints: 19007 sinusoidal: 8430 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 19004 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 4489 0.094 - 0.188: 372 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 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: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 32.030 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 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= 0.471 Angle : 0.935 41.773 42595 Z= 0.531 Chirality : 0.053 0.469 4879 Planarity : 0.006 0.076 5259 Dihedral : 17.415 172.190 12189 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/Z covalent geometry : bond 0.00950 / 0.47 (31269) covalent geometry : angle 0.88038 / 0.53 (42583) hydrogen bonds : bond 0.17181 / 11.88 ( 1321) hydrogen bonds : angle 6.91948 / 4.86 ( 3737) metal coordination : bond 0.01314 / 0.68 ( 8) metal coordination : angle 18.81852 / 9.43 ( 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 : 0.995 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: 0.1530 time to fit residues: 96.5232 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 : 0.965 ------------------------------------------------------------------------------- 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... G 132 HIS H 194 GLN I 808 ASN 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 = 0.3652 r_free = 0.3652 target = 0.079242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.050549 restraints weight = 115638.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.052154 restraints weight = 58559.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.053107 restraints weight = 38828.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.053745 restraints weight = 30886.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.054103 restraints weight = 27017.333| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 31277 Z= 0.135 Angle : 0.694 38.656 42595 Z= 0.344 Chirality : 0.043 0.187 4879 Planarity : 0.005 0.071 5259 Dihedral : 16.060 166.227 5122 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.14 % Favored : 93.78 % Rotamer: Outliers : 4.49 % Allowed : 15.60 % Favored : 79.92 % 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: -1.39 (0.13), residues: 3651 helix: 0.63 (0.14), residues: 1401 sheet: -1.52 (0.23), residues: 458 loop : -2.09 (0.13), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 637 TYR 0.015 0.001 TYR G 177 PHE 0.012 0.001 PHE L 302 TRP 0.026 0.001 TRP L 326 HIS 0.005 0.001 HIS J 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (31269) covalent geometry : angle 0.63175 / 0.34 (42583) hydrogen bonds : bond 0.04673 / 3.25 ( 1321) hydrogen bonds : angle 5.22897 / 3.62 ( 3737) metal coordination : bond 0.01225 / 0.55 ( 8) metal coordination : angle 17.10078 / 7.96 ( 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 293 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 152 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 118 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.7982 (ptmt) REVERT: I 213 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8837 (tt) REVERT: I 240 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7615 (pm20) REVERT: I 315 MET cc_start: 0.8094 (mmm) cc_final: 0.7882 (mmm) REVERT: I 369 MET cc_start: 0.8698 (tmm) cc_final: 0.8199 (tmm) REVERT: I 492 MET cc_start: 0.8396 (pmm) cc_final: 0.7638 (pmm) REVERT: I 515 MET cc_start: 0.8680 (ttp) cc_final: 0.8387 (ttp) REVERT: I 653 MET cc_start: 0.8625 (ttt) cc_final: 0.8361 (ttt) REVERT: I 658 GLN cc_start: 0.9311 (OUTLIER) cc_final: 0.7408 (pp30) REVERT: I 800 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7490 (mtm) REVERT: I 1244 HIS cc_start: 0.8750 (OUTLIER) cc_final: 0.8316 (p-80) REVERT: I 1274 GLU cc_start: 0.8132 (mp0) cc_final: 0.7895 (mm-30) REVERT: I 1287 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8485 (tp) REVERT: J 255 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8588 (mm) REVERT: J 596 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9277 (mm) REVERT: J 706 VAL cc_start: 0.8697 (OUTLIER) cc_final: 0.8425 (m) REVERT: J 746 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8949 (mp) REVERT: J 1040 MET cc_start: 0.8214 (mpp) cc_final: 0.7484 (mpp) REVERT: L 291 CYS cc_start: 0.0843 (OUTLIER) cc_final: 0.0529 (m) REVERT: L 365 MET cc_start: 0.9247 (mmt) cc_final: 0.8859 (mmt) REVERT: L 379 MET cc_start: 0.8725 (ppp) cc_final: 0.8363 (ppp) REVERT: L 487 MET cc_start: 0.8851 (mmt) cc_final: 0.8538 (mmt) outliers start: 141 outliers final: 86 residues processed: 281 average time/residue: 0.1489 time to fit residues: 72.9296 Evaluate side-chains 236 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 138 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 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 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 207 THR Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 62 TYR 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 213 LEU 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 512 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 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 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 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 20 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 255 LEU Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 429 LEU 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 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 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 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 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 1237 VAL Chi-restraints excluded: chain J residue 1326 GLN Chi-restraints excluded: chain J residue 1366 HIS 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 580 PHE 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: 6.9990 chunk 366 optimal weight: 50.0000 chunk 34 optimal weight: 0.6980 chunk 359 optimal weight: 8.9990 chunk 213 optimal weight: 0.8980 chunk 190 optimal weight: 7.9990 chunk 238 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 275 optimal weight: 30.0000 chunk 225 optimal weight: 5.9990 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 314 ASN I 832 HIS I1268 GLN ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN J 861 ASN ** 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 = 0.3625 r_free = 0.3625 target = 0.078092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.049262 restraints weight = 117010.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.050823 restraints weight = 59766.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.051791 restraints weight = 39883.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.052407 restraints weight = 31615.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.052686 restraints weight = 27721.790| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1094 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= 0.215 Angle : 0.684 30.168 42595 Z= 0.340 Chirality : 0.043 0.207 4879 Planarity : 0.004 0.064 5259 Dihedral : 15.831 166.039 5039 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.67 % Favored : 92.25 % Rotamer: Outliers : 4.52 % Allowed : 16.96 % Favored : 78.52 % 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: -1.09 (0.14), residues: 3651 helix: 0.98 (0.14), residues: 1400 sheet: -1.48 (0.24), residues: 449 loop : -1.97 (0.14), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 637 TYR 0.014 0.001 TYR L 430 PHE 0.016 0.001 PHE J1199 TRP 0.012 0.001 TRP L 326 HIS 0.005 0.001 HIS I1313 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.21 (31269) covalent geometry : angle 0.63869 / 0.34 (42583) hydrogen bonds : bond 0.04368 / 3.06 ( 1321) hydrogen bonds : angle 4.98289 / 3.44 ( 3737) metal coordination : bond 0.01328 / 0.66 ( 8) metal coordination : angle 14.63091 / 7.00 ( 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 283 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 141 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 41 ASN cc_start: 0.8656 (t0) cc_final: 0.8392 (t0) REVERT: I 240 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7616 (pm20) REVERT: I 369 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8054 (tmm) REVERT: I 492 MET cc_start: 0.8450 (pmm) cc_final: 0.7670 (pmm) REVERT: I 513 GLN cc_start: 0.9189 (OUTLIER) cc_final: 0.8975 (pm20) REVERT: I 515 MET cc_start: 0.8662 (ttp) cc_final: 0.8413 (ttp) REVERT: I 658 GLN cc_start: 0.9350 (OUTLIER) cc_final: 0.7330 (pp30) REVERT: I 800 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.7433 (mtm) REVERT: I 1244 HIS cc_start: 0.8747 (OUTLIER) cc_final: 0.8363 (p-80) REVERT: I 1274 GLU cc_start: 0.8100 (mp0) cc_final: 0.7872 (mm-30) REVERT: I 1287 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8688 (tp) REVERT: J 130 MET cc_start: 0.8337 (mmm) cc_final: 0.8086 (mmm) REVERT: J 157 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8747 (mm110) REVERT: J 255 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8603 (mm) REVERT: J 534 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8535 (tm-30) REVERT: J 596 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.9244 (mm) REVERT: J 706 VAL cc_start: 0.8789 (OUTLIER) cc_final: 0.8538 (m) REVERT: J 746 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8946 (mp) REVERT: J 898 CYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7594 (m) REVERT: J 1040 MET cc_start: 0.8156 (mpp) cc_final: 0.7351 (mpp) REVERT: J 1095 MET cc_start: 0.7181 (tpp) cc_final: 0.6972 (tpp) REVERT: J 1215 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7858 (mp0) REVERT: L 291 CYS cc_start: 0.0592 (OUTLIER) cc_final: -0.0079 (m) REVERT: L 365 MET cc_start: 0.9210 (mmt) cc_final: 0.8857 (mmt) REVERT: L 567 MET cc_start: 0.8178 (ppp) cc_final: 0.7699 (ppp) outliers start: 142 outliers final: 96 residues processed: 275 average time/residue: 0.1518 time to fit residues: 72.3880 Evaluate side-chains 246 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 134 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 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 62 TYR 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 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 589 THR Chi-restraints excluded: chain I residue 606 LEU 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 819 SER Chi-restraints excluded: chain I residue 822 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 1038 GLN Chi-restraints excluded: chain I residue 1046 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 20 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 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 255 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 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 596 LEU 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 707 ILE 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 966 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 1237 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain K residue 4 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 511 ILE Chi-restraints excluded: chain L residue 561 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 161 optimal weight: 3.9990 chunk 92 optimal weight: 20.0000 chunk 150 optimal weight: 5.9990 chunk 226 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 249 optimal weight: 2.9990 chunk 152 optimal weight: 6.9990 chunk 370 optimal weight: 50.0000 chunk 252 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 314 ASN ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 861 ASN K 75 GLN ** 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 = 0.3589 r_free = 0.3589 target = 0.077047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.048445 restraints weight = 115642.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.049951 restraints weight = 60307.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.050928 restraints weight = 40642.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.051514 restraints weight = 32134.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.051790 restraints weight = 28219.607| |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 31277 Z= 0.194 Angle : 0.635 22.426 42595 Z= 0.323 Chirality : 0.043 0.207 4879 Planarity : 0.004 0.062 5259 Dihedral : 15.745 166.194 5026 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.15 % Favored : 92.77 % Rotamer: Outliers : 4.84 % Allowed : 17.35 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.11 % Twisted Proline : 0.70 % Twisted General : 0.06 % 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: -0.92 (0.14), residues: 3651 helix: 1.14 (0.14), residues: 1404 sheet: -1.43 (0.23), residues: 461 loop : -1.88 (0.14), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 352 TYR 0.012 0.001 TYR L 430 PHE 0.014 0.001 PHE J1199 TRP 0.008 0.001 TRP L 326 HIS 0.004 0.001 HIS I1313 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (31269) covalent geometry : angle 0.60695 / 0.32 (42583) hydrogen bonds : bond 0.04038 / 2.83 ( 1321) hydrogen bonds : angle 4.81233 / 3.33 ( 3737) metal coordination : bond 0.01354 / 0.69 ( 8) metal coordination : angle 11.04338 / 5.30 ( 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 288 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 136 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 27 THR cc_start: 0.9120 (OUTLIER) cc_final: 0.8864 (p) REVERT: G 41 ASN cc_start: 0.8663 (t0) cc_final: 0.8363 (t0) REVERT: I 240 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7077 (pm20) REVERT: I 369 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8134 (tmm) REVERT: I 492 MET cc_start: 0.8475 (pmm) cc_final: 0.7654 (pmm) REVERT: I 513 GLN cc_start: 0.9239 (OUTLIER) cc_final: 0.9038 (pm20) REVERT: I 515 MET cc_start: 0.8601 (ttp) cc_final: 0.8395 (ttp) REVERT: I 658 GLN cc_start: 0.9386 (OUTLIER) cc_final: 0.7361 (pp30) REVERT: I 800 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7427 (mtm) REVERT: I 1244 HIS cc_start: 0.8719 (OUTLIER) cc_final: 0.8322 (p-80) REVERT: I 1274 GLU cc_start: 0.8144 (mp0) cc_final: 0.7882 (mm-30) REVERT: I 1287 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8692 (tp) REVERT: J 130 MET cc_start: 0.8240 (mmm) cc_final: 0.7945 (mmm) REVERT: J 157 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8756 (mm110) REVERT: J 180 MET cc_start: 0.6654 (ttt) cc_final: 0.6341 (tpt) REVERT: J 534 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8572 (tm-30) REVERT: J 706 VAL cc_start: 0.8779 (OUTLIER) cc_final: 0.8537 (m) REVERT: J 746 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8947 (mp) REVERT: J 898 CYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7665 (m) REVERT: J 1040 MET cc_start: 0.8077 (mpp) cc_final: 0.7872 (mpp) REVERT: J 1095 MET cc_start: 0.7246 (tpp) cc_final: 0.7023 (tpp) REVERT: J 1215 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7883 (mp0) REVERT: L 291 CYS cc_start: 0.0618 (OUTLIER) cc_final: 0.0184 (m) REVERT: L 365 MET cc_start: 0.9164 (mmt) cc_final: 0.8956 (mmt) REVERT: L 379 MET cc_start: 0.8724 (ppp) cc_final: 0.8396 (ppp) REVERT: L 470 MET cc_start: 0.9005 (mtp) cc_final: 0.8617 (tpp) REVERT: L 567 MET cc_start: 0.8186 (ppp) cc_final: 0.7673 (ppp) outliers start: 152 outliers final: 93 residues processed: 276 average time/residue: 0.1481 time to fit residues: 71.5270 Evaluate side-chains 246 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 138 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 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 I residue 30 ILE Chi-restraints excluded: chain I residue 62 TYR 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 455 SER Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 606 LEU Chi-restraints excluded: chain I residue 643 SER Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 658 GLN Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 819 SER Chi-restraints excluded: chain I residue 822 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 830 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 1038 GLN 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 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 434 ILE Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 534 GLU Chi-restraints excluded: chain J residue 536 LEU 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 654 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 869 CYS 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 1046 ILE Chi-restraints excluded: chain J residue 1215 GLU Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1267 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 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 354 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 310 optimal weight: 0.6980 chunk 370 optimal weight: 50.0000 chunk 238 optimal weight: 3.9990 chunk 358 optimal weight: 10.0000 chunk 192 optimal weight: 9.9990 chunk 317 optimal weight: 10.0000 chunk 273 optimal weight: 8.9990 chunk 114 optimal weight: 1.9990 chunk 38 optimal weight: 20.0000 chunk 34 optimal weight: 3.9990 chunk 326 optimal weight: 40.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3589 r_free = 0.3589 target = 0.077010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.048566 restraints weight = 116099.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.050068 restraints weight = 60300.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.051034 restraints weight = 40497.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.051623 restraints weight = 31971.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.051903 restraints weight = 27947.476| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 31277 Z= 0.192 Angle : 0.623 17.437 42595 Z= 0.320 Chirality : 0.043 0.208 4879 Planarity : 0.004 0.061 5259 Dihedral : 15.614 165.840 5009 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.50 % Favored : 92.44 % Rotamer: Outliers : 5.12 % Allowed : 18.11 % Favored : 76.77 % 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: -0.81 (0.14), residues: 3651 helix: 1.23 (0.14), residues: 1402 sheet: -1.39 (0.23), residues: 462 loop : -1.81 (0.14), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 197 TYR 0.011 0.001 TYR L 430 PHE 0.015 0.001 PHE L 302 TRP 0.006 0.001 TRP L 326 HIS 0.004 0.001 HIS I1313 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 (31269) covalent geometry : angle 0.60626 / 0.32 (42583) hydrogen bonds : bond 0.03941 / 2.76 ( 1321) hydrogen bonds : angle 4.70496 / 3.26 ( 3737) metal coordination : bond 0.01434 / 0.73 ( 8) metal coordination : angle 8.48395 / 4.02 ( 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 302 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 141 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 27 THR cc_start: 0.9132 (OUTLIER) cc_final: 0.8883 (p) REVERT: G 41 ASN cc_start: 0.8678 (t0) cc_final: 0.8354 (t0) REVERT: I 240 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.6980 (pm20) REVERT: I 369 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8231 (tmm) REVERT: I 492 MET cc_start: 0.8461 (pmm) cc_final: 0.7644 (pmm) REVERT: I 513 GLN cc_start: 0.9267 (OUTLIER) cc_final: 0.9046 (pm20) REVERT: I 658 GLN cc_start: 0.9372 (OUTLIER) cc_final: 0.7297 (pp30) REVERT: I 697 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7561 (ttmm) REVERT: I 800 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7461 (mtm) REVERT: I 1229 TYR cc_start: 0.8611 (m-80) cc_final: 0.8404 (m-80) REVERT: I 1244 HIS cc_start: 0.8727 (OUTLIER) cc_final: 0.8334 (p-80) REVERT: I 1274 GLU cc_start: 0.8146 (mp0) cc_final: 0.7878 (mm-30) REVERT: I 1287 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8655 (tp) REVERT: J 130 MET cc_start: 0.8253 (mmm) cc_final: 0.7947 (mmm) REVERT: J 157 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8734 (mm110) REVERT: J 534 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8573 (tm-30) REVERT: J 706 VAL cc_start: 0.8775 (OUTLIER) cc_final: 0.8540 (m) REVERT: J 746 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8957 (mp) REVERT: J 898 CYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7659 (m) REVERT: J 1095 MET cc_start: 0.7196 (tpp) cc_final: 0.6975 (tpp) REVERT: J 1215 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7886 (mp0) REVERT: L 291 CYS cc_start: 0.0485 (OUTLIER) cc_final: -0.0056 (m) REVERT: L 379 MET cc_start: 0.8656 (ppp) cc_final: 0.8294 (ppp) REVERT: L 567 MET cc_start: 0.8294 (ppp) cc_final: 0.7756 (ppp) outliers start: 161 outliers final: 110 residues processed: 290 average time/residue: 0.1497 time to fit residues: 75.4986 Evaluate side-chains 264 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 138 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 65 LEU 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 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 207 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 62 TYR 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 512 SER Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 606 LEU Chi-restraints excluded: chain I residue 643 SER Chi-restraints excluded: chain I residue 650 VAL 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 765 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 819 SER 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 830 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 1038 GLN Chi-restraints excluded: chain I residue 1047 LEU Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1206 THR 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 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 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 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 558 ASP 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 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 869 CYS 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 1215 GLU Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 39 VAL 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 354 THR Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 558 VAL Chi-restraints excluded: chain L residue 561 MET Chi-restraints excluded: chain L residue 573 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 249 optimal weight: 10.0000 chunk 358 optimal weight: 9.9990 chunk 158 optimal weight: 0.5980 chunk 88 optimal weight: 10.0000 chunk 350 optimal weight: 10.0000 chunk 256 optimal weight: 20.0000 chunk 192 optimal weight: 10.0000 chunk 349 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 chunk 26 optimal weight: 0.6980 chunk 334 optimal weight: 9.9990 overall best weight: 5.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 193 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.076323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.047937 restraints weight = 116098.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.049410 restraints weight = 60806.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.050354 restraints weight = 41000.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.050879 restraints weight = 32470.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.051256 restraints weight = 28533.019| |-----------------------------------------------------------------------------| r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 31277 Z= 0.260 Angle : 0.675 16.016 42595 Z= 0.343 Chirality : 0.044 0.208 4879 Planarity : 0.004 0.060 5259 Dihedral : 15.630 165.852 5008 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.97 % Favored : 91.95 % Rotamer: Outliers : 5.19 % Allowed : 18.62 % Favored : 76.19 % 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: -0.85 (0.14), residues: 3651 helix: 1.20 (0.14), residues: 1407 sheet: -1.41 (0.24), residues: 450 loop : -1.84 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 678 TYR 0.012 0.001 TYR I 578 PHE 0.014 0.001 PHE I1144 TRP 0.005 0.001 TRP L 315 HIS 0.005 0.001 HIS I1313 Details of bonding type rmsd/Z covalent geometry : bond 0.00583 / 0.26 (31269) covalent geometry : angle 0.66208 / 0.34 (42583) hydrogen bonds : bond 0.04102 / 2.88 ( 1321) hydrogen bonds : angle 4.77045 / 3.31 ( 3737) metal coordination : bond 0.01737 / 0.87 ( 8) metal coordination : angle 7.72661 / 3.68 ( 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 300 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 137 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 27 THR cc_start: 0.9121 (OUTLIER) cc_final: 0.8869 (p) REVERT: G 41 ASN cc_start: 0.8715 (t0) cc_final: 0.8406 (t0) REVERT: G 204 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7940 (tm-30) REVERT: I 240 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7070 (tm-30) REVERT: I 369 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.8170 (tmm) REVERT: I 448 LEU cc_start: 0.9565 (OUTLIER) cc_final: 0.8946 (tt) REVERT: I 492 MET cc_start: 0.8483 (pmm) cc_final: 0.7714 (pmm) REVERT: I 658 GLN cc_start: 0.9372 (OUTLIER) cc_final: 0.7683 (pp30) REVERT: I 697 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7606 (ttmm) REVERT: I 704 MET cc_start: 0.8312 (tmm) cc_final: 0.8045 (tmm) REVERT: I 800 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7476 (mtm) REVERT: I 1244 HIS cc_start: 0.8752 (OUTLIER) cc_final: 0.8358 (p-80) REVERT: I 1274 GLU cc_start: 0.8144 (mp0) cc_final: 0.7877 (mm-30) REVERT: I 1287 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8770 (tp) REVERT: I 1290 MET cc_start: 0.9264 (tpp) cc_final: 0.8635 (tpt) REVERT: I 1331 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8219 (ttm170) REVERT: J 130 MET cc_start: 0.8260 (mmm) cc_final: 0.7921 (mmm) REVERT: J 157 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8754 (mm110) REVERT: J 534 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8608 (tm-30) REVERT: J 746 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8818 (mp) REVERT: J 898 CYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7702 (m) REVERT: J 1095 MET cc_start: 0.7142 (tpp) cc_final: 0.6926 (tpp) REVERT: J 1215 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7904 (mp0) REVERT: K 69 ARG cc_start: 0.9206 (tpp80) cc_final: 0.8729 (tpp80) REVERT: L 291 CYS cc_start: 0.0520 (OUTLIER) cc_final: -0.0092 (m) REVERT: L 379 MET cc_start: 0.8728 (ppp) cc_final: 0.8358 (ppp) REVERT: L 470 MET cc_start: 0.8986 (mtp) cc_final: 0.8767 (tpp) REVERT: L 567 MET cc_start: 0.8284 (ppp) cc_final: 0.7772 (ppp) outliers start: 163 outliers final: 121 residues processed: 289 average time/residue: 0.1531 time to fit residues: 77.0244 Evaluate side-chains 274 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 136 time to evaluate : 1.185 ------------------------------------------------------------------------------- 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 65 LEU 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 204 GLU Chi-restraints excluded: chain G residue 222 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 59 VAL Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 62 TYR 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 448 LEU Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 512 SER Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 606 LEU Chi-restraints excluded: chain I residue 643 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 765 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 819 SER 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 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 924 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1036 ILE Chi-restraints excluded: chain I residue 1038 GLN Chi-restraints excluded: chain I residue 1047 LEU Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1141 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 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 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 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 558 ASP 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 654 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 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 869 CYS 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 1215 GLU Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1326 GLN 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 39 VAL 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 354 THR Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 558 VAL Chi-restraints excluded: chain L residue 561 MET Chi-restraints excluded: chain L residue 573 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 14 optimal weight: 3.9990 chunk 319 optimal weight: 0.0370 chunk 44 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 370 optimal weight: 50.0000 chunk 9 optimal weight: 4.9990 chunk 181 optimal weight: 4.9990 chunk 172 optimal weight: 0.6980 chunk 266 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 340 optimal weight: 6.9990 overall best weight: 2.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1336 ASN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.077815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.049268 restraints weight = 115619.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.050818 restraints weight = 59877.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.051804 restraints weight = 40072.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.052352 restraints weight = 31672.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.052751 restraints weight = 27792.053| |-----------------------------------------------------------------------------| r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31277 Z= 0.133 Angle : 0.591 13.695 42595 Z= 0.305 Chirality : 0.042 0.207 4879 Planarity : 0.004 0.061 5259 Dihedral : 15.511 165.624 5007 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.66 % Favored : 93.29 % Rotamer: Outliers : 4.07 % Allowed : 19.83 % 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: -0.63 (0.14), residues: 3651 helix: 1.35 (0.14), residues: 1408 sheet: -1.29 (0.24), residues: 456 loop : -1.68 (0.14), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 678 TYR 0.013 0.001 TYR J 512 PHE 0.011 0.001 PHE L 302 TRP 0.007 0.001 TRP I 807 HIS 0.003 0.001 HIS I1313 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (31269) covalent geometry : angle 0.58177 / 0.30 (42583) hydrogen bonds : bond 0.03665 / 2.56 ( 1321) hydrogen bonds : angle 4.52365 / 3.13 ( 3737) metal coordination : bond 0.01149 / 0.57 ( 8) metal coordination : angle 6.33223 / 2.97 ( 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 274 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 146 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 27 THR cc_start: 0.9169 (OUTLIER) cc_final: 0.8926 (p) REVERT: I 240 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.6995 (tm-30) REVERT: I 369 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8204 (tmm) REVERT: I 492 MET cc_start: 0.8435 (pmm) cc_final: 0.7662 (pmm) REVERT: I 658 GLN cc_start: 0.9339 (OUTLIER) cc_final: 0.7288 (pp30) REVERT: I 800 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.7402 (mtm) REVERT: I 1244 HIS cc_start: 0.8641 (OUTLIER) cc_final: 0.8295 (p-80) REVERT: I 1274 GLU cc_start: 0.8119 (mp0) cc_final: 0.7819 (mm-30) REVERT: I 1287 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8595 (tp) REVERT: I 1290 MET cc_start: 0.9215 (tpp) cc_final: 0.8556 (tpt) REVERT: J 130 MET cc_start: 0.8269 (mmm) cc_final: 0.8011 (mmm) REVERT: J 157 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8729 (mm110) REVERT: J 534 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8573 (tm-30) REVERT: J 746 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8958 (mp) REVERT: J 898 CYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7673 (m) REVERT: J 1040 MET cc_start: 0.8264 (mpp) cc_final: 0.7995 (mpp) REVERT: J 1095 MET cc_start: 0.7210 (tpp) cc_final: 0.6978 (tpp) REVERT: K 25 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.8030 (tmm-80) REVERT: K 69 ARG cc_start: 0.9200 (tpp80) cc_final: 0.8711 (tpp80) REVERT: L 291 CYS cc_start: 0.0489 (OUTLIER) cc_final: -0.0111 (m) REVERT: L 379 MET cc_start: 0.8737 (ppp) cc_final: 0.8392 (ppp) REVERT: L 470 MET cc_start: 0.8969 (mtp) cc_final: 0.8738 (tpp) REVERT: L 567 MET cc_start: 0.8304 (ppp) cc_final: 0.7769 (ppp) outliers start: 128 outliers final: 83 residues processed: 265 average time/residue: 0.1595 time to fit residues: 72.6574 Evaluate side-chains 236 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 140 time to evaluate : 1.241 ------------------------------------------------------------------------------- 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 65 LEU 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 I residue 30 ILE Chi-restraints excluded: chain I residue 62 TYR 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 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 765 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 829 THR 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 1036 ILE Chi-restraints excluded: chain I residue 1038 GLN Chi-restraints excluded: chain I residue 1047 LEU Chi-restraints excluded: chain I residue 1141 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 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 157 GLN 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 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 545 HIS Chi-restraints excluded: chain J residue 554 GLU Chi-restraints excluded: chain J residue 558 ASP 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 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 869 CYS 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 913 GLU 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 1298 VAL Chi-restraints excluded: chain J residue 1326 GLN 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 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 354 THR Chi-restraints excluded: chain L residue 511 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 339 optimal weight: 3.9990 chunk 308 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 260 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 352 optimal weight: 8.9990 chunk 109 optimal weight: 0.9980 chunk 223 optimal weight: 6.9990 chunk 266 optimal weight: 7.9990 chunk 131 optimal weight: 0.9980 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3602 r_free = 0.3602 target = 0.077611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.049234 restraints weight = 115527.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.050763 restraints weight = 59787.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.051735 restraints weight = 39934.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.052268 restraints weight = 31487.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.052662 restraints weight = 27738.462| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31277 Z= 0.153 Angle : 0.600 12.053 42595 Z= 0.308 Chirality : 0.042 0.205 4879 Planarity : 0.004 0.075 5259 Dihedral : 15.418 165.340 4988 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.18 % Favored : 92.77 % Rotamer: Outliers : 3.72 % Allowed : 20.02 % Favored : 76.26 % 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: -0.58 (0.14), residues: 3651 helix: 1.38 (0.14), residues: 1409 sheet: -1.22 (0.24), residues: 448 loop : -1.66 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 637 TYR 0.018 0.001 TYR I1229 PHE 0.012 0.001 PHE J1199 TRP 0.006 0.001 TRP L 326 HIS 0.004 0.001 HIS J 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (31269) covalent geometry : angle 0.59167 / 0.31 (42583) hydrogen bonds : bond 0.03650 / 2.56 ( 1321) hydrogen bonds : angle 4.47563 / 3.10 ( 3737) metal coordination : bond 0.01239 / 0.63 ( 8) metal coordination : angle 5.88119 / 2.79 ( 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 261 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 144 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 27 THR cc_start: 0.9215 (OUTLIER) cc_final: 0.8990 (p) REVERT: I 256 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8362 (mp0) REVERT: I 369 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8163 (tmm) REVERT: I 492 MET cc_start: 0.8538 (pmm) cc_final: 0.7713 (pmm) REVERT: I 658 GLN cc_start: 0.9347 (OUTLIER) cc_final: 0.7280 (pp30) REVERT: I 800 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7463 (mtm) REVERT: I 1244 HIS cc_start: 0.8637 (OUTLIER) cc_final: 0.8282 (p-80) REVERT: I 1274 GLU cc_start: 0.8135 (mp0) cc_final: 0.7847 (mm-30) REVERT: I 1287 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8631 (tp) REVERT: I 1331 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8175 (ttm170) REVERT: J 130 MET cc_start: 0.8268 (mmm) cc_final: 0.8016 (mmm) REVERT: J 157 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8728 (mm110) REVERT: J 534 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8552 (tm-30) REVERT: J 706 VAL cc_start: 0.8772 (OUTLIER) cc_final: 0.8539 (m) REVERT: J 746 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8950 (mp) REVERT: J 898 CYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7596 (m) REVERT: J 1095 MET cc_start: 0.7212 (tpp) cc_final: 0.6977 (tpp) REVERT: K 25 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.8058 (tmm-80) REVERT: K 69 ARG cc_start: 0.9200 (tpp80) cc_final: 0.8698 (tpp80) REVERT: L 252 LEU cc_start: 0.6852 (OUTLIER) cc_final: 0.6427 (mt) REVERT: L 277 MET cc_start: 0.8875 (mpt) cc_final: 0.8665 (mpt) REVERT: L 291 CYS cc_start: 0.0389 (OUTLIER) cc_final: -0.0124 (m) REVERT: L 379 MET cc_start: 0.8745 (ppp) cc_final: 0.8390 (ppp) REVERT: L 470 MET cc_start: 0.8973 (mtp) cc_final: 0.8657 (tpp) REVERT: L 561 MET cc_start: 0.8842 (tpt) cc_final: 0.8626 (tpt) REVERT: L 567 MET cc_start: 0.8314 (ppp) cc_final: 0.7820 (ppp) outliers start: 117 outliers final: 90 residues processed: 251 average time/residue: 0.1592 time to fit residues: 68.3004 Evaluate side-chains 247 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 141 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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 65 LEU 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 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 217 THR Chi-restraints excluded: chain I residue 222 ASP 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 538 LEU 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 829 THR 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 1036 ILE Chi-restraints excluded: chain I residue 1038 GLN Chi-restraints excluded: chain I residue 1047 LEU Chi-restraints excluded: chain I residue 1141 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 1331 ARG Chi-restraints excluded: chain I residue 1337 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 157 GLN Chi-restraints excluded: chain J residue 160 LEU 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 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 545 HIS Chi-restraints excluded: chain J residue 554 GLU Chi-restraints excluded: chain J residue 558 ASP 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 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 869 CYS 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 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 1298 VAL Chi-restraints excluded: chain J residue 1326 GLN 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 25 ARG Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 252 LEU 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 354 THR Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 558 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 98 optimal weight: 10.0000 chunk 298 optimal weight: 4.9990 chunk 271 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 340 optimal weight: 7.9990 chunk 277 optimal weight: 8.9990 chunk 48 optimal weight: 8.9990 chunk 182 optimal weight: 0.4980 chunk 120 optimal weight: 8.9990 chunk 156 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 overall best weight: 5.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3578 r_free = 0.3578 target = 0.076553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.048142 restraints weight = 116106.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.049625 restraints weight = 60753.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.050564 restraints weight = 40876.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.051098 restraints weight = 32415.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.051454 restraints weight = 28476.660| |-----------------------------------------------------------------------------| r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 31277 Z= 0.251 Angle : 0.673 13.450 42595 Z= 0.342 Chirality : 0.043 0.207 4879 Planarity : 0.004 0.073 5259 Dihedral : 15.448 165.624 4984 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.83 % Favored : 92.11 % Rotamer: Outliers : 3.79 % Allowed : 20.15 % 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: -0.68 (0.14), residues: 3651 helix: 1.29 (0.14), residues: 1414 sheet: -1.32 (0.24), residues: 452 loop : -1.71 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 678 TYR 0.018 0.001 TYR I1229 PHE 0.015 0.001 PHE I1144 TRP 0.047 0.001 TRP I 997 HIS 0.004 0.001 HIS I1313 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.25 (31269) covalent geometry : angle 0.66540 / 0.34 (42583) hydrogen bonds : bond 0.03936 / 2.75 ( 1321) hydrogen bonds : angle 4.61624 / 3.20 ( 3737) metal coordination : bond 0.01664 / 0.83 ( 8) metal coordination : angle 6.07191 / 2.95 ( 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 259 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 140 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 27 THR cc_start: 0.9193 (OUTLIER) cc_final: 0.8952 (p) REVERT: G 41 ASN cc_start: 0.8673 (t0) cc_final: 0.8406 (t0) REVERT: I 239 MET cc_start: 0.5217 (mtm) cc_final: 0.4776 (mtp) REVERT: I 256 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8630 (mp0) REVERT: I 369 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8160 (tmm) REVERT: I 492 MET cc_start: 0.8560 (pmm) cc_final: 0.7750 (pmm) REVERT: I 658 GLN cc_start: 0.9382 (OUTLIER) cc_final: 0.7669 (pp30) REVERT: I 800 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7509 (mtm) REVERT: I 1244 HIS cc_start: 0.8727 (OUTLIER) cc_final: 0.8317 (p-80) REVERT: I 1274 GLU cc_start: 0.8151 (mp0) cc_final: 0.7866 (mm-30) REVERT: I 1287 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8783 (tp) REVERT: I 1290 MET cc_start: 0.9216 (tpp) cc_final: 0.8565 (tpt) REVERT: I 1331 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8248 (ttm170) REVERT: J 130 MET cc_start: 0.8293 (mmm) cc_final: 0.7999 (mmm) REVERT: J 157 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8717 (mm110) REVERT: J 180 MET cc_start: 0.6873 (tpt) cc_final: 0.5919 (tpt) REVERT: J 534 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8624 (tm-30) REVERT: J 706 VAL cc_start: 0.8841 (OUTLIER) cc_final: 0.8614 (m) REVERT: J 746 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8790 (mp) REVERT: J 898 CYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7687 (m) REVERT: J 1095 MET cc_start: 0.7135 (tpp) cc_final: 0.6919 (tpp) REVERT: K 25 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8161 (ttp80) REVERT: K 69 ARG cc_start: 0.9202 (tpp80) cc_final: 0.8703 (tpp80) REVERT: L 252 LEU cc_start: 0.6866 (OUTLIER) cc_final: 0.6434 (mt) REVERT: L 277 MET cc_start: 0.8883 (mpt) cc_final: 0.8674 (mpt) REVERT: L 291 CYS cc_start: 0.0550 (OUTLIER) cc_final: -0.0056 (m) REVERT: L 379 MET cc_start: 0.8774 (ppp) cc_final: 0.8407 (ppp) REVERT: L 470 MET cc_start: 0.9000 (mtp) cc_final: 0.8723 (tpp) REVERT: L 561 MET cc_start: 0.8798 (tpt) cc_final: 0.8546 (tpt) REVERT: L 567 MET cc_start: 0.8262 (ppp) cc_final: 0.7704 (ppp) outliers start: 119 outliers final: 96 residues processed: 250 average time/residue: 0.1519 time to fit residues: 65.2212 Evaluate side-chains 252 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 140 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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 65 LEU 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 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 217 THR Chi-restraints excluded: chain I residue 222 ASP 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 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 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 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 1038 GLN Chi-restraints excluded: chain I residue 1047 LEU Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1141 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 1331 ARG Chi-restraints excluded: chain I residue 1337 ILE Chi-restraints excluded: chain J residue 20 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 157 GLN 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 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 558 ASP Chi-restraints excluded: chain J residue 596 LEU 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 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 869 CYS 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 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 1273 ASP Chi-restraints excluded: chain J residue 1298 VAL Chi-restraints excluded: chain J residue 1326 GLN 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 25 ARG Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 252 LEU 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 354 THR Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 558 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 157 optimal weight: 2.9990 chunk 285 optimal weight: 0.8980 chunk 274 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 237 optimal weight: 0.8980 chunk 34 optimal weight: 20.0000 chunk 117 optimal weight: 0.7980 chunk 154 optimal weight: 0.9980 chunk 265 optimal weight: 7.9990 chunk 269 optimal weight: 0.9990 chunk 133 optimal weight: 0.0870 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.078826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.050593 restraints weight = 114410.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.052125 restraints weight = 58794.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.053090 restraints weight = 39149.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.053692 restraints weight = 30906.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.054007 restraints weight = 27008.409| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 31277 Z= 0.111 Angle : 0.596 12.341 42595 Z= 0.307 Chirality : 0.042 0.207 4879 Planarity : 0.004 0.063 5259 Dihedral : 15.317 165.439 4984 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.61 % Favored : 94.33 % Rotamer: Outliers : 2.90 % Allowed : 21.04 % 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: -0.47 (0.14), residues: 3651 helix: 1.42 (0.14), residues: 1417 sheet: -1.16 (0.24), residues: 451 loop : -1.56 (0.14), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 637 TYR 0.016 0.001 TYR I1229 PHE 0.011 0.001 PHE J1037 TRP 0.039 0.001 TRP I 997 HIS 0.004 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (31269) covalent geometry : angle 0.59052 / 0.31 (42583) hydrogen bonds : bond 0.03448 / 2.40 ( 1321) hydrogen bonds : angle 4.37034 / 3.02 ( 3737) metal coordination : bond 0.00871 / 0.45 ( 8) metal coordination : angle 4.94483 / 2.30 ( 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 239 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 148 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 27 THR cc_start: 0.9167 (OUTLIER) cc_final: 0.8946 (p) REVERT: I 239 MET cc_start: 0.5163 (mtm) cc_final: 0.4771 (mtp) REVERT: I 369 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8261 (tmm) REVERT: I 492 MET cc_start: 0.8517 (pmm) cc_final: 0.7672 (pmm) REVERT: I 658 GLN cc_start: 0.9365 (OUTLIER) cc_final: 0.7271 (pp30) REVERT: I 800 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.7439 (mtm) REVERT: I 1274 GLU cc_start: 0.8269 (mp0) cc_final: 0.7924 (mm-30) REVERT: I 1287 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8531 (tp) REVERT: J 130 MET cc_start: 0.8350 (mmm) cc_final: 0.8069 (mmm) REVERT: J 180 MET cc_start: 0.6803 (tpt) cc_final: 0.5887 (tpt) REVERT: J 534 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8603 (tm-30) REVERT: J 706 VAL cc_start: 0.8676 (OUTLIER) cc_final: 0.8458 (m) REVERT: J 746 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8976 (mp) REVERT: J 898 CYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7618 (m) REVERT: J 1095 MET cc_start: 0.7211 (tpp) cc_final: 0.6989 (tpp) REVERT: K 25 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7977 (tmm-80) REVERT: K 43 ASN cc_start: 0.8455 (t0) cc_final: 0.8154 (t0) REVERT: K 49 ILE cc_start: 0.8785 (mt) cc_final: 0.8577 (mt) REVERT: L 252 LEU cc_start: 0.7123 (OUTLIER) cc_final: 0.6700 (mt) REVERT: L 277 MET cc_start: 0.8864 (mpt) cc_final: 0.8561 (mpt) REVERT: L 291 CYS cc_start: 0.0536 (OUTLIER) cc_final: 0.0074 (m) REVERT: L 379 MET cc_start: 0.8798 (ppp) cc_final: 0.8478 (ppp) REVERT: L 470 MET cc_start: 0.8918 (mtp) cc_final: 0.8615 (tpp) REVERT: L 561 MET cc_start: 0.8737 (tpt) cc_final: 0.8472 (tpt) REVERT: L 567 MET cc_start: 0.8327 (ppp) cc_final: 0.7832 (ppp) outliers start: 91 outliers final: 67 residues processed: 230 average time/residue: 0.1535 time to fit residues: 60.4735 Evaluate side-chains 220 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 141 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 65 LEU Chi-restraints excluded: chain G residue 70 THR 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 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 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 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 823 VAL Chi-restraints excluded: chain I residue 829 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 1141 LEU 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 262 THR Chi-restraints excluded: chain J residue 506 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 558 ASP Chi-restraints excluded: chain J residue 596 LEU 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 1046 ILE Chi-restraints excluded: chain J residue 1237 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 25 ARG Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 252 LEU 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 558 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 12 optimal weight: 0.9990 chunk 223 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 325 optimal weight: 0.9990 chunk 228 optimal weight: 2.9990 chunk 280 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 248 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 79 optimal weight: 20.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3607 r_free = 0.3607 target = 0.077825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.049414 restraints weight = 115696.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.050957 restraints weight = 59883.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.051934 restraints weight = 39956.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.052499 restraints weight = 31497.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.052881 restraints weight = 27549.647| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1857 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= 0.161 Angle : 0.619 16.615 42595 Z= 0.315 Chirality : 0.042 0.233 4879 Planarity : 0.004 0.064 5259 Dihedral : 15.297 165.294 4979 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.60 % Favored : 93.34 % Rotamer: Outliers : 2.86 % Allowed : 21.20 % Favored : 75.94 % 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: 1.41 (0.14), residues: 1417 sheet: -1.21 (0.24), residues: 438 loop : -1.53 (0.14), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 637 TYR 0.012 0.001 TYR L 430 PHE 0.012 0.001 PHE J 988 TRP 0.036 0.001 TRP I 997 HIS 0.005 0.001 HIS I1244 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (31269) covalent geometry : angle 0.61384 / 0.31 (42583) hydrogen bonds : bond 0.03545 / 2.47 ( 1321) hydrogen bonds : angle 4.41165 / 3.06 ( 3737) metal coordination : bond 0.01221 / 0.62 ( 8) metal coordination : angle 4.88584 / 2.35 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5202.38 seconds wall clock time: 90 minutes 22.18 seconds (5422.18 seconds total)