Starting phenix.real_space_refine on Sat Jun 6 22:14:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ymx_73125/06_2026/9ymx_73125.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ymx_73125/06_2026/9ymx_73125.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ymx_73125/06_2026/9ymx_73125.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ymx_73125/06_2026/9ymx_73125.map" model { file = "/net/cci-nas-00/data/ceres_data/9ymx_73125/06_2026/9ymx_73125.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ymx_73125/06_2026/9ymx_73125.cif" } resolution = 2.7 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= 0.000 sd= 0.019 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 75 5.49 5 Mg 1 5.21 5 S 129 5.16 5 C 18815 2.51 5 N 5380 2.21 5 O 6673 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31075 Number of models: 1 Model: "" Number of chains: 20 Chain: "I" Number of atoms: 10567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10567 Classifications: {'peptide': 1340} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 104 Classifications: {'RNA': 5} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 3} Link IDs: {'rna3p': 4} Chain: "P" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 684 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain breaks: 1 Chain: "G" Number of atoms: 1755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1755 Classifications: {'peptide': 227} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 217} Chain breaks: 1 Chain: "H" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1710 Classifications: {'peptide': 222} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 212} Chain breaks: 1 Chain: "J" Number of atoms: 10385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1336, 10385 Classifications: {'peptide': 1336} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1280} Chain breaks: 2 Chain: "L" Number of atoms: 3837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3837 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 15, 'TRANS': 455} Chain breaks: 2 Chain: "Q" Number of atoms: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 711 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain breaks: 2 Chain: "I" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'POP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 324 Classifications: {'water': 324} Link IDs: {None: 323} Chain: "K" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "R" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "J" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 233 Classifications: {'water': 233} Link IDs: {None: 232} Chain: "L" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "Q" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15896 SG CYS J 70 52.805 37.265 117.564 1.00 87.92 S ATOM 15910 SG CYS J 72 54.829 36.400 120.600 1.00104.97 S ATOM 16018 SG CYS J 85 51.115 36.662 120.943 1.00103.16 S ATOM 16042 SG CYS J 88 53.240 39.732 120.399 1.00 95.12 S ATOM 21730 SG CYS J 814 25.791 93.133 87.299 1.00 71.54 S ATOM 22295 SG CYS J 888 29.131 91.809 88.349 1.00 54.40 S ATOM 22346 SG CYS J 895 27.568 90.692 85.164 1.00 52.75 S ATOM 22367 SG CYS J 898 28.861 94.164 85.430 1.00 70.67 S Time building chain proxies: 6.57, per 1000 atoms: 0.21 Number of scatterers: 31075 At special positions: 0 Unit cell: (159.96, 168.56, 194.36, 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 129 16.00 P 75 15.00 Mg 1 11.99 O 6673 8.00 N 5380 7.00 C 18815 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: 2.44 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 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " 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: 6820 Finding SS restraints... Secondary structure from input PDB file: 137 helices and 47 sheets defined 44.2% alpha, 16.3% beta 26 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 3.90 Creating SS restraints... Processing helix chain 'I' and resid 4 through 9 Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.536A pdb=" N LEU I 32 " --> pdb=" O LEU I 28 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 57 removed outlier: 3.576A 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: 3.741A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 288 through 293 Processing helix chain 'I' and resid 318 through 327 removed outlier: 3.808A pdb=" N GLN I 327 " --> pdb=" O ALA I 323 " (cutoff:3.500A) Processing helix chain 'I' and resid 345 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 3.893A pdb=" N GLU I 382 " --> pdb=" O ARG I 378 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 397 through 409 Processing helix chain 'I' and resid 421 through 438 removed outlier: 3.585A pdb=" N ILE I 425 " --> pdb=" O SER I 421 " (cutoff:3.500A) Processing helix chain 'I' and resid 455 through 482 removed outlier: 3.564A pdb=" N GLN I 463 " --> pdb=" O MET I 459 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG I 473 " --> pdb=" O VAL I 469 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 488 through 493 removed outlier: 3.653A pdb=" N MET I 492 " --> pdb=" O MET I 488 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE I 493 " --> pdb=" O PRO I 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 488 through 493' Processing helix chain 'I' and resid 495 through 509 removed outlier: 3.842A pdb=" N ALA I 501 " --> pdb=" O PRO I 497 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL I 502 " --> pdb=" O ILE I 498 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER I 509 " --> pdb=" O PHE I 505 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 539 through 543 removed outlier: 3.783A pdb=" N ALA I 543 " --> pdb=" O ARG I 540 " (cutoff:3.500A) Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.530A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 608 through 612 removed outlier: 3.716A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 612' Processing helix chain 'I' and resid 648 through 650 No H-bonds generated for 'chain 'I' and resid 648 through 650' Processing helix chain 'I' and resid 664 through 668 removed outlier: 3.575A pdb=" N LEU I 667 " --> pdb=" O GLY I 664 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE I 668 " --> pdb=" O ALA I 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 664 through 668' Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 686 Processing helix chain 'I' and resid 687 through 689 No H-bonds generated for 'chain 'I' and resid 687 through 689' Processing helix chain 'I' and resid 704 through 713 removed outlier: 4.054A pdb=" N GLY I 713 " --> pdb=" O ALA I 709 " (cutoff:3.500A) Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 896 through 907 Processing helix chain 'I' and resid 942 through 961 Processing helix chain 'I' and resid 963 through 979 removed outlier: 4.487A pdb=" N LEU I 967 " --> pdb=" O GLU I 963 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU I 979 " --> pdb=" O ILE I 975 " (cutoff:3.500A) Processing helix chain 'I' and resid 993 through 1000 removed outlier: 4.018A pdb=" N LEU I 998 " --> pdb=" O ASP I 995 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU I1000 " --> pdb=" O TRP I 997 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1037 removed outlier: 4.230A pdb=" N ASN I1009 " --> pdb=" O GLU I1005 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA I1031 " --> pdb=" O LYS I1027 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS I1032 " --> pdb=" O LYS I1028 " (cutoff:3.500A) Processing helix chain 'I' and resid 1081 through 1085 removed outlier: 3.566A pdb=" N MET I1085 " --> pdb=" O ILE I1082 " (cutoff:3.500A) Processing helix chain 'I' and resid 1099 through 1103 Processing helix chain 'I' and resid 1109 through 1134 Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.626A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 3.840A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1176 Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1283 through 1292 Processing helix chain 'I' and resid 1297 through 1310 removed outlier: 3.529A pdb=" N ARG I1301 " --> pdb=" O ASP I1297 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1332 removed outlier: 3.854A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 14 removed outlier: 3.521A pdb=" N LYS K 12 " --> pdb=" O ASP K 8 " (cutoff:3.500A) Processing helix chain 'K' and resid 15 through 33 removed outlier: 3.590A 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 80 Processing helix chain 'G' and resid 34 through 51 removed outlier: 3.592A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER G 49 " --> pdb=" O ARG G 45 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N MET G 51 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.686A 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 158 Processing helix chain 'G' and resid 212 through 233 removed outlier: 3.621A pdb=" N GLU G 229 " --> pdb=" O ALA G 225 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP G 233 " --> pdb=" O GLU G 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.589A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 removed outlier: 3.702A pdb=" N GLY H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 212 through 228 Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 58 through 63 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.530A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 173 Processing helix chain 'J' and resid 180 through 191 removed outlier: 3.753A pdb=" N ALA J 184 " --> pdb=" O MET J 180 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 208 Processing helix chain 'J' and resid 210 through 230 removed outlier: 3.884A pdb=" N LYS J 216 " --> pdb=" O THR J 212 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 286 removed outlier: 4.380A pdb=" N ASP J 267 " --> pdb=" O SER J 263 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU J 268 " --> pdb=" O ASP J 264 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 327 through 331 Processing helix chain 'J' and resid 336 through 342 Processing helix chain 'J' and resid 370 through 377 removed outlier: 3.658A pdb=" N GLU J 375 " --> pdb=" O LYS J 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 405 through 416 removed outlier: 3.965A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 450 through 452 No H-bonds generated for 'chain 'J' and resid 450 through 452' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 485 through 489 Processing helix chain 'J' and resid 504 through 514 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 580 Processing helix chain 'J' and resid 581 through 583 No H-bonds generated for 'chain 'J' and resid 581 through 583' Processing helix chain 'J' and resid 588 through 592 Processing helix chain 'J' and resid 597 through 612 Processing helix chain 'J' and resid 613 through 636 removed outlier: 3.681A pdb=" N THR J 617 " --> pdb=" O GLY J 613 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP J 622 " --> pdb=" O VAL J 618 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER J 635 " --> pdb=" O TYR J 631 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (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 Processing helix chain 'J' and resid 768 through 805 removed outlier: 4.018A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA J 779 " --> pdb=" O SER J 775 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR J 790 " --> pdb=" O THR J 786 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) Processing helix chain 'J' and resid 835 through 840 Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 884 through 888 Processing helix chain 'J' and resid 914 through 925 removed outlier: 3.519A 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 1068 through 1073 removed outlier: 4.596A pdb=" N ASP J1073 " --> pdb=" O ALA J1069 " (cutoff:3.500A) 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 1243 removed outlier: 3.595A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU J1243 " --> pdb=" O ASP J1239 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.306A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1318 through 1326 Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1353 removed outlier: 3.772A pdb=" N ASN J1350 " --> pdb=" O GLY J1346 " (cutoff:3.500A) Processing helix chain 'J' and resid 1359 through 1361 No H-bonds generated for 'chain 'J' and resid 1359 through 1361' Processing helix chain 'J' and resid 1362 through 1375 removed outlier: 3.672A pdb=" N HIS J1366 " --> pdb=" O GLY J1362 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 106 Processing helix chain 'L' and resid 112 through 136 removed outlier: 3.593A pdb=" N GLU L 136 " --> pdb=" O CYS L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 153 removed outlier: 3.555A pdb=" N ILE L 141 " --> pdb=" O TYR L 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 215 through 236 removed outlier: 3.626A pdb=" N LYS L 236 " --> pdb=" O ARG L 232 " (cutoff:3.500A) Processing helix chain 'L' and resid 245 through 259 Processing helix chain 'L' and resid 262 through 296 removed outlier: 4.001A pdb=" N GLU L 293 " --> pdb=" O LYS L 289 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLN L 294 " --> pdb=" O LEU L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 307 Processing helix chain 'L' and resid 313 through 319 Processing helix chain 'L' and resid 324 through 330 Processing helix chain 'L' and resid 333 through 352 removed outlier: 3.506A pdb=" N GLU L 348 " --> pdb=" O LEU L 344 " (cutoff:3.500A) Processing helix chain 'L' and resid 354 through 381 removed outlier: 4.444A pdb=" N ASP L 360 " --> pdb=" O GLU L 356 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG L 363 " --> pdb=" O LYS L 359 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG L 364 " --> pdb=" O ASP L 360 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET L 365 " --> pdb=" O ILE L 361 " (cutoff:3.500A) Processing helix chain 'L' and resid 383 through 392 Processing helix chain 'L' and resid 393 through 395 No H-bonds generated for 'chain 'L' and resid 393 through 395' Processing helix chain 'L' and resid 400 through 419 removed outlier: 3.598A pdb=" N ILE L 410 " --> pdb=" O GLN L 406 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY L 411 " --> pdb=" O GLU L 407 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS L 418 " --> pdb=" O LYS L 414 " (cutoff:3.500A) Processing helix chain 'L' and resid 420 through 424 Processing helix chain 'L' and resid 426 through 447 removed outlier: 3.850A pdb=" N TYR L 430 " --> pdb=" O LYS L 426 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N TRP L 433 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TRP L 434 " --> pdb=" O TYR L 430 " (cutoff:3.500A) Processing helix chain 'L' and resid 453 through 475 removed outlier: 3.650A pdb=" N GLN L 472 " --> pdb=" O ARG L 468 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU L 473 " --> pdb=" O GLN L 469 " (cutoff:3.500A) Processing helix chain 'L' and resid 479 through 488 removed outlier: 3.623A pdb=" N GLU L 485 " --> pdb=" O GLU L 481 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG L 486 " --> pdb=" O GLU L 482 " (cutoff:3.500A) Processing helix chain 'L' and resid 490 through 500 Processing helix chain 'L' and resid 518 through 523 removed outlier: 3.621A pdb=" N ILE L 523 " --> pdb=" O GLY L 520 " (cutoff:3.500A) Processing helix chain 'L' and resid 530 through 550 Processing helix chain 'L' and resid 554 through 564 Processing helix chain 'L' and resid 574 through 581 Processing helix chain 'L' and resid 583 through 600 removed outlier: 3.971A pdb=" N HIS L 600 " --> pdb=" O ARG L 596 " (cutoff:3.500A) Processing helix chain 'L' and resid 606 through 611 removed outlier: 3.509A pdb=" N PHE L 610 " --> pdb=" O VAL L 606 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU L 611 " --> pdb=" O LEU L 607 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 606 through 611' Processing sheet with id=AA1, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.672A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 59 through 60 removed outlier: 6.736A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 136 through 138 Processing sheet with id=AA4, first strand: chain 'I' and resid 451 through 454 removed outlier: 3.535A pdb=" N SER I 147 " --> pdb=" O ARG I 529 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 154 through 159 removed outlier: 5.260A pdb=" N TYR I 172 " --> pdb=" O PHE I 188 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 227 through 231 Processing sheet with id=AA7, first strand: chain 'I' and resid 238 through 240 Processing sheet with id=AA8, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.534A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 301 through 302 Processing sheet with id=AB1, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.427A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR I 595 " --> pdb=" O THR I 600 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N THR I 600 " --> pdb=" O THR I 595 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AB3, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.515A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.174A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AB6, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AB7, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.103A pdb=" N ILE I 816 " --> pdb=" O LYS I1078 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ASN I1080 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL I 818 " --> pdb=" O ASN I1080 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.662A pdb=" N LYS I1048 " --> pdb=" O SER I 840 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.798A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 887 through 889 Processing sheet with id=AC2, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 6.526A pdb=" N CYS J 366 " --> pdb=" O VAL J 440 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ILE J 442 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU J 368 " --> pdb=" O ILE J 442 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AC4, first strand: chain 'I' and resid 1335 through 1340 Processing sheet with id=AC5, first strand: chain 'G' and resid 12 through 18 removed outlier: 5.180A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LYS G 200 " --> pdb=" O VAL G 187 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL G 187 " --> pdb=" O LYS G 200 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL G 202 " --> pdb=" O TYR G 185 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TYR G 185 " --> pdb=" O VAL G 202 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLU G 204 " --> pdb=" O ILE G 183 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ILE G 183 " --> pdb=" O GLU G 204 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLU G 206 " --> pdb=" O GLU G 181 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 97 through 105 removed outlier: 7.522A pdb=" N SER G 141 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ILE G 61 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AC8, first strand: chain 'G' and resid 108 through 111 removed outlier: 6.590A pdb=" N GLY G 108 " --> pdb=" O HIS G 132 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N HIS G 132 " --> pdb=" O GLY G 108 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL G 110 " --> pdb=" O ILE G 130 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 152 through 153 Processing sheet with id=AD1, first strand: chain 'H' and resid 13 through 20 removed outlier: 6.303A pdb=" N HIS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N THR H 196 " --> pdb=" O ARG H 191 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ARG H 191 " --> pdb=" O THR H 196 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU H 198 " --> pdb=" O ALA H 189 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA H 189 " --> pdb=" O LEU H 198 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LYS H 200 " --> pdb=" O VAL H 187 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL H 187 " --> pdb=" O LYS H 200 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL H 202 " --> pdb=" O TYR H 185 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N TYR H 185 " --> pdb=" O VAL H 202 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLU H 204 " --> pdb=" O ILE H 183 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE H 183 " --> pdb=" O GLU H 204 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLU H 206 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 97 through 105 removed outlier: 6.567A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 90 through 92 Processing sheet with id=AD4, first strand: chain 'H' and resid 108 through 111 removed outlier: 6.441A pdb=" N GLY H 108 " --> pdb=" O HIS H 132 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N HIS H 132 " --> pdb=" O GLY H 108 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL H 110 " --> pdb=" O ILE H 130 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AD6, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.569A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 10.078A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.305A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 159 through 160 removed outlier: 6.983A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 252 through 254 removed outlier: 6.681A pdb=" N PHE J 260 " --> pdb=" O ILE L 505 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AE1, first strand: chain 'J' and resid 703 through 707 Processing sheet with id=AE2, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AE3, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE4, first strand: chain 'J' and resid 825 through 827 removed outlier: 7.031A pdb=" N GLU J 827 " --> pdb=" O VAL J 831 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL J 831 " --> pdb=" O GLU J 827 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 848 through 849 removed outlier: 6.831A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 949 through 951 removed outlier: 6.598A pdb=" N ILE J 950 " --> pdb=" O VAL J1017 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 991 through 997 removed outlier: 6.481A pdb=" N LEU J 984 " --> pdb=" O LYS J 992 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N SER J 994 " --> pdb=" O LEU J 982 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU J 982 " --> pdb=" O SER J 994 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LYS J 996 " --> pdb=" O THR J 980 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N THR J 980 " --> pdb=" O LYS J 996 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 1026 through 1028 removed outlier: 6.700A pdb=" N VAL J1027 " --> pdb=" O LEU J1121 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 1098 through 1100 Processing sheet with id=AF1, first strand: chain 'J' and resid 1186 through 1191 Processing sheet with id=AF2, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.639A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1316 hydrogen bonds defined for protein. 3711 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 66 hydrogen bonds 132 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 7.96 Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9606 1.34 - 1.45: 3852 1.45 - 1.57: 17157 1.57 - 1.69: 142 1.69 - 1.81: 227 Bond restraints: 30984 Sorted by residual: bond pdb=" O POP I1401 " pdb=" P2 POP I1401 " ideal model delta sigma weight residual 1.661 1.611 0.050 2.00e-02 2.50e+03 6.32e+00 bond pdb=" O POP I1401 " pdb=" P1 POP I1401 " ideal model delta sigma weight residual 1.660 1.610 0.050 2.00e-02 2.50e+03 6.26e+00 bond pdb=" CA GLY J 828 " pdb=" C GLY J 828 " ideal model delta sigma weight residual 1.514 1.531 -0.016 1.41e-02 5.03e+03 1.32e+00 bond pdb=" O2 POP I1401 " pdb=" P1 POP I1401 " ideal model delta sigma weight residual 1.531 1.509 0.022 2.00e-02 2.50e+03 1.19e+00 bond pdb=" O5 POP I1401 " pdb=" P2 POP I1401 " ideal model delta sigma weight residual 1.530 1.509 0.021 2.00e-02 2.50e+03 1.08e+00 ... (remaining 30979 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.69: 42094 3.69 - 7.37: 32 7.37 - 11.06: 1 11.06 - 14.75: 0 14.75 - 18.44: 1 Bond angle restraints: 42128 Sorted by residual: angle pdb=" P1 POP I1401 " pdb=" O POP I1401 " pdb=" P2 POP I1401 " ideal model delta sigma weight residual 139.66 121.22 18.44 3.00e+00 1.11e-01 3.78e+01 angle pdb=" CA GLU J1110 " pdb=" C GLU J1110 " pdb=" N ASP J1111 " ideal model delta sigma weight residual 116.25 120.32 -4.07 1.30e+00 5.92e-01 9.81e+00 angle pdb=" C ILE J 737 " pdb=" N ARG J 738 " pdb=" CA ARG J 738 " ideal model delta sigma weight residual 121.54 127.36 -5.82 1.91e+00 2.74e-01 9.29e+00 angle pdb=" C SER I1165 " pdb=" N ASP I1166 " pdb=" CA ASP I1166 " ideal model delta sigma weight residual 121.54 126.75 -5.21 1.91e+00 2.74e-01 7.43e+00 angle pdb=" CA GLU J1110 " pdb=" C GLU J1110 " pdb=" O GLU J1110 " ideal model delta sigma weight residual 121.55 118.20 3.35 1.26e+00 6.30e-01 7.08e+00 ... (remaining 42123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 17391 17.99 - 35.98: 1089 35.98 - 53.97: 352 53.97 - 71.96: 77 71.96 - 89.95: 15 Dihedral angle restraints: 18924 sinusoidal: 8345 harmonic: 10579 Sorted by residual: dihedral pdb=" CA GLN J 736 " pdb=" C GLN J 736 " pdb=" N ILE J 737 " pdb=" CA ILE J 737 " ideal model delta harmonic sigma weight residual 180.00 153.06 26.94 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA PHE I1164 " pdb=" C PHE I1164 " pdb=" N SER I1165 " pdb=" CA SER I1165 " ideal model delta harmonic sigma weight residual -180.00 -161.27 -18.73 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA TYR J 75 " pdb=" C TYR J 75 " pdb=" N LYS J 76 " pdb=" CA LYS J 76 " ideal model delta harmonic sigma weight residual -180.00 -162.79 -17.21 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 18921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2989 0.029 - 0.057: 1148 0.057 - 0.086: 381 0.086 - 0.114: 239 0.114 - 0.143: 54 Chirality restraints: 4811 Sorted by residual: chirality pdb=" CA ILE J1090 " pdb=" N ILE J1090 " pdb=" C ILE J1090 " pdb=" CB ILE J1090 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" CA VAL J 440 " pdb=" N VAL J 440 " pdb=" C VAL J 440 " pdb=" CB VAL J 440 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CA GLU I 813 " pdb=" N GLU I 813 " pdb=" C GLU I 813 " pdb=" CB GLU I 813 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.88e-01 ... (remaining 4808 not shown) Planarity restraints: 5251 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR I 589 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.48e+00 pdb=" N PRO I 590 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO I 590 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO I 590 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL J 858 " -0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO J 859 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO J 859 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO J 859 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU J 245 " 0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO J 246 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO J 246 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO J 246 " 0.022 5.00e-02 4.00e+02 ... (remaining 5248 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 567 2.68 - 3.23: 27778 3.23 - 3.79: 46727 3.79 - 4.34: 67519 4.34 - 4.90: 109123 Nonbonded interactions: 251714 Sorted by model distance: nonbonded pdb=" O3' A R 5 " pdb="MG MG J1501 " model vdw 2.124 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1501 " model vdw 2.164 2.170 nonbonded pdb="MG MG J1501 " pdb=" O HOH J1617 " model vdw 2.170 2.170 nonbonded pdb=" OG SER J 977 " pdb=" OG1 THR J 980 " model vdw 2.213 3.040 nonbonded pdb=" OG1 THR I 843 " pdb=" O GLY I 846 " model vdw 2.235 3.040 ... (remaining 251709 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'G' and (resid 4 through 158 or resid 167 through 233)) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.730 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: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 35.450 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 30992 Z= 0.121 Angle : 0.496 18.436 42140 Z= 0.274 Chirality : 0.040 0.143 4811 Planarity : 0.004 0.047 5251 Dihedral : 13.626 89.946 12104 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.59 % Allowed : 5.85 % Favored : 92.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.14), residues: 3651 helix: 1.75 (0.14), residues: 1417 sheet: 0.61 (0.24), residues: 466 loop : -0.44 (0.14), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 798 TYR 0.012 0.001 TYR I1281 PHE 0.012 0.001 PHE I 514 TRP 0.007 0.001 TRP L 326 HIS 0.005 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (30984) covalent geometry : angle 0.49564 / 0.27 (42128) hydrogen bonds : bond 0.12695 / 8.64 ( 1380) hydrogen bonds : angle 5.30997 / 3.80 ( 3843) metal coordination : bond 0.05043 / 2.42 ( 8) metal coordination : angle 0.06170 / 0.03 ( 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 431 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 381 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 253 PHE cc_start: 0.8579 (p90) cc_final: 0.8256 (p90) REVERT: I 332 ARG cc_start: 0.8130 (mtp85) cc_final: 0.7915 (ttm-80) REVERT: I 357 ASN cc_start: 0.8812 (p0) cc_final: 0.8588 (p0) REVERT: I 481 LEU cc_start: 0.7943 (pp) cc_final: 0.7107 (pp) REVERT: I 600 THR cc_start: 0.8844 (OUTLIER) cc_final: 0.8611 (p) REVERT: I 899 GLU cc_start: 0.8956 (mt-10) cc_final: 0.8585 (mt-10) REVERT: I 1025 PHE cc_start: 0.8115 (t80) cc_final: 0.7703 (t80) REVERT: J 1040 MET cc_start: 0.5838 (mmm) cc_final: 0.5542 (mmt) REVERT: J 1162 ILE cc_start: 0.8387 (tp) cc_final: 0.8004 (pp) REVERT: L 274 ARG cc_start: 0.9214 (ttm110) cc_final: 0.9004 (ttp-110) outliers start: 50 outliers final: 14 residues processed: 421 average time/residue: 0.9532 time to fit residues: 453.7806 Evaluate side-chains 243 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 228 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 470 ARG Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 940 GLU Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 961 SER Chi-restraints excluded: chain J residue 1316 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 518 ASN I 573 ASN G 127 GLN H 147 GLN J 430 HIS J 560 ASN L 338 HIS L 357 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.108681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.063312 restraints weight = 61198.661| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.64 r_work: 0.2757 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 30992 Z= 0.246 Angle : 0.588 10.936 42140 Z= 0.312 Chirality : 0.044 0.169 4811 Planarity : 0.005 0.066 5251 Dihedral : 13.068 132.629 4854 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.03 % Allowed : 10.81 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.14), residues: 3651 helix: 1.82 (0.14), residues: 1446 sheet: 0.64 (0.24), residues: 470 loop : -0.40 (0.14), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 978 TYR 0.016 0.001 TYR I1281 PHE 0.013 0.001 PHE I 514 TRP 0.010 0.001 TRP L 326 HIS 0.009 0.001 HIS I1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.25 (30984) covalent geometry : angle 0.58668 / 0.31 (42128) hydrogen bonds : bond 0.05278 / 3.52 ( 1380) hydrogen bonds : angle 4.46031 / 3.15 ( 3843) metal coordination : bond 0.01060 / 0.52 ( 8) metal coordination : angle 2.44230 / 1.20 ( 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 309 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 245 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 62 TYR cc_start: 0.8650 (OUTLIER) cc_final: 0.8433 (m-80) REVERT: I 158 ASP cc_start: 0.8389 (t0) cc_final: 0.8124 (t0) REVERT: I 161 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8956 (mtpt) REVERT: I 253 PHE cc_start: 0.8676 (p90) cc_final: 0.8378 (p90) REVERT: I 332 ARG cc_start: 0.8663 (mtp85) cc_final: 0.8331 (ttm-80) REVERT: I 477 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8502 (tm-30) REVERT: I 478 ARG cc_start: 0.8559 (tpp80) cc_final: 0.8025 (tpt90) REVERT: I 481 LEU cc_start: 0.7716 (pp) cc_final: 0.7435 (pp) REVERT: I 600 THR cc_start: 0.8950 (OUTLIER) cc_final: 0.8345 (p) REVERT: I 779 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.8718 (ttt-90) REVERT: I 813 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8611 (tp30) REVERT: I 899 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8425 (mt-10) REVERT: I 1025 PHE cc_start: 0.8724 (t80) cc_final: 0.8510 (t80) REVERT: I 1329 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8779 (mt-10) REVERT: K 3 ARG cc_start: 0.8697 (mtt90) cc_final: 0.8286 (mtt180) REVERT: K 41 GLU cc_start: 0.8590 (pt0) cc_final: 0.8348 (tt0) REVERT: J 133 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.7305 (mpt90) REVERT: J 499 ILE cc_start: 0.9374 (OUTLIER) cc_final: 0.9059 (tt) REVERT: J 1040 MET cc_start: 0.6696 (mmm) cc_final: 0.6312 (mmt) REVERT: J 1152 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7987 (mm-30) REVERT: J 1162 ILE cc_start: 0.8599 (tp) cc_final: 0.8293 (pp) REVERT: L 144 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8410 (pp) REVERT: L 489 MET cc_start: 0.8231 (ttm) cc_final: 0.8005 (ttp) REVERT: L 603 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7553 (mpp80) outliers start: 64 outliers final: 26 residues processed: 293 average time/residue: 0.8420 time to fit residues: 283.8941 Evaluate side-chains 253 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 216 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 161 LYS Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 413 GLU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 626 GLU Chi-restraints excluded: chain I residue 779 ARG Chi-restraints excluded: chain I residue 813 GLU Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain H residue 25 LYS Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 499 ILE Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 822 MET Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 961 SER Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1152 GLU Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 603 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 300 optimal weight: 20.0000 chunk 359 optimal weight: 0.9980 chunk 221 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 307 optimal weight: 2.9990 chunk 318 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 200 optimal weight: 0.9980 chunk 249 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 317 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 677 ASN G 127 GLN G 137 ASN ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 338 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.110513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.065465 restraints weight = 61054.843| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.64 r_work: 0.2795 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 30992 Z= 0.114 Angle : 0.500 9.777 42140 Z= 0.265 Chirality : 0.041 0.156 4811 Planarity : 0.004 0.055 5251 Dihedral : 12.805 84.324 4843 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.72 % Allowed : 11.57 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.14), residues: 3651 helix: 2.13 (0.14), residues: 1443 sheet: 0.84 (0.24), residues: 458 loop : -0.24 (0.14), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 235 TYR 0.010 0.001 TYR I1281 PHE 0.012 0.001 PHE I 405 TRP 0.011 0.001 TRP L 326 HIS 0.006 0.001 HIS I 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (30984) covalent geometry : angle 0.49880 / 0.26 (42128) hydrogen bonds : bond 0.03804 / 2.54 ( 1380) hydrogen bonds : angle 4.16339 / 2.95 ( 3843) metal coordination : bond 0.00385 / 0.21 ( 8) metal coordination : angle 1.95311 / 1.00 ( 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 298 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 244 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 62 TYR cc_start: 0.8693 (OUTLIER) cc_final: 0.8459 (m-80) REVERT: I 158 ASP cc_start: 0.8353 (t0) cc_final: 0.8077 (t0) REVERT: I 253 PHE cc_start: 0.8615 (p90) cc_final: 0.8253 (p90) REVERT: I 315 MET cc_start: 0.8687 (ttm) cc_final: 0.8091 (mtm) REVERT: I 477 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8547 (tm-30) REVERT: I 600 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8355 (p) REVERT: I 813 GLU cc_start: 0.8808 (tt0) cc_final: 0.8566 (tp30) REVERT: I 856 ASN cc_start: 0.8007 (t0) cc_final: 0.7803 (t0) REVERT: I 899 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8377 (mt-10) REVERT: I 903 ARG cc_start: 0.8851 (tmm-80) cc_final: 0.8589 (mmm-85) REVERT: I 908 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8113 (mp0) REVERT: I 1032 LYS cc_start: 0.9383 (tppp) cc_final: 0.9160 (tppp) REVERT: I 1329 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8776 (mt-10) REVERT: I 1340 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7558 (mt-10) REVERT: H 95 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8426 (ptmt) REVERT: J 133 ARG cc_start: 0.7472 (mpt180) cc_final: 0.7266 (mpt90) REVERT: J 229 GLN cc_start: 0.8976 (mm-40) cc_final: 0.8729 (mm-40) REVERT: J 1040 MET cc_start: 0.6788 (mmm) cc_final: 0.6407 (mmt) REVERT: J 1152 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7992 (tp30) REVERT: J 1162 ILE cc_start: 0.8546 (tp) cc_final: 0.8180 (pp) REVERT: J 1334 GLU cc_start: 0.8340 (tp30) cc_final: 0.7978 (tp30) REVERT: L 144 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8411 (pp) REVERT: L 273 MET cc_start: 0.8984 (tpt) cc_final: 0.8447 (tpt) REVERT: L 277 MET cc_start: 0.9067 (tpt) cc_final: 0.8563 (tmm) REVERT: L 489 MET cc_start: 0.8235 (ttm) cc_final: 0.7841 (ttp) REVERT: L 603 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7222 (mtm-85) outliers start: 54 outliers final: 19 residues processed: 288 average time/residue: 0.8392 time to fit residues: 278.4282 Evaluate side-chains 257 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 229 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 470 ARG Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 626 GLU Chi-restraints excluded: chain I residue 908 GLU Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain I residue 1340 GLU Chi-restraints excluded: chain H residue 25 LYS Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 822 MET Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 1152 GLU Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1247 LYS Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 357 GLN Chi-restraints excluded: chain L residue 603 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 1 optimal weight: 5.9990 chunk 250 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 322 optimal weight: 5.9990 chunk 140 optimal weight: 0.9980 chunk 325 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 361 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 127 GLN G 137 ASN ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 430 HIS L 338 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.108081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.062870 restraints weight = 60961.487| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.57 r_work: 0.2762 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 30992 Z= 0.241 Angle : 0.563 9.232 42140 Z= 0.297 Chirality : 0.043 0.168 4811 Planarity : 0.004 0.060 5251 Dihedral : 12.954 81.605 4837 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.13 % Allowed : 12.27 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.14), residues: 3651 helix: 1.99 (0.14), residues: 1455 sheet: 0.66 (0.24), residues: 457 loop : -0.34 (0.14), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 235 TYR 0.015 0.001 TYR I1281 PHE 0.016 0.001 PHE I1025 TRP 0.008 0.001 TRP L 326 HIS 0.006 0.001 HIS I1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.24 (30984) covalent geometry : angle 0.56116 / 0.30 (42128) hydrogen bonds : bond 0.05152 / 3.43 ( 1380) hydrogen bonds : angle 4.27798 / 3.02 ( 3843) metal coordination : bond 0.00910 / 0.45 ( 8) metal coordination : angle 2.42046 / 1.22 ( 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 294 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 227 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 62 TYR cc_start: 0.8749 (OUTLIER) cc_final: 0.8396 (m-80) REVERT: I 161 LYS cc_start: 0.9275 (OUTLIER) cc_final: 0.9011 (mtpt) REVERT: I 253 PHE cc_start: 0.8676 (p90) cc_final: 0.8253 (p90) REVERT: I 315 MET cc_start: 0.8787 (ttm) cc_final: 0.8207 (mtp) REVERT: I 477 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8612 (tm-30) REVERT: I 600 THR cc_start: 0.9046 (OUTLIER) cc_final: 0.8525 (p) REVERT: I 813 GLU cc_start: 0.9013 (OUTLIER) cc_final: 0.8794 (tp30) REVERT: I 856 ASN cc_start: 0.8293 (t0) cc_final: 0.8090 (t0) REVERT: I 899 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8535 (mt-10) REVERT: I 903 ARG cc_start: 0.8926 (tmm-80) cc_final: 0.8568 (ttm110) REVERT: I 908 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8308 (OUTLIER) REVERT: I 1032 LYS cc_start: 0.9459 (tppp) cc_final: 0.9230 (tppp) REVERT: I 1034 ARG cc_start: 0.8977 (ptp-110) cc_final: 0.8685 (ptp-110) REVERT: I 1329 GLU cc_start: 0.9155 (OUTLIER) cc_final: 0.8939 (mt-10) REVERT: H 95 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8416 (ptmt) REVERT: J 183 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8873 (mm-30) REVERT: J 204 GLU cc_start: 0.8719 (tp30) cc_final: 0.8518 (tp30) REVERT: J 229 GLN cc_start: 0.9083 (mm-40) cc_final: 0.8822 (mm-40) REVERT: J 499 ILE cc_start: 0.9413 (OUTLIER) cc_final: 0.9099 (tt) REVERT: J 1040 MET cc_start: 0.6870 (mmm) cc_final: 0.6512 (mmt) REVERT: J 1152 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8082 (tp30) REVERT: J 1162 ILE cc_start: 0.8606 (tp) cc_final: 0.8254 (pp) REVERT: J 1196 LEU cc_start: 0.9360 (mp) cc_final: 0.8757 (tt) REVERT: J 1334 GLU cc_start: 0.8577 (tp30) cc_final: 0.8235 (tp30) REVERT: L 144 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8443 (pp) REVERT: L 273 MET cc_start: 0.8603 (tpt) cc_final: 0.8208 (tpt) REVERT: L 277 MET cc_start: 0.9066 (tpt) cc_final: 0.8671 (tmm) REVERT: L 489 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.7905 (ttp) REVERT: L 603 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7202 (mtm-85) outliers start: 67 outliers final: 29 residues processed: 278 average time/residue: 0.8141 time to fit residues: 260.9616 Evaluate side-chains 259 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 219 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 161 LYS Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 413 GLU Chi-restraints excluded: chain I residue 470 ARG Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 541 GLU Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 788 SER Chi-restraints excluded: chain I residue 813 GLU Chi-restraints excluded: chain I residue 908 GLU Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain H residue 25 LYS Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 499 ILE Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1152 GLU Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1247 LYS Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 489 MET Chi-restraints excluded: chain L residue 603 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 28 optimal weight: 9.9990 chunk 220 optimal weight: 1.9990 chunk 315 optimal weight: 4.9990 chunk 337 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 320 optimal weight: 6.9990 chunk 279 optimal weight: 0.0870 chunk 302 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 628 HIS I 922 ASN G 127 GLN G 137 ASN ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 430 HIS L 265 GLN L 338 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.108304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.063030 restraints weight = 61550.583| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.64 r_work: 0.2761 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 30992 Z= 0.200 Angle : 0.542 11.867 42140 Z= 0.286 Chirality : 0.042 0.163 4811 Planarity : 0.004 0.064 5251 Dihedral : 12.983 81.917 4834 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.10 % Allowed : 12.68 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.14), residues: 3651 helix: 2.08 (0.14), residues: 1449 sheet: 0.65 (0.24), residues: 467 loop : -0.32 (0.14), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 235 TYR 0.013 0.001 TYR I1281 PHE 0.011 0.001 PHE I1025 TRP 0.010 0.001 TRP L 326 HIS 0.005 0.001 HIS L 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.20 (30984) covalent geometry : angle 0.54108 / 0.29 (42128) hydrogen bonds : bond 0.04625 / 3.08 ( 1380) hydrogen bonds : angle 4.18810 / 2.96 ( 3843) metal coordination : bond 0.00746 / 0.37 ( 8) metal coordination : angle 2.16840 / 1.11 ( 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 295 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 229 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 62 TYR cc_start: 0.8726 (OUTLIER) cc_final: 0.8334 (m-80) REVERT: I 161 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.8999 (mtpt) REVERT: I 253 PHE cc_start: 0.8634 (p90) cc_final: 0.8132 (p90) REVERT: I 315 MET cc_start: 0.8763 (ttm) cc_final: 0.8164 (mtp) REVERT: I 332 ARG cc_start: 0.8699 (mtp85) cc_final: 0.8405 (mtp85) REVERT: I 371 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7901 (mtt180) REVERT: I 477 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8585 (tm-30) REVERT: I 478 ARG cc_start: 0.8628 (tpp80) cc_final: 0.8132 (tpt90) REVERT: I 600 THR cc_start: 0.8993 (OUTLIER) cc_final: 0.8491 (p) REVERT: I 813 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8655 (tp30) REVERT: I 899 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8487 (mt-10) REVERT: I 903 ARG cc_start: 0.8893 (tmm-80) cc_final: 0.8585 (ttm110) REVERT: I 908 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8367 (mp0) REVERT: I 1032 LYS cc_start: 0.9458 (tppp) cc_final: 0.9209 (tppp) REVERT: I 1219 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8460 (mp0) REVERT: I 1329 GLU cc_start: 0.9056 (OUTLIER) cc_final: 0.8826 (mt-10) REVERT: H 95 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8505 (ptmt) REVERT: J 204 GLU cc_start: 0.8727 (tp30) cc_final: 0.8521 (tp30) REVERT: J 229 GLN cc_start: 0.9023 (mm-40) cc_final: 0.8737 (mm-40) REVERT: J 1040 MET cc_start: 0.6781 (mmm) cc_final: 0.6429 (mmt) REVERT: J 1095 MET cc_start: 0.3250 (tmt) cc_final: 0.2817 (tmm) REVERT: J 1152 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7954 (tp30) REVERT: J 1162 ILE cc_start: 0.8549 (tp) cc_final: 0.8187 (pp) REVERT: J 1196 LEU cc_start: 0.9349 (mp) cc_final: 0.8719 (tt) REVERT: J 1265 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.8235 (p) REVERT: L 144 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8448 (pp) REVERT: L 277 MET cc_start: 0.9052 (tpt) cc_final: 0.8680 (tmm) REVERT: L 489 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.7823 (ttp) REVERT: L 551 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7598 (tp) REVERT: L 603 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7272 (mtm-85) outliers start: 66 outliers final: 29 residues processed: 277 average time/residue: 0.8438 time to fit residues: 269.0203 Evaluate side-chains 262 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 219 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 7 GLU Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 161 LYS Chi-restraints excluded: chain I residue 371 ARG Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 470 ARG Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 541 GLU Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 788 SER Chi-restraints excluded: chain I residue 813 GLU Chi-restraints excluded: chain I residue 908 GLU Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain H residue 25 LYS Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1152 GLU Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1247 LYS Chi-restraints excluded: chain J residue 1265 THR Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 357 GLN Chi-restraints excluded: chain L residue 489 MET Chi-restraints excluded: chain L residue 551 LEU Chi-restraints excluded: chain L residue 603 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 341 optimal weight: 20.0000 chunk 84 optimal weight: 0.7980 chunk 148 optimal weight: 0.9980 chunk 177 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 287 optimal weight: 6.9990 chunk 351 optimal weight: 4.9990 chunk 340 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 273 HIS I 922 ASN G 127 GLN ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 338 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.108493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.063347 restraints weight = 61148.396| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.64 r_work: 0.2769 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 30992 Z= 0.171 Angle : 0.529 11.804 42140 Z= 0.279 Chirality : 0.042 0.156 4811 Planarity : 0.004 0.067 5251 Dihedral : 12.965 82.506 4833 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.88 % Allowed : 13.25 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.14), residues: 3651 helix: 2.13 (0.14), residues: 1449 sheet: 0.69 (0.24), residues: 467 loop : -0.30 (0.14), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG G 235 TYR 0.011 0.001 TYR I1281 PHE 0.019 0.001 PHE I1025 TRP 0.010 0.001 TRP L 326 HIS 0.006 0.001 HIS L 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 (30984) covalent geometry : angle 0.52834 / 0.28 (42128) hydrogen bonds : bond 0.04360 / 2.91 ( 1380) hydrogen bonds : angle 4.11349 / 2.91 ( 3843) metal coordination : bond 0.00618 / 0.31 ( 8) metal coordination : angle 2.03692 / 1.04 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 232 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 62 TYR cc_start: 0.8754 (OUTLIER) cc_final: 0.8329 (m-80) REVERT: I 253 PHE cc_start: 0.8657 (p90) cc_final: 0.8123 (p90) REVERT: I 315 MET cc_start: 0.8778 (ttm) cc_final: 0.8199 (mtp) REVERT: I 332 ARG cc_start: 0.8691 (mtp85) cc_final: 0.8306 (ttm-80) REVERT: I 371 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7899 (mtt180) REVERT: I 477 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8586 (tm-30) REVERT: I 600 THR cc_start: 0.8979 (OUTLIER) cc_final: 0.8470 (p) REVERT: I 813 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8648 (tp30) REVERT: I 899 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8366 (mt-10) REVERT: I 903 ARG cc_start: 0.8928 (tmm-80) cc_final: 0.8670 (mmm-85) REVERT: I 908 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8313 (mp0) REVERT: I 1025 PHE cc_start: 0.8668 (t80) cc_final: 0.8369 (t80) REVERT: I 1032 LYS cc_start: 0.9471 (tppp) cc_final: 0.9220 (tppp) REVERT: I 1034 ARG cc_start: 0.8906 (ptp-110) cc_final: 0.8676 (ptp-110) REVERT: I 1219 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8447 (mp0) REVERT: I 1329 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8806 (mt-10) REVERT: H 95 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8509 (ptmt) REVERT: J 204 GLU cc_start: 0.8756 (tp30) cc_final: 0.8522 (tp30) REVERT: J 229 GLN cc_start: 0.9045 (mm-40) cc_final: 0.8721 (mm-40) REVERT: J 1040 MET cc_start: 0.6943 (mmm) cc_final: 0.6611 (mmt) REVERT: J 1095 MET cc_start: 0.3295 (tmt) cc_final: 0.2844 (tmm) REVERT: J 1152 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7909 (tp30) REVERT: J 1162 ILE cc_start: 0.8520 (tp) cc_final: 0.8133 (pp) REVERT: J 1196 LEU cc_start: 0.9346 (mp) cc_final: 0.8704 (tt) REVERT: J 1249 ASN cc_start: 0.9141 (OUTLIER) cc_final: 0.8892 (t0) REVERT: J 1265 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8236 (p) REVERT: J 1334 GLU cc_start: 0.8390 (tp30) cc_final: 0.8032 (tp30) REVERT: L 144 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8437 (pp) REVERT: L 273 MET cc_start: 0.8551 (tpt) cc_final: 0.8318 (tpt) REVERT: L 277 MET cc_start: 0.8998 (tpt) cc_final: 0.8682 (tmm) REVERT: L 489 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.8043 (ttm) REVERT: L 551 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7564 (tp) REVERT: L 603 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7328 (mtm-85) outliers start: 59 outliers final: 29 residues processed: 276 average time/residue: 0.8343 time to fit residues: 264.8420 Evaluate side-chains 261 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 218 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 7 GLU Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 371 ARG Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 413 GLU Chi-restraints excluded: chain I residue 470 ARG Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 541 GLU Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 788 SER Chi-restraints excluded: chain I residue 813 GLU Chi-restraints excluded: chain I residue 908 GLU Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain H residue 25 LYS Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1152 GLU Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1247 LYS Chi-restraints excluded: chain J residue 1249 ASN Chi-restraints excluded: chain J residue 1265 THR Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 489 MET Chi-restraints excluded: chain L residue 551 LEU Chi-restraints excluded: chain L residue 603 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 97 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 32 optimal weight: 8.9990 chunk 196 optimal weight: 2.9990 chunk 223 optimal weight: 0.8980 chunk 351 optimal weight: 5.9990 chunk 347 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 25 optimal weight: 0.4980 chunk 282 optimal weight: 10.0000 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 922 ASN G 137 ASN H 66 HIS L 338 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.108612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.063469 restraints weight = 61414.090| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.64 r_work: 0.2774 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 30992 Z= 0.166 Angle : 0.538 11.408 42140 Z= 0.282 Chirality : 0.042 0.166 4811 Planarity : 0.004 0.074 5251 Dihedral : 12.946 82.749 4833 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.94 % Allowed : 13.54 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.14), residues: 3651 helix: 2.17 (0.14), residues: 1447 sheet: 0.79 (0.24), residues: 459 loop : -0.29 (0.14), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG G 235 TYR 0.012 0.001 TYR I1281 PHE 0.010 0.001 PHE I1025 TRP 0.010 0.001 TRP L 326 HIS 0.006 0.001 HIS L 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (30984) covalent geometry : angle 0.53681 / 0.28 (42128) hydrogen bonds : bond 0.04299 / 2.87 ( 1380) hydrogen bonds : angle 4.08131 / 2.89 ( 3843) metal coordination : bond 0.00594 / 0.30 ( 8) metal coordination : angle 2.01117 / 1.03 ( 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 287 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 226 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 62 TYR cc_start: 0.8760 (OUTLIER) cc_final: 0.8330 (m-80) REVERT: I 145 ILE cc_start: 0.9425 (OUTLIER) cc_final: 0.9084 (mm) REVERT: I 253 PHE cc_start: 0.8636 (p90) cc_final: 0.8010 (p90) REVERT: I 315 MET cc_start: 0.8772 (ttm) cc_final: 0.8183 (mtp) REVERT: I 332 ARG cc_start: 0.8713 (mtp85) cc_final: 0.8323 (ttm-80) REVERT: I 371 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7909 (mtt180) REVERT: I 477 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8593 (tm-30) REVERT: I 478 ARG cc_start: 0.8622 (tpp80) cc_final: 0.8072 (tpt90) REVERT: I 600 THR cc_start: 0.8985 (OUTLIER) cc_final: 0.8485 (p) REVERT: I 813 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8635 (tp30) REVERT: I 899 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8357 (mt-10) REVERT: I 903 ARG cc_start: 0.8961 (tmm-80) cc_final: 0.8668 (mmm-85) REVERT: I 908 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8331 (mp0) REVERT: I 1025 PHE cc_start: 0.8623 (t80) cc_final: 0.8365 (t80) REVERT: I 1032 LYS cc_start: 0.9467 (tppp) cc_final: 0.9212 (tppp) REVERT: I 1219 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8460 (mp0) REVERT: I 1329 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8804 (mt-10) REVERT: H 95 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8488 (ptmt) REVERT: J 204 GLU cc_start: 0.8733 (tp30) cc_final: 0.8498 (tp30) REVERT: J 229 GLN cc_start: 0.9042 (mm-40) cc_final: 0.8725 (mm-40) REVERT: J 1040 MET cc_start: 0.6801 (mmm) cc_final: 0.6498 (mmt) REVERT: J 1152 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7903 (tp30) REVERT: J 1162 ILE cc_start: 0.8494 (tp) cc_final: 0.8099 (pp) REVERT: J 1196 LEU cc_start: 0.9348 (mp) cc_final: 0.8751 (tt) REVERT: J 1249 ASN cc_start: 0.9135 (OUTLIER) cc_final: 0.8885 (t0) REVERT: J 1265 THR cc_start: 0.8602 (OUTLIER) cc_final: 0.8231 (p) REVERT: J 1334 GLU cc_start: 0.8385 (tp30) cc_final: 0.8027 (tp30) REVERT: L 264 LYS cc_start: 0.9367 (OUTLIER) cc_final: 0.9090 (pptt) REVERT: L 277 MET cc_start: 0.9031 (tpt) cc_final: 0.8668 (tmm) REVERT: L 551 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7524 (tp) REVERT: L 603 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7304 (mtm-85) outliers start: 61 outliers final: 34 residues processed: 266 average time/residue: 0.8442 time to fit residues: 258.4202 Evaluate side-chains 270 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 222 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 7 GLU Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 371 ARG Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 413 GLU Chi-restraints excluded: chain I residue 470 ARG Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 541 GLU Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 788 SER Chi-restraints excluded: chain I residue 813 GLU Chi-restraints excluded: chain I residue 857 VAL Chi-restraints excluded: chain I residue 908 GLU Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain H residue 25 LYS Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1152 GLU Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1247 LYS Chi-restraints excluded: chain J residue 1249 ASN Chi-restraints excluded: chain J residue 1265 THR Chi-restraints excluded: chain L residue 264 LYS Chi-restraints excluded: chain L residue 551 LEU Chi-restraints excluded: chain L residue 583 THR Chi-restraints excluded: chain L residue 603 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 96 optimal weight: 0.0870 chunk 189 optimal weight: 1.9990 chunk 191 optimal weight: 0.8980 chunk 244 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 229 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 233 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 922 ASN H 66 HIS ** L 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 338 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.109884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.065172 restraints weight = 61245.787| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.63 r_work: 0.2799 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 30992 Z= 0.108 Angle : 0.517 11.565 42140 Z= 0.268 Chirality : 0.040 0.158 4811 Planarity : 0.004 0.075 5251 Dihedral : 12.848 83.868 4833 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.43 % Allowed : 13.99 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.14), residues: 3651 helix: 2.27 (0.14), residues: 1450 sheet: 0.80 (0.25), residues: 463 loop : -0.20 (0.15), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG G 235 TYR 0.010 0.001 TYR J 679 PHE 0.011 0.001 PHE I 405 TRP 0.010 0.001 TRP L 326 HIS 0.006 0.001 HIS L 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (30984) covalent geometry : angle 0.51629 / 0.27 (42128) hydrogen bonds : bond 0.03527 / 2.36 ( 1380) hydrogen bonds : angle 3.96668 / 2.82 ( 3843) metal coordination : bond 0.00310 / 0.16 ( 8) metal coordination : angle 1.70103 / 0.88 ( 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 282 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 237 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 253 PHE cc_start: 0.8646 (p90) cc_final: 0.8069 (p90) REVERT: I 315 MET cc_start: 0.8698 (ttm) cc_final: 0.8128 (mtp) REVERT: I 332 ARG cc_start: 0.8744 (mtp85) cc_final: 0.8348 (ttm-80) REVERT: I 477 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8567 (tm-30) REVERT: I 478 ARG cc_start: 0.8570 (tpp80) cc_final: 0.8041 (tpt90) REVERT: I 498 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8711 (mt) REVERT: I 600 THR cc_start: 0.8895 (OUTLIER) cc_final: 0.8418 (p) REVERT: I 813 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8591 (tp30) REVERT: I 899 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8355 (mt-10) REVERT: I 903 ARG cc_start: 0.8952 (tmm-80) cc_final: 0.8656 (mmm-85) REVERT: I 1025 PHE cc_start: 0.8610 (t80) cc_final: 0.8358 (t80) REVERT: I 1219 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8441 (mp0) REVERT: I 1329 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8737 (mt-10) REVERT: H 95 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8478 (ptmt) REVERT: J 130 MET cc_start: 0.8944 (ttp) cc_final: 0.8707 (ttm) REVERT: J 204 GLU cc_start: 0.8701 (tp30) cc_final: 0.8454 (tp30) REVERT: J 229 GLN cc_start: 0.9030 (mm-40) cc_final: 0.8698 (mm-40) REVERT: J 674 THR cc_start: 0.8274 (OUTLIER) cc_final: 0.7962 (p) REVERT: J 1040 MET cc_start: 0.6745 (mmm) cc_final: 0.6433 (mmt) REVERT: J 1095 MET cc_start: 0.3712 (tmm) cc_final: 0.3504 (tmm) REVERT: J 1152 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7906 (tp30) REVERT: J 1162 ILE cc_start: 0.8417 (tp) cc_final: 0.7989 (pp) REVERT: J 1196 LEU cc_start: 0.9349 (mp) cc_final: 0.8760 (tt) REVERT: J 1249 ASN cc_start: 0.9034 (OUTLIER) cc_final: 0.8804 (t0) REVERT: J 1265 THR cc_start: 0.8496 (OUTLIER) cc_final: 0.8119 (p) REVERT: J 1334 GLU cc_start: 0.8314 (tp30) cc_final: 0.7945 (tp30) REVERT: L 264 LYS cc_start: 0.9354 (pptt) cc_final: 0.9080 (pptt) REVERT: L 277 MET cc_start: 0.9123 (tpt) cc_final: 0.8708 (tmm) REVERT: L 551 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7667 (tp) outliers start: 45 outliers final: 24 residues processed: 266 average time/residue: 0.8423 time to fit residues: 258.2688 Evaluate side-chains 261 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 227 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 7 GLU Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 470 ARG Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 813 GLU Chi-restraints excluded: chain I residue 857 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain H residue 25 LYS Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1152 GLU Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1247 LYS Chi-restraints excluded: chain J residue 1249 ASN Chi-restraints excluded: chain J residue 1265 THR Chi-restraints excluded: chain L residue 551 LEU Chi-restraints excluded: chain L residue 583 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 141 optimal weight: 10.0000 chunk 322 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 318 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 357 optimal weight: 5.9990 chunk 153 optimal weight: 0.5980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 922 ASN G 137 ASN H 66 HIS ** L 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 338 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.108588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.063414 restraints weight = 61359.703| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.63 r_work: 0.2769 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 30992 Z= 0.170 Angle : 0.553 10.846 42140 Z= 0.288 Chirality : 0.042 0.145 4811 Planarity : 0.004 0.084 5251 Dihedral : 12.861 82.884 4832 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.37 % Allowed : 14.46 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.14), residues: 3651 helix: 2.25 (0.14), residues: 1446 sheet: 0.82 (0.25), residues: 455 loop : -0.23 (0.14), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG G 235 TYR 0.011 0.001 TYR I1281 PHE 0.009 0.001 PHE J1319 TRP 0.009 0.001 TRP L 326 HIS 0.006 0.001 HIS L 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 (30984) covalent geometry : angle 0.55168 / 0.29 (42128) hydrogen bonds : bond 0.04237 / 2.83 ( 1380) hydrogen bonds : angle 4.01680 / 2.85 ( 3843) metal coordination : bond 0.00629 / 0.31 ( 8) metal coordination : angle 2.08697 / 1.07 ( 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 272 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 229 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 145 ILE cc_start: 0.9378 (OUTLIER) cc_final: 0.9022 (mm) REVERT: I 253 PHE cc_start: 0.8676 (p90) cc_final: 0.8046 (p90) REVERT: I 315 MET cc_start: 0.8714 (ttm) cc_final: 0.8130 (mtp) REVERT: I 332 ARG cc_start: 0.8728 (mtp85) cc_final: 0.8322 (ttm-80) REVERT: I 477 GLU cc_start: 0.8878 (tm-30) cc_final: 0.8625 (tm-30) REVERT: I 478 ARG cc_start: 0.8594 (tpp80) cc_final: 0.8065 (tpt90) REVERT: I 498 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8710 (mt) REVERT: I 600 THR cc_start: 0.8947 (OUTLIER) cc_final: 0.8480 (p) REVERT: I 813 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8612 (tp30) REVERT: I 899 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8376 (mt-10) REVERT: I 903 ARG cc_start: 0.8927 (tmm-80) cc_final: 0.8668 (mmm-85) REVERT: I 951 MET cc_start: 0.8992 (ttp) cc_final: 0.8768 (tmm) REVERT: I 1025 PHE cc_start: 0.8660 (t80) cc_final: 0.8380 (t80) REVERT: I 1219 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8466 (mp0) REVERT: I 1329 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8757 (mt-10) REVERT: H 95 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8446 (ptmt) REVERT: J 204 GLU cc_start: 0.8699 (tp30) cc_final: 0.8471 (tp30) REVERT: J 215 LYS cc_start: 0.9032 (mmpt) cc_final: 0.8693 (mmtt) REVERT: J 229 GLN cc_start: 0.9052 (mm-40) cc_final: 0.8736 (mm-40) REVERT: J 674 THR cc_start: 0.8247 (OUTLIER) cc_final: 0.7942 (p) REVERT: J 1040 MET cc_start: 0.6834 (mmm) cc_final: 0.6520 (mmt) REVERT: J 1152 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7905 (tp30) REVERT: J 1162 ILE cc_start: 0.8469 (tp) cc_final: 0.8037 (pp) REVERT: J 1196 LEU cc_start: 0.9353 (mp) cc_final: 0.8766 (tt) REVERT: J 1249 ASN cc_start: 0.9100 (OUTLIER) cc_final: 0.8865 (t0) REVERT: J 1265 THR cc_start: 0.8519 (OUTLIER) cc_final: 0.8150 (p) REVERT: J 1334 GLU cc_start: 0.8359 (tp30) cc_final: 0.7983 (tp30) REVERT: L 144 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8453 (pp) REVERT: L 264 LYS cc_start: 0.9378 (pptt) cc_final: 0.9112 (pptt) REVERT: L 277 MET cc_start: 0.9111 (tpt) cc_final: 0.8751 (tmm) REVERT: L 489 MET cc_start: 0.8203 (mtt) cc_final: 0.7989 (mtp) REVERT: L 551 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7629 (tp) outliers start: 43 outliers final: 22 residues processed: 260 average time/residue: 0.8565 time to fit residues: 255.9255 Evaluate side-chains 258 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 224 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 7 GLU Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 470 ARG Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 541 GLU Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 813 GLU Chi-restraints excluded: chain I residue 857 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain H residue 25 LYS Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1152 GLU Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1249 ASN Chi-restraints excluded: chain J residue 1265 THR Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 551 LEU Chi-restraints excluded: chain L residue 583 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 141 optimal weight: 10.0000 chunk 54 optimal weight: 0.3980 chunk 323 optimal weight: 8.9990 chunk 286 optimal weight: 7.9990 chunk 300 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 206 optimal weight: 6.9990 chunk 181 optimal weight: 0.0670 chunk 42 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 554 HIS I 922 ASN H 66 HIS ** L 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 338 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.110034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.064992 restraints weight = 61346.313| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.64 r_work: 0.2804 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30992 Z= 0.111 Angle : 0.534 11.854 42140 Z= 0.276 Chirality : 0.040 0.187 4811 Planarity : 0.004 0.084 5251 Dihedral : 12.788 83.927 4832 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.18 % Allowed : 14.75 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.14), residues: 3651 helix: 2.29 (0.14), residues: 1454 sheet: 0.85 (0.25), residues: 457 loop : -0.14 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG G 235 TYR 0.009 0.001 TYR J 679 PHE 0.011 0.001 PHE I 405 TRP 0.010 0.001 TRP L 326 HIS 0.006 0.001 HIS L 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (30984) covalent geometry : angle 0.53341 / 0.28 (42128) hydrogen bonds : bond 0.03417 / 2.29 ( 1380) hydrogen bonds : angle 3.92674 / 2.78 ( 3843) metal coordination : bond 0.00331 / 0.17 ( 8) metal coordination : angle 1.69805 / 0.87 ( 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 275 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 238 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 145 ILE cc_start: 0.9333 (OUTLIER) cc_final: 0.8980 (mm) REVERT: I 253 PHE cc_start: 0.8640 (p90) cc_final: 0.8000 (p90) REVERT: I 275 ARG cc_start: 0.9145 (ptm-80) cc_final: 0.8861 (tmm160) REVERT: I 315 MET cc_start: 0.8716 (ttm) cc_final: 0.8163 (mtp) REVERT: I 332 ARG cc_start: 0.8746 (mtp85) cc_final: 0.8342 (ttm-80) REVERT: I 477 GLU cc_start: 0.8865 (tm-30) cc_final: 0.8622 (tm-30) REVERT: I 478 ARG cc_start: 0.8563 (tpp80) cc_final: 0.8087 (tpt90) REVERT: I 498 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8699 (mt) REVERT: I 600 THR cc_start: 0.8881 (OUTLIER) cc_final: 0.8415 (p) REVERT: I 813 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8556 (tp30) REVERT: I 844 LYS cc_start: 0.9175 (pptt) cc_final: 0.8952 (ptpp) REVERT: I 899 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8364 (mt-10) REVERT: I 903 ARG cc_start: 0.8962 (tmm-80) cc_final: 0.8720 (mmm-85) REVERT: I 951 MET cc_start: 0.8996 (ttp) cc_final: 0.8766 (tmm) REVERT: I 1219 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8430 (mp0) REVERT: I 1329 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8714 (mt-10) REVERT: H 86 LYS cc_start: 0.9096 (ttpt) cc_final: 0.8777 (tttt) REVERT: H 95 LYS cc_start: 0.8661 (ptmt) cc_final: 0.8361 (ptmt) REVERT: J 204 GLU cc_start: 0.8678 (tp30) cc_final: 0.8467 (tp30) REVERT: J 229 GLN cc_start: 0.9059 (mm-40) cc_final: 0.8739 (mm-40) REVERT: J 322 ARG cc_start: 0.8674 (ttm-80) cc_final: 0.8434 (tpp80) REVERT: J 674 THR cc_start: 0.8213 (OUTLIER) cc_final: 0.7944 (p) REVERT: J 1040 MET cc_start: 0.6871 (mmm) cc_final: 0.6561 (mmt) REVERT: J 1152 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7904 (tp30) REVERT: J 1162 ILE cc_start: 0.8434 (tp) cc_final: 0.7978 (pp) REVERT: J 1196 LEU cc_start: 0.9347 (mp) cc_final: 0.8747 (tt) REVERT: J 1249 ASN cc_start: 0.9029 (OUTLIER) cc_final: 0.8794 (t0) REVERT: J 1265 THR cc_start: 0.8481 (OUTLIER) cc_final: 0.8107 (p) REVERT: J 1334 GLU cc_start: 0.8307 (tp30) cc_final: 0.7940 (tp30) REVERT: L 144 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8453 (pp) REVERT: L 264 LYS cc_start: 0.9367 (pptt) cc_final: 0.9104 (pptt) REVERT: L 277 MET cc_start: 0.9122 (tpt) cc_final: 0.8754 (tmm) REVERT: L 360 ASP cc_start: 0.9221 (m-30) cc_final: 0.8816 (p0) REVERT: L 489 MET cc_start: 0.8144 (mtt) cc_final: 0.7903 (mtp) REVERT: L 551 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7611 (tp) outliers start: 37 outliers final: 18 residues processed: 264 average time/residue: 0.8033 time to fit residues: 245.4487 Evaluate side-chains 252 residues out of total 3146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 223 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 470 ARG Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 541 GLU Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 813 GLU Chi-restraints excluded: chain I residue 857 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1152 GLU Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1249 ASN Chi-restraints excluded: chain J residue 1265 THR Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 551 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 13 optimal weight: 3.9990 chunk 271 optimal weight: 0.0070 chunk 61 optimal weight: 4.9990 chunk 332 optimal weight: 7.9990 chunk 146 optimal weight: 6.9990 chunk 351 optimal weight: 1.9990 chunk 321 optimal weight: 1.9990 chunk 280 optimal weight: 8.9990 chunk 145 optimal weight: 0.9990 chunk 201 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN H 66 HIS ** L 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 338 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.109172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.064049 restraints weight = 61647.135| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.65 r_work: 0.2783 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30992 Z= 0.139 Angle : 0.550 11.792 42140 Z= 0.285 Chirality : 0.041 0.175 4811 Planarity : 0.004 0.087 5251 Dihedral : 12.794 83.387 4832 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.08 % Allowed : 15.13 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.14), residues: 3651 helix: 2.30 (0.14), residues: 1449 sheet: 0.85 (0.25), residues: 461 loop : -0.14 (0.15), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG G 235 TYR 0.010 0.001 TYR I1281 PHE 0.013 0.001 PHE I1025 TRP 0.009 0.001 TRP L 326 HIS 0.006 0.001 HIS L 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (30984) covalent geometry : angle 0.54933 / 0.29 (42128) hydrogen bonds : bond 0.03825 / 2.56 ( 1380) hydrogen bonds : angle 3.95706 / 2.80 ( 3843) metal coordination : bond 0.00486 / 0.24 ( 8) metal coordination : angle 1.87156 / 0.95 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13392.65 seconds wall clock time: 227 minutes 49.96 seconds (13669.96 seconds total)