Starting phenix.real_space_refine on Sat Jun 6 08:56:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10ma_75279/06_2026/10ma_75279.cif Found real_map, /net/cci-nas-00/data/ceres_data/10ma_75279/06_2026/10ma_75279.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/10ma_75279/06_2026/10ma_75279.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10ma_75279/06_2026/10ma_75279.map" model { file = "/net/cci-nas-00/data/ceres_data/10ma_75279/06_2026/10ma_75279.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10ma_75279/06_2026/10ma_75279.cif" } resolution = 2.9 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= 0.001 sd= 0.010 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 63 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 16289 2.51 5 N 4646 2.21 5 O 5793 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s 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: 26900 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 472 Classifications: {'DNA': 23} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 22} Chain breaks: 1 Chain: "B" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 627 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "G" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1685 Classifications: {'peptide': 218} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 208} Chain breaks: 1 Chain: "H" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1693 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 8, 'TRANS': 210} Chain breaks: 1 Chain: "I" Number of atoms: 10381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1316, 10381 Classifications: {'peptide': 1316} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1260} Chain breaks: 1 Chain: "J" Number of atoms: 10533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1358, 10533 Classifications: {'peptide': 1358} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1302} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 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: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 214 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna3p': 9} Chain: "I" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'1N7': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'1N7:plan-1': 2} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "G" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "H" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "I" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 268 Classifications: {'water': 268} Link IDs: {None: 267} Chain: "J" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 205 Classifications: {'water': 205} Link IDs: {None: 204} Chain: "K" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "R" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15307 SG CYS J 70 115.253 54.603 67.852 1.00122.44 S ATOM 15321 SG CYS J 72 116.022 50.861 67.351 1.00140.69 S ATOM 15429 SG CYS J 85 117.075 52.544 65.004 1.00138.89 S ATOM 15453 SG CYS J 88 113.972 52.798 64.719 1.00132.73 S ATOM 21133 SG CYS J 814 87.681 117.645 68.275 1.00 45.90 S ATOM 21698 SG CYS J 888 86.279 114.027 68.553 1.00 38.86 S ATOM 21749 SG CYS J 895 87.378 115.926 71.753 1.00 49.89 S ATOM 21770 SG CYS J 898 84.925 116.299 70.611 1.00 45.00 S Time building chain proxies: 6.23, per 1000 atoms: 0.23 Number of scatterers: 26900 At special positions: 0 Unit cell: (143.312, 157.508, 163.592, 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 106 16.00 P 63 15.00 Mg 1 11.99 O 5793 8.00 N 4646 7.00 C 16289 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: 2.38 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " Number of angles added : 12 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5884 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 45 sheets defined 39.2% alpha, 17.6% beta 27 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 3.56 Creating SS restraints... Processing helix chain 'G' and resid 34 through 51 removed outlier: 3.634A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN G 41 " --> pdb=" O HIS G 37 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER G 49 " --> pdb=" O ARG G 45 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N MET G 51 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 86 Processing helix chain 'G' and resid 154 through 159 removed outlier: 3.800A pdb=" N ARG G 158 " --> pdb=" O PRO G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 229 Processing helix chain 'H' and resid 34 through 51 removed outlier: 3.831A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N MET H 51 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 removed outlier: 3.701A 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 removed outlier: 3.662A pdb=" N GLN H 227 " --> pdb=" O ILE H 223 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 229 through 232 removed outlier: 4.254A pdb=" N VAL H 232 " --> pdb=" O GLU H 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 229 through 232' Processing helix chain 'I' and resid 4 through 9 removed outlier: 3.654A pdb=" N LYS I 9 " --> pdb=" O TYR I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.740A pdb=" N LEU I 32 " --> pdb=" O LEU I 28 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 55 removed outlier: 3.582A pdb=" N ALA I 51 " --> pdb=" O TYR I 47 " (cutoff:3.500A) removed outlier: 3.609A 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 163 through 167 removed outlier: 4.168A pdb=" N SER I 167 " --> pdb=" O THR I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.779A 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 279 Processing helix chain 'I' and resid 288 through 293 removed outlier: 3.691A pdb=" N ILE I 292 " --> pdb=" O PRO I 288 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA I 293 " --> pdb=" O VAL I 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 288 through 293' Processing helix chain 'I' and resid 318 through 328 Processing helix chain 'I' and resid 345 through 353 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 4.193A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE I 390 " --> pdb=" O GLU I 386 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 removed outlier: 3.654A pdb=" N ILE I 425 " --> pdb=" O SER I 421 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY I 438 " --> pdb=" O ASP I 434 " (cutoff:3.500A) Processing helix chain 'I' and resid 455 through 482 removed outlier: 3.545A pdb=" N ARG I 470 " --> pdb=" O VAL I 466 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 488 through 493 removed outlier: 3.791A pdb=" N MET I 492 " --> pdb=" O MET I 488 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 509 removed outlier: 3.502A pdb=" N SER I 499 " --> pdb=" O ALA I 495 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER I 509 " --> pdb=" O PHE I 505 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 527 removed outlier: 3.791A pdb=" N LYS I 527 " --> pdb=" O GLU I 523 " (cutoff:3.500A) Processing helix chain 'I' and resid 539 through 543 removed outlier: 3.707A pdb=" N ALA I 543 " --> pdb=" O ARG I 540 " (cutoff:3.500A) Processing helix chain 'I' and resid 551 through 555 Processing helix chain 'I' and resid 608 through 613 removed outlier: 3.998A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 613' 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 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 712 Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 942 through 981 removed outlier: 3.791A pdb=" N ALA I 981 " --> pdb=" O ALA I 977 " (cutoff:3.500A) Processing helix chain 'I' and resid 984 through 992 removed outlier: 4.359A pdb=" N LYS I 988 " --> pdb=" O VAL I 984 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS I 991 " --> pdb=" O GLU I 987 " (cutoff:3.500A) Processing helix chain 'I' and resid 997 through 1001 removed outlier: 3.576A pdb=" N GLY I1001 " --> pdb=" O LEU I 998 " (cutoff:3.500A) Processing helix chain 'I' and resid 1006 through 1037 removed outlier: 3.897A pdb=" N THR I1037 " --> pdb=" O ARG I1033 " (cutoff:3.500A) Processing helix chain 'I' and resid 1081 through 1085 removed outlier: 3.536A pdb=" N ASP I1084 " --> pdb=" O PRO I1081 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET I1085 " --> pdb=" O ILE I1082 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1081 through 1085' Processing helix chain 'I' and resid 1099 through 1103 removed outlier: 3.610A pdb=" N VAL I1103 " --> pdb=" O PRO I1100 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.643A pdb=" N LEU I1113 " --> pdb=" O ILE I1109 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1150 removed outlier: 3.966A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1165 through 1177 Processing helix chain 'I' and resid 1191 through 1202 removed outlier: 3.501A pdb=" N GLY I1202 " --> pdb=" O LEU I1198 " (cutoff:3.500A) Processing helix chain 'I' and resid 1238 through 1242 Processing helix chain 'I' and resid 1271 through 1282 removed outlier: 3.578A pdb=" N VAL I1275 " --> pdb=" O GLY I1271 " (cutoff:3.500A) Processing helix chain 'I' and resid 1283 through 1292 removed outlier: 3.580A pdb=" N LEU I1287 " --> pdb=" O ALA I1283 " (cutoff:3.500A) Processing helix chain 'I' and resid 1297 through 1310 removed outlier: 3.715A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR I1305 " --> pdb=" O ARG I1301 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1332 removed outlier: 3.849A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) 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 removed outlier: 3.640A pdb=" N HIS J 80 " --> pdb=" O ARG J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 100 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 removed outlier: 3.527A pdb=" N ILE J 135 " --> pdb=" O PRO J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 167 Processing helix chain 'J' and resid 168 through 176 removed outlier: 3.670A pdb=" N GLY J 173 " --> pdb=" O GLU J 170 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASP J 174 " --> pdb=" O GLU J 171 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE J 176 " --> pdb=" O GLY J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 191 removed outlier: 3.649A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 208 removed outlier: 3.677A pdb=" N GLU J 197 " --> pdb=" O ASP J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 230 removed outlier: 3.604A pdb=" N SER J 230 " --> pdb=" O ALA J 226 " (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 264 through 285 Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 318 through 322 Processing helix chain 'J' and resid 327 through 331 removed outlier: 3.544A pdb=" N MET J 330 " --> pdb=" O LEU J 327 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE J 331 " --> pdb=" O ALA J 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 327 through 331' Processing helix chain 'J' and resid 336 through 342 removed outlier: 3.502A pdb=" N LEU J 342 " --> pdb=" O PHE J 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 370 through 377 removed outlier: 3.586A 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 406 through 416 removed outlier: 3.985A 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 removed outlier: 3.746A pdb=" N TYR J 457 " --> pdb=" O VAL J 453 " (cutoff:3.500A) Processing helix chain 'J' and resid 473 through 483 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 removed outlier: 3.796A pdb=" N ILE J 591 " --> pdb=" O PRO J 588 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 612 Processing helix chain 'J' and resid 613 through 634 removed outlier: 3.831A pdb=" N THR J 617 " --> pdb=" O GLY J 613 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP J 622 " --> pdb=" O VAL J 618 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG J 634 " --> pdb=" O ALA J 630 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 removed outlier: 3.831A pdb=" N ILE J 653 " --> pdb=" O LYS J 649 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER J 670 " --> pdb=" O GLU J 666 " (cutoff:3.500A) Processing helix chain 'J' and resid 674 through 703 removed outlier: 3.562A pdb=" N MET J 698 " --> pdb=" O SER J 694 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN J 700 " --> pdb=" O ALA J 696 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 removed outlier: 4.443A pdb=" N GLN J 739 " --> pdb=" O ALA J 735 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU J 740 " --> pdb=" O GLN J 736 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 805 removed outlier: 3.567A pdb=" N ILE J 774 " --> pdb=" O LEU J 770 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 Processing helix chain 'J' and resid 865 through 876 Processing helix chain 'J' and resid 896 through 900 Processing helix chain 'J' and resid 914 through 932 removed outlier: 3.714A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Proline residue: J 926 - end of helix removed outlier: 3.665A pdb=" N MET J 932 " --> pdb=" O THR J 928 " (cutoff:3.500A) Processing helix chain 'J' and resid 1068 through 1072 Processing helix chain 'J' and resid 1133 through 1147 Proline residue: J1139 - end of helix Processing helix chain 'J' and resid 1168 through 1170 No H-bonds generated for 'chain 'J' and resid 1168 through 1170' Processing helix chain 'J' and resid 1216 through 1224 Processing helix chain 'J' and resid 1225 through 1243 removed outlier: 3.832A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR J1230 " --> pdb=" O VAL J1226 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG J1231 " --> pdb=" O HIS J1227 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL J1240 " --> pdb=" O GLU J1236 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR J1241 " --> pdb=" O VAL J1237 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU J1243 " --> pdb=" O ASP J1239 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1260 removed outlier: 3.547A pdb=" N ILE J1256 " --> pdb=" O HIS J1252 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1294 Processing helix chain 'J' and resid 1310 through 1315 Processing helix chain 'J' and resid 1319 through 1324 Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1348 through 1354 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 1373 removed outlier: 3.537A pdb=" N ARG J1369 " --> pdb=" O TYR J1365 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG J1373 " --> pdb=" O ARG J1369 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 15 through 33 removed outlier: 3.553A pdb=" N LEU K 19 " --> pdb=" O ASN K 15 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL K 20 " --> pdb=" O ARG K 16 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 57 Processing helix chain 'K' and resid 60 through 80 removed outlier: 4.057A pdb=" N LEU K 80 " --> pdb=" O GLU K 76 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 12 through 20 removed outlier: 6.889A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLN G 18 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N HIS G 23 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.862A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLY G 149 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N CYS G 54 " --> pdb=" O GLY G 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.624A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'H' and resid 17 through 20 removed outlier: 5.368A pdb=" N GLN H 18 " --> pdb=" O LYS H 25 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LYS H 25 " --> pdb=" O GLN H 18 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG H 182 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 98 through 105 removed outlier: 3.928A pdb=" N GLU H 58 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 90 through 92 Processing sheet with id=AA9, first strand: chain 'H' and resid 108 through 111 removed outlier: 6.957A pdb=" N GLY H 108 " --> pdb=" O HIS H 132 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N HIS H 132 " --> pdb=" O GLY H 108 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL H 110 " --> pdb=" O ILE H 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.758A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 59 through 60 removed outlier: 4.161A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE I 104 " --> pdb=" O ASP I 116 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB5, first strand: chain 'I' and resid 451 through 454 removed outlier: 6.536A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 154 through 158 removed outlier: 3.567A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU I 204 " --> pdb=" O VAL I 196 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 284 through 286 removed outlier: 3.768A pdb=" N GLN I 238 " --> pdb=" O GLU I 231 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ILE I 229 " --> pdb=" O GLU I 240 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 256 through 257 Processing sheet with id=AB9, first strand: chain 'I' and resid 301 through 302 Processing sheet with id=AC1, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.600A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N THR I 595 " --> pdb=" O THR I 600 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N THR I 600 " --> pdb=" O THR I 595 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC3, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.618A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 749 through 752 removed outlier: 6.232A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AC6, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC7, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.422A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 8.872A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.912A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 882 through 884 removed outlier: 3.982A pdb=" N VAL I 884 " --> pdb=" O LEU I 918 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 1244 through 1245 Processing sheet with id=AD2, first strand: chain 'I' and resid 1268 through 1270 removed outlier: 3.770A pdb=" N GLN I1268 " --> pdb=" O VAL J 347 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 1335 through 1340 removed outlier: 3.554A pdb=" N ALA J 19 " --> pdb=" O GLU I1340 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.669A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY J 103 " --> pdb=" O VAL J 244 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 10.222A pdb=" N SER J 109 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 9.906A pdb=" N ILE J 238 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 159 through 160 Processing sheet with id=AD6, first strand: chain 'J' and resid 526 through 527 removed outlier: 3.689A pdb=" N ARG J 551 " --> pdb=" O LEU J 527 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 705 through 709 removed outlier: 4.232A pdb=" N THR J 705 " --> pdb=" O GLN J 716 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AD9, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE1, first strand: chain 'J' and resid 825 through 826 removed outlier: 7.324A pdb=" N VAL J 825 " --> pdb=" O LYS J 832 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 848 through 849 removed outlier: 7.112A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 949 through 951 removed outlier: 6.563A pdb=" N ILE J 950 " --> pdb=" O VAL J1017 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 991 through 995 removed outlier: 3.552A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY J 956 " --> pdb=" O VAL J1011 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 1024 through 1028 removed outlier: 3.699A pdb=" N ALA J1122 " --> pdb=" O VAL J1027 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 1098 through 1100 removed outlier: 3.531A pdb=" N GLY J1033 " --> pdb=" O ILE J1115 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 1046 through 1050 removed outlier: 3.882A pdb=" N LEU J1059 " --> pdb=" O VAL J1107 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 1188 through 1191 Processing sheet with id=AE9, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 7.038A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1031 hydrogen bonds defined for protein. 2883 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 67 hydrogen bonds 134 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 7.37 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7613 1.33 - 1.45: 3873 1.45 - 1.57: 15022 1.57 - 1.69: 123 1.69 - 1.81: 184 Bond restraints: 26815 Sorted by residual: bond pdb=" C3' DG A 24 " pdb=" O3' DG A 24 " ideal model delta sigma weight residual 1.422 1.463 -0.041 3.00e-02 1.11e+03 1.85e+00 bond pdb=" C4 1N7 I1402 " pdb=" O4 1N7 I1402 " ideal model delta sigma weight residual 1.415 1.442 -0.027 2.00e-02 2.50e+03 1.83e+00 bond pdb=" C13 1N7 I1402 " pdb=" O2 1N7 I1402 " ideal model delta sigma weight residual 1.416 1.441 -0.025 2.00e-02 2.50e+03 1.51e+00 bond pdb=" C17 1N7 I1402 " pdb=" O3 1N7 I1402 " ideal model delta sigma weight residual 1.417 1.441 -0.024 2.00e-02 2.50e+03 1.49e+00 bond pdb=" N GLN J 504 " pdb=" CA GLN J 504 " ideal model delta sigma weight residual 1.457 1.473 -0.015 1.29e-02 6.01e+03 1.43e+00 ... (remaining 26810 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 34815 1.11 - 2.22: 1369 2.22 - 3.34: 246 3.34 - 4.45: 66 4.45 - 5.56: 8 Bond angle restraints: 36504 Sorted by residual: angle pdb=" N THR J 240 " pdb=" CA THR J 240 " pdb=" C THR J 240 " ideal model delta sigma weight residual 114.04 109.61 4.43 1.24e+00 6.50e-01 1.27e+01 angle pdb=" CA GLY I1068 " pdb=" C GLY I1068 " pdb=" N ARG I1069 " ideal model delta sigma weight residual 114.65 117.58 -2.93 9.20e-01 1.18e+00 1.02e+01 angle pdb=" C GLN J 504 " pdb=" CA GLN J 504 " pdb=" CB GLN J 504 " ideal model delta sigma weight residual 110.42 115.98 -5.56 1.99e+00 2.53e-01 7.80e+00 angle pdb=" C ASP J 710 " pdb=" CA ASP J 710 " pdb=" CB ASP J 710 " ideal model delta sigma weight residual 110.42 115.78 -5.36 1.99e+00 2.53e-01 7.24e+00 angle pdb=" CA VAL K 39 " pdb=" C VAL K 39 " pdb=" N PRO K 40 " ideal model delta sigma weight residual 116.57 119.16 -2.59 9.80e-01 1.04e+00 6.99e+00 ... (remaining 36499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.41: 16044 33.41 - 66.83: 418 66.83 - 100.24: 18 100.24 - 133.66: 3 133.66 - 167.07: 1 Dihedral angle restraints: 16484 sinusoidal: 7333 harmonic: 9151 Sorted by residual: dihedral pdb=" CA ILE I 561 " pdb=" C ILE I 561 " pdb=" N GLU I 562 " pdb=" CA GLU I 562 " ideal model delta harmonic sigma weight residual 180.00 158.32 21.68 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA ARG J 425 " pdb=" C ARG J 425 " pdb=" N ALA J 426 " pdb=" CA ALA J 426 " ideal model delta harmonic sigma weight residual 180.00 -159.24 -20.76 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA ASN I1236 " pdb=" C ASN I1236 " pdb=" N HIS I1237 " pdb=" CA HIS I1237 " ideal model delta harmonic sigma weight residual 180.00 159.78 20.22 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 16481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2619 0.031 - 0.061: 1012 0.061 - 0.092: 303 0.092 - 0.122: 209 0.122 - 0.153: 44 Chirality restraints: 4187 Sorted by residual: chirality pdb=" CA ILE I 117 " pdb=" N ILE I 117 " pdb=" C ILE I 117 " pdb=" CB ILE I 117 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.83e-01 chirality pdb=" CA ILE J 105 " pdb=" N ILE J 105 " pdb=" C ILE J 105 " pdb=" CB ILE J 105 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.42e-01 chirality pdb=" CA ILE I 530 " pdb=" N ILE I 530 " pdb=" C ILE I 530 " pdb=" CB ILE I 530 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.36e-01 ... (remaining 4184 not shown) Planarity restraints: 4547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER J 492 " 0.031 5.00e-02 4.00e+02 4.71e-02 3.55e+00 pdb=" N PRO J 493 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO J 493 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO J 493 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU J 245 " 0.028 5.00e-02 4.00e+02 4.23e-02 2.86e+00 pdb=" N PRO J 246 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO J 246 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO J 246 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR I 589 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.71e+00 pdb=" N PRO I 590 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO I 590 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO I 590 " -0.023 5.00e-02 4.00e+02 ... (remaining 4544 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4628 2.77 - 3.30: 24673 3.30 - 3.84: 41054 3.84 - 4.37: 51120 4.37 - 4.90: 88248 Nonbonded interactions: 209723 Sorted by model distance: nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1501 " model vdw 2.238 2.170 nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1501 " model vdw 2.256 2.170 nonbonded pdb=" O3' C R 18 " pdb="MG MG J1501 " model vdw 2.296 2.170 nonbonded pdb=" OD1 ASP J 464 " pdb="MG MG J1501 " model vdw 2.329 2.170 nonbonded pdb=" O SER J 492 " pdb=" O ASN J 495 " model vdw 2.374 3.040 ... (remaining 209718 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 8 through 158 or resid 170 through 231)) selection = (chain 'H' and resid 8 through 231) } 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: 3.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.680 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 31.560 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 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 : 0.004 0.102 26823 Z= 0.152 Angle : 0.614 34.626 36516 Z= 0.309 Chirality : 0.042 0.153 4187 Planarity : 0.004 0.047 4547 Dihedral : 13.558 167.075 10600 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.99 % Allowed : 5.54 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.20 (0.15), residues: 3174 helix: 1.20 (0.17), residues: 1059 sheet: -0.39 (0.24), residues: 461 loop : -0.94 (0.14), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 10 TYR 0.013 0.001 TYR J 457 PHE 0.017 0.001 PHE I 514 TRP 0.006 0.001 TRP J 409 HIS 0.004 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (26815) covalent geometry : angle 0.53627 / 0.30 (36504) hydrogen bonds : bond 0.15537 / 7.62 ( 1096) hydrogen bonds : angle 5.64670 / 3.67 ( 3017) metal coordination : bond 0.07989 / 4.00 ( 8) metal coordination : angle 16.48955 / 10.99 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 467 time to evaluate : 1.059 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: G 143 ARG cc_start: 0.7561 (mtp85) cc_final: 0.7185 (mtm-85) REVERT: H 191 ARG cc_start: 0.8543 (ptt90) cc_final: 0.8228 (ptt90) REVERT: I 54 ARG cc_start: 0.7151 (mtt180) cc_final: 0.6947 (mtp-110) REVERT: I 197 ARG cc_start: 0.7304 (ttt180) cc_final: 0.7100 (ttp-170) REVERT: I 392 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7646 (mm-30) REVERT: I 394 ARG cc_start: 0.7945 (mmm160) cc_final: 0.7442 (mpp-170) REVERT: I 658 GLN cc_start: 0.7691 (mt0) cc_final: 0.7381 (pt0) REVERT: I 954 LYS cc_start: 0.8545 (tppp) cc_final: 0.8295 (tptt) REVERT: I 1114 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.7242 (tm-30) REVERT: I 1158 LYS cc_start: 0.8263 (tmtp) cc_final: 0.7791 (mttp) REVERT: I 1225 VAL cc_start: 0.8895 (OUTLIER) cc_final: 0.8681 (t) REVERT: J 66 LYS cc_start: 0.8058 (mttt) cc_final: 0.7780 (tttm) REVERT: J 137 ARG cc_start: 0.7159 (mtm180) cc_final: 0.6736 (mtt180) REVERT: J 142 GLU cc_start: 0.7279 (mt-10) cc_final: 0.6832 (tm-30) REVERT: J 222 LYS cc_start: 0.8682 (tppt) cc_final: 0.8417 (mmtm) REVERT: J 301 GLU cc_start: 0.6768 (mt-10) cc_final: 0.6520 (mt-10) REVERT: J 316 ILE cc_start: 0.7727 (tt) cc_final: 0.7447 (mt) REVERT: J 399 LYS cc_start: 0.8042 (ttmm) cc_final: 0.7502 (ttpp) REVERT: J 497 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7671 (mp0) REVERT: J 568 SER cc_start: 0.8213 (t) cc_final: 0.7995 (p) REVERT: J 599 LYS cc_start: 0.8151 (mttp) cc_final: 0.7743 (mmmt) REVERT: J 925 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8119 (tm-30) REVERT: J 932 MET cc_start: 0.8514 (mtm) cc_final: 0.8207 (mtm) REVERT: J 996 LYS cc_start: 0.8003 (mttt) cc_final: 0.7642 (mptt) REVERT: J 1028 ILE cc_start: 0.7247 (OUTLIER) cc_final: 0.6836 (pt) REVERT: J 1106 ILE cc_start: 0.8039 (tt) cc_final: 0.7816 (mt) REVERT: J 1155 ILE cc_start: 0.8392 (mm) cc_final: 0.8183 (mt) REVERT: J 1286 LYS cc_start: 0.7995 (mmmm) cc_final: 0.7673 (ttpp) REVERT: J 1345 ARG cc_start: 0.8296 (ttm-80) cc_final: 0.8090 (mtp85) outliers start: 81 outliers final: 27 residues processed: 539 average time/residue: 0.7872 time to fit residues: 482.8996 Evaluate side-chains 368 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 337 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1114 GLU Chi-restraints excluded: chain I residue 1154 ASP Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 52 GLU Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 709 ARG Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 925 GLU Chi-restraints excluded: chain J residue 937 ILE Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1028 ILE Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1313 SER Chi-restraints excluded: chain K residue 59 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.0370 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 0.0070 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 5.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 103 ASN I 387 ASN I1090 ASN J 865 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.199430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.147075 restraints weight = 28875.949| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.59 r_work: 0.3296 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 26823 Z= 0.113 Angle : 0.546 14.376 36516 Z= 0.284 Chirality : 0.042 0.240 4187 Planarity : 0.004 0.065 4547 Dihedral : 13.370 173.407 4433 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.18 % Allowed : 13.00 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.15 (0.15), residues: 3174 helix: 1.54 (0.16), residues: 1082 sheet: -0.11 (0.24), residues: 453 loop : -0.83 (0.14), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 88 TYR 0.015 0.001 TYR J 140 PHE 0.011 0.001 PHE I 514 TRP 0.006 0.001 TRP J1193 HIS 0.003 0.000 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (26815) covalent geometry : angle 0.53584 / 0.28 (36504) hydrogen bonds : bond 0.04437 / 2.18 ( 1096) hydrogen bonds : angle 4.29928 / 2.84 ( 3017) metal coordination : bond 0.00624 / 0.32 ( 8) metal coordination : angle 5.81983 / 3.88 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 352 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8246 (mtmt) REVERT: G 127 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7616 (mp10) REVERT: G 143 ARG cc_start: 0.7520 (mtp85) cc_final: 0.7207 (mtm-85) REVERT: H 191 ARG cc_start: 0.8598 (ptt90) cc_final: 0.8366 (ptt90) REVERT: I 14 ASP cc_start: 0.8753 (OUTLIER) cc_final: 0.8472 (t70) REVERT: I 54 ARG cc_start: 0.7201 (mtt180) cc_final: 0.6924 (mtp-110) REVERT: I 392 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7689 (mm-30) REVERT: I 394 ARG cc_start: 0.8140 (mmm160) cc_final: 0.7504 (mpp-170) REVERT: I 658 GLN cc_start: 0.7619 (mt0) cc_final: 0.7401 (pt0) REVERT: I 693 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8614 (mp) REVERT: I 719 LYS cc_start: 0.8329 (mtmt) cc_final: 0.8118 (mttt) REVERT: I 954 LYS cc_start: 0.8643 (tppp) cc_final: 0.8406 (tptt) REVERT: I 1114 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7360 (tm-30) REVERT: I 1158 LYS cc_start: 0.8301 (tmtp) cc_final: 0.7897 (mttp) REVERT: I 1168 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7408 (mm-30) REVERT: J 52 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6881 (mt-10) REVERT: J 60 ARG cc_start: 0.8035 (ttm170) cc_final: 0.7795 (mmm-85) REVERT: J 66 LYS cc_start: 0.8111 (mttt) cc_final: 0.7848 (tttm) REVERT: J 137 ARG cc_start: 0.7356 (mtm180) cc_final: 0.6955 (mtt180) REVERT: J 142 GLU cc_start: 0.7323 (mt-10) cc_final: 0.6859 (tm-30) REVERT: J 316 ILE cc_start: 0.7738 (tt) cc_final: 0.7379 (mt) REVERT: J 399 LYS cc_start: 0.7907 (ttmm) cc_final: 0.7496 (ttpt) REVERT: J 497 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7764 (mp0) REVERT: J 599 LYS cc_start: 0.8321 (mttp) cc_final: 0.7960 (mmmt) REVERT: J 751 ASP cc_start: 0.6482 (OUTLIER) cc_final: 0.5722 (p0) REVERT: J 802 ASP cc_start: 0.7553 (t70) cc_final: 0.7113 (m-30) REVERT: J 925 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8134 (tm-30) REVERT: J 932 MET cc_start: 0.8498 (mtm) cc_final: 0.8224 (mtm) REVERT: J 996 LYS cc_start: 0.8011 (mttt) cc_final: 0.7701 (mptt) REVERT: J 1028 ILE cc_start: 0.7303 (OUTLIER) cc_final: 0.6925 (pt) REVERT: J 1286 LYS cc_start: 0.8186 (mmmm) cc_final: 0.7857 (mtpt) outliers start: 86 outliers final: 35 residues processed: 404 average time/residue: 0.7301 time to fit residues: 338.1970 Evaluate side-chains 363 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 319 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 25 LYS Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain I residue 14 ASP Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 772 SER Chi-restraints excluded: chain I residue 1114 GLU Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 52 GLU Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 700 ASN Chi-restraints excluded: chain J residue 718 SER Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 864 LEU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 925 GLU Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1003 LEU Chi-restraints excluded: chain J residue 1011 VAL Chi-restraints excluded: chain J residue 1028 ILE Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1239 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 314 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 304 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 230 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 174 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN I 766 ASN J 430 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.194960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.152177 restraints weight = 28590.596| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 3.23 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 26823 Z= 0.210 Angle : 0.642 11.505 36516 Z= 0.332 Chirality : 0.046 0.172 4187 Planarity : 0.005 0.064 4547 Dihedral : 13.461 172.410 4414 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.40 % Allowed : 14.07 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.09 (0.15), residues: 3174 helix: 1.30 (0.16), residues: 1078 sheet: -0.18 (0.23), residues: 474 loop : -0.95 (0.14), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 88 TYR 0.020 0.002 TYR J 457 PHE 0.015 0.002 PHE I 514 TRP 0.007 0.001 TRP J 686 HIS 0.006 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.21 (26815) covalent geometry : angle 0.63813 / 0.33 (36504) hydrogen bonds : bond 0.06045 / 2.97 ( 1096) hydrogen bonds : angle 4.30625 / 2.83 ( 3017) metal coordination : bond 0.00642 / 0.35 ( 8) metal coordination : angle 3.74527 / 2.50 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 314 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8061 (mtmt) REVERT: G 127 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.7108 (mp10) REVERT: G 145 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7956 (tttm) REVERT: I 104 ILE cc_start: 0.6424 (OUTLIER) cc_final: 0.6053 (pp) REVERT: I 452 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.8163 (mtp-110) REVERT: I 1114 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7634 (tt0) REVERT: I 1219 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7230 (mt-10) REVERT: I 1274 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8122 (mm-30) REVERT: J 205 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8325 (tp) REVERT: J 298 MET cc_start: 0.7084 (mmm) cc_final: 0.6744 (mmm) REVERT: J 497 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7372 (mp0) REVERT: J 792 ASN cc_start: 0.7960 (p0) cc_final: 0.7620 (p0) REVERT: J 925 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7907 (tm-30) outliers start: 119 outliers final: 58 residues processed: 398 average time/residue: 0.6966 time to fit residues: 321.7341 Evaluate side-chains 371 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 303 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 25 LYS Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 145 LYS Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 229 GLU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain I residue 14 ASP Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 118 LYS Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 388 LEU Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 452 ARG Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 757 THR Chi-restraints excluded: chain I residue 772 SER Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1114 GLU Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1274 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1322 SER Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 700 ASN Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 864 LEU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 886 VAL Chi-restraints excluded: chain J residue 925 GLU Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 994 SER Chi-restraints excluded: chain J residue 1011 VAL Chi-restraints excluded: chain J residue 1028 ILE Chi-restraints excluded: chain J residue 1060 VAL Chi-restraints excluded: chain J residue 1106 ILE Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain K residue 59 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 31 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 chunk 179 optimal weight: 0.9980 chunk 219 optimal weight: 0.0270 chunk 120 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 296 optimal weight: 30.0000 chunk 108 optimal weight: 1.9990 overall best weight: 1.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 266 ASN J 430 HIS J1249 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.196957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.153129 restraints weight = 28531.308| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 3.38 r_work: 0.3084 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26823 Z= 0.122 Angle : 0.537 10.896 36516 Z= 0.282 Chirality : 0.042 0.182 4187 Planarity : 0.004 0.062 4547 Dihedral : 13.142 174.840 4410 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.80 % Allowed : 15.52 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.09 (0.15), residues: 3174 helix: 1.50 (0.16), residues: 1080 sheet: -0.04 (0.24), residues: 449 loop : -0.90 (0.14), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 88 TYR 0.013 0.001 TYR J 457 PHE 0.012 0.001 PHE I 514 TRP 0.005 0.001 TRP J 409 HIS 0.004 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (26815) covalent geometry : angle 0.53526 / 0.28 (36504) hydrogen bonds : bond 0.04522 / 2.22 ( 1096) hydrogen bonds : angle 4.08048 / 2.69 ( 3017) metal coordination : bond 0.00421 / 0.24 ( 8) metal coordination : angle 2.75560 / 1.84 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 304 time to evaluate : 1.069 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: G 25 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8187 (mtmt) REVERT: G 127 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7665 (mp10) REVERT: G 145 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8037 (tttm) REVERT: I 88 ARG cc_start: 0.8095 (ttm110) cc_final: 0.7580 (mtt-85) REVERT: I 189 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7604 (m-30) REVERT: I 434 ASP cc_start: 0.7618 (m-30) cc_final: 0.7405 (m-30) REVERT: I 451 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.8163 (mtt180) REVERT: I 518 ASN cc_start: 0.8580 (OUTLIER) cc_final: 0.8353 (m-40) REVERT: I 739 ASP cc_start: 0.8577 (t0) cc_final: 0.8163 (m-30) REVERT: I 1114 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.7527 (tm-30) REVERT: I 1219 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8276 (mm-30) REVERT: J 60 ARG cc_start: 0.8048 (mmm-85) cc_final: 0.7754 (mmm160) REVERT: J 137 ARG cc_start: 0.7414 (mtt180) cc_final: 0.6972 (mmt90) REVERT: J 205 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8122 (tp) REVERT: J 497 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7871 (mp0) REVERT: J 709 ARG cc_start: 0.7684 (ppt-90) cc_final: 0.7105 (ppt90) REVERT: J 792 ASN cc_start: 0.8009 (p0) cc_final: 0.7716 (p0) REVERT: J 925 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8183 (tm-30) REVERT: J 1028 ILE cc_start: 0.7481 (OUTLIER) cc_final: 0.7015 (pt) outliers start: 103 outliers final: 57 residues processed: 377 average time/residue: 0.7216 time to fit residues: 314.2901 Evaluate side-chains 361 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 293 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 25 LYS Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 145 LYS Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain I residue 14 ASP Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 118 LYS Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 451 ARG Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 601 ASP Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 631 GLU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 772 SER Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1114 GLU Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 700 ASN Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 846 GLU Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 864 LEU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 886 VAL Chi-restraints excluded: chain J residue 890 THR Chi-restraints excluded: chain J residue 925 GLU Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1011 VAL Chi-restraints excluded: chain J residue 1028 ILE Chi-restraints excluded: chain J residue 1060 VAL Chi-restraints excluded: chain J residue 1106 ILE Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1249 ASN Chi-restraints excluded: chain K residue 59 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 257 optimal weight: 20.0000 chunk 59 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 221 optimal weight: 2.9990 chunk 313 optimal weight: 0.9980 chunk 147 optimal weight: 7.9990 chunk 187 optimal weight: 0.1980 chunk 241 optimal weight: 0.0060 chunk 240 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 chunk 70 optimal weight: 40.0000 overall best weight: 1.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN J 430 HIS J1249 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.196933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 128)---------------| | r_work = 0.3553 r_free = 0.3553 target = 0.132829 restraints weight = 28673.927| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.89 r_work: 0.3264 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26823 Z= 0.113 Angle : 0.517 10.153 36516 Z= 0.272 Chirality : 0.041 0.171 4187 Planarity : 0.004 0.059 4547 Dihedral : 13.051 174.277 4410 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.77 % Allowed : 15.96 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.21 (0.15), residues: 3174 helix: 1.63 (0.16), residues: 1080 sheet: 0.02 (0.24), residues: 460 loop : -0.85 (0.14), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J1123 TYR 0.014 0.001 TYR I 70 PHE 0.012 0.001 PHE I 514 TRP 0.005 0.001 TRP J 409 HIS 0.003 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (26815) covalent geometry : angle 0.51479 / 0.27 (36504) hydrogen bonds : bond 0.04173 / 2.05 ( 1096) hydrogen bonds : angle 3.95904 / 2.61 ( 3017) metal coordination : bond 0.00363 / 0.20 ( 8) metal coordination : angle 2.37731 / 1.58 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 305 time to evaluate : 0.938 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: G 25 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8093 (mtmt) REVERT: G 127 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7583 (mp10) REVERT: G 143 ARG cc_start: 0.7599 (mmm-85) cc_final: 0.7009 (mtm-85) REVERT: G 145 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7968 (tttm) REVERT: I 189 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7382 (m-30) REVERT: I 451 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.8124 (mtt180) REVERT: I 452 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8224 (mtp-110) REVERT: I 697 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.7680 (pmtt) REVERT: I 719 LYS cc_start: 0.8221 (mtmt) cc_final: 0.7753 (mttt) REVERT: I 739 ASP cc_start: 0.8554 (t0) cc_final: 0.8153 (m-30) REVERT: I 1114 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.7417 (tm-30) REVERT: I 1219 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8093 (mm-30) REVERT: J 60 ARG cc_start: 0.7966 (mmm-85) cc_final: 0.7751 (mmm160) REVERT: J 137 ARG cc_start: 0.7234 (mtt180) cc_final: 0.6872 (mmt90) REVERT: J 200 GLN cc_start: 0.8949 (tt0) cc_final: 0.8529 (mm110) REVERT: J 244 VAL cc_start: 0.8364 (m) cc_final: 0.7898 (t) REVERT: J 301 GLU cc_start: 0.7097 (tp30) cc_final: 0.6792 (mt-10) REVERT: J 497 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7724 (mp0) REVERT: J 709 ARG cc_start: 0.7653 (ppt-90) cc_final: 0.7210 (ppt90) REVERT: J 737 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8023 (mp) REVERT: J 925 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8215 (tm-30) REVERT: J 1189 MET cc_start: 0.6891 (ptm) cc_final: 0.6575 (mmm) REVERT: J 1249 ASN cc_start: 0.8636 (OUTLIER) cc_final: 0.8432 (t0) REVERT: J 1371 ARG cc_start: 0.7922 (tmm160) cc_final: 0.7460 (ttp80) outliers start: 102 outliers final: 56 residues processed: 379 average time/residue: 0.6997 time to fit residues: 305.7992 Evaluate side-chains 362 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 294 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 25 LYS Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 145 LYS Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 229 GLU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain I residue 14 ASP Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 118 LYS Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 451 ARG Chi-restraints excluded: chain I residue 452 ARG Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 601 ASP Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 631 GLU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 772 SER Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1114 GLU Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 700 ASN Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 864 LEU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 886 VAL Chi-restraints excluded: chain J residue 890 THR Chi-restraints excluded: chain J residue 925 GLU Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 994 SER Chi-restraints excluded: chain J residue 1011 VAL Chi-restraints excluded: chain J residue 1028 ILE Chi-restraints excluded: chain J residue 1060 VAL Chi-restraints excluded: chain J residue 1106 ILE Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1249 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 51 optimal weight: 0.0980 chunk 41 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 189 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 157 optimal weight: 0.0770 chunk 122 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 overall best weight: 1.4344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 430 HIS J1249 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.196329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.149869 restraints weight = 28758.557| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 3.61 r_work: 0.3069 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26823 Z= 0.127 Angle : 0.530 11.708 36516 Z= 0.277 Chirality : 0.042 0.172 4187 Planarity : 0.004 0.070 4547 Dihedral : 13.053 173.633 4408 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.92 % Allowed : 16.40 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.22 (0.15), residues: 3174 helix: 1.64 (0.16), residues: 1080 sheet: 0.06 (0.24), residues: 455 loop : -0.85 (0.14), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG I 88 TYR 0.013 0.001 TYR J 457 PHE 0.012 0.001 PHE I 514 TRP 0.005 0.001 TRP J 409 HIS 0.003 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (26815) covalent geometry : angle 0.52840 / 0.28 (36504) hydrogen bonds : bond 0.04397 / 2.16 ( 1096) hydrogen bonds : angle 3.94134 / 2.59 ( 3017) metal coordination : bond 0.00359 / 0.20 ( 8) metal coordination : angle 2.24227 / 1.49 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 302 time to evaluate : 0.873 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: G 25 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8155 (mtmt) REVERT: G 127 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7643 (mp10) REVERT: G 145 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.8011 (tttm) REVERT: I 88 ARG cc_start: 0.8005 (ttm110) cc_final: 0.7401 (mtt-85) REVERT: I 189 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7415 (m-30) REVERT: I 434 ASP cc_start: 0.7609 (m-30) cc_final: 0.7398 (m-30) REVERT: I 451 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.8159 (mtt180) REVERT: I 452 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8266 (mtp-110) REVERT: I 697 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.7728 (pmtt) REVERT: I 739 ASP cc_start: 0.8598 (t0) cc_final: 0.8190 (m-30) REVERT: I 955 GLN cc_start: 0.8018 (tp40) cc_final: 0.7805 (tp-100) REVERT: I 959 ASP cc_start: 0.7669 (m-30) cc_final: 0.7445 (m-30) REVERT: I 1114 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.7585 (tm-30) REVERT: I 1219 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8155 (mm-30) REVERT: J 137 ARG cc_start: 0.7358 (mtt180) cc_final: 0.7034 (mtt90) REVERT: J 205 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8147 (tt) REVERT: J 244 VAL cc_start: 0.8410 (m) cc_final: 0.7940 (t) REVERT: J 301 GLU cc_start: 0.7276 (tp30) cc_final: 0.6917 (mt-10) REVERT: J 413 ASP cc_start: 0.7438 (OUTLIER) cc_final: 0.7113 (m-30) REVERT: J 497 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7773 (mp0) REVERT: J 709 ARG cc_start: 0.7679 (ppt-90) cc_final: 0.7289 (ppt90) REVERT: J 712 GLN cc_start: 0.7254 (OUTLIER) cc_final: 0.6782 (mp10) REVERT: J 737 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8112 (mp) REVERT: J 751 ASP cc_start: 0.6463 (OUTLIER) cc_final: 0.5700 (p0) REVERT: J 802 ASP cc_start: 0.7618 (m-30) cc_final: 0.7273 (m-30) REVERT: J 925 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8256 (tm-30) REVERT: J 1189 MET cc_start: 0.6984 (ptm) cc_final: 0.6743 (mmm) REVERT: J 1249 ASN cc_start: 0.8770 (OUTLIER) cc_final: 0.8567 (t0) outliers start: 106 outliers final: 65 residues processed: 382 average time/residue: 0.6928 time to fit residues: 304.9745 Evaluate side-chains 375 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 294 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 25 LYS Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 145 LYS Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 229 GLU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain I residue 14 ASP Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 118 LYS Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 451 ARG Chi-restraints excluded: chain I residue 452 ARG Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 601 ASP Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 631 GLU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 772 SER Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1114 GLU Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 413 ASP Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 700 ASN Chi-restraints excluded: chain J residue 712 GLN Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 864 LEU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 886 VAL Chi-restraints excluded: chain J residue 890 THR Chi-restraints excluded: chain J residue 925 GLU Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 994 SER Chi-restraints excluded: chain J residue 1011 VAL Chi-restraints excluded: chain J residue 1028 ILE Chi-restraints excluded: chain J residue 1060 VAL Chi-restraints excluded: chain J residue 1106 ILE Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1249 ASN Chi-restraints excluded: chain K residue 59 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 208 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 204 optimal weight: 6.9990 chunk 125 optimal weight: 0.0970 chunk 147 optimal weight: 10.0000 chunk 169 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 275 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 430 HIS J1249 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.196894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.151674 restraints weight = 28543.592| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 3.41 r_work: 0.3092 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26823 Z= 0.134 Angle : 0.537 11.705 36516 Z= 0.281 Chirality : 0.042 0.169 4187 Planarity : 0.004 0.059 4547 Dihedral : 13.070 173.523 4408 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.10 % Allowed : 16.99 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.23 (0.15), residues: 3174 helix: 1.59 (0.16), residues: 1086 sheet: 0.11 (0.24), residues: 445 loop : -0.82 (0.14), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 88 TYR 0.014 0.001 TYR I 70 PHE 0.012 0.001 PHE I 514 TRP 0.005 0.001 TRP I 807 HIS 0.004 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 (26815) covalent geometry : angle 0.53587 / 0.28 (36504) hydrogen bonds : bond 0.04495 / 2.21 ( 1096) hydrogen bonds : angle 3.95458 / 2.60 ( 3017) metal coordination : bond 0.00405 / 0.22 ( 8) metal coordination : angle 2.11813 / 1.41 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 300 time to evaluate : 0.976 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: G 25 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8190 (mtmt) REVERT: G 127 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7682 (mp10) REVERT: G 145 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.7991 (tttm) REVERT: I 88 ARG cc_start: 0.8000 (ttm110) cc_final: 0.7496 (mtt-85) REVERT: I 189 ASP cc_start: 0.7763 (OUTLIER) cc_final: 0.7436 (m-30) REVERT: I 434 ASP cc_start: 0.7626 (m-30) cc_final: 0.7405 (m-30) REVERT: I 451 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8185 (mtt180) REVERT: I 452 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8277 (mtp-110) REVERT: I 492 MET cc_start: 0.7412 (OUTLIER) cc_final: 0.7052 (ptm) REVERT: I 632 ASP cc_start: 0.7810 (OUTLIER) cc_final: 0.7610 (t0) REVERT: I 697 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.7767 (pmtt) REVERT: I 739 ASP cc_start: 0.8567 (t0) cc_final: 0.8218 (m-30) REVERT: I 1114 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.7597 (tm-30) REVERT: I 1156 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7211 (ptt180) REVERT: I 1219 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8224 (mm-30) REVERT: J 48 THR cc_start: 0.8106 (OUTLIER) cc_final: 0.7832 (p) REVERT: J 66 LYS cc_start: 0.7894 (tttm) cc_final: 0.7558 (tttm) REVERT: J 137 ARG cc_start: 0.7489 (mtt180) cc_final: 0.7038 (mmt90) REVERT: J 205 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8386 (tt) REVERT: J 298 MET cc_start: 0.7527 (mmm) cc_final: 0.7200 (mtm) REVERT: J 301 GLU cc_start: 0.7354 (tp30) cc_final: 0.6987 (mt-10) REVERT: J 413 ASP cc_start: 0.7470 (OUTLIER) cc_final: 0.7151 (m-30) REVERT: J 497 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7847 (mp0) REVERT: J 709 ARG cc_start: 0.7717 (ppt-90) cc_final: 0.7394 (ppt90) REVERT: J 712 GLN cc_start: 0.7371 (OUTLIER) cc_final: 0.6888 (mp10) REVERT: J 737 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8191 (mp) REVERT: J 751 ASP cc_start: 0.6457 (OUTLIER) cc_final: 0.5724 (p0) REVERT: J 802 ASP cc_start: 0.7646 (m-30) cc_final: 0.7296 (m-30) REVERT: J 842 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8295 (mtt180) REVERT: J 925 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8232 (tm-30) REVERT: J 1138 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8142 (tt) REVERT: J 1371 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7056 (tmm160) outliers start: 111 outliers final: 71 residues processed: 386 average time/residue: 0.7039 time to fit residues: 313.7289 Evaluate side-chains 382 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 289 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 25 LYS Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 145 LYS Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 229 GLU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain I residue 14 ASP Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 118 LYS Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 451 ARG Chi-restraints excluded: chain I residue 452 ARG Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 492 MET Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 601 ASP Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 631 GLU Chi-restraints excluded: chain I residue 632 ASP Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 772 SER Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1114 GLU Chi-restraints excluded: chain I residue 1156 ARG Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1322 SER Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain J residue 413 ASP Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 700 ASN Chi-restraints excluded: chain J residue 712 GLN Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 842 ARG Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 857 LEU Chi-restraints excluded: chain J residue 864 LEU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 886 VAL Chi-restraints excluded: chain J residue 890 THR Chi-restraints excluded: chain J residue 925 GLU Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 994 SER Chi-restraints excluded: chain J residue 1011 VAL Chi-restraints excluded: chain J residue 1028 ILE Chi-restraints excluded: chain J residue 1060 VAL Chi-restraints excluded: chain J residue 1106 ILE Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain J residue 1138 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1371 ARG Chi-restraints excluded: chain K residue 59 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 56 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 29 optimal weight: 0.3980 chunk 153 optimal weight: 2.9990 chunk 305 optimal weight: 5.9990 chunk 213 optimal weight: 3.9990 chunk 317 optimal weight: 0.0050 chunk 201 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 302 optimal weight: 4.9990 chunk 188 optimal weight: 0.5980 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 762 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.199913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.156365 restraints weight = 28808.924| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 3.38 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 26823 Z= 0.099 Angle : 0.502 13.212 36516 Z= 0.262 Chirality : 0.040 0.167 4187 Planarity : 0.004 0.076 4547 Dihedral : 12.914 173.876 4408 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.14 % Allowed : 17.99 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.44 (0.15), residues: 3174 helix: 1.81 (0.16), residues: 1087 sheet: 0.21 (0.25), residues: 441 loop : -0.73 (0.14), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG J 60 TYR 0.010 0.001 TYR J 679 PHE 0.010 0.001 PHE J 892 TRP 0.005 0.001 TRP J 33 HIS 0.003 0.000 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (26815) covalent geometry : angle 0.50100 / 0.26 (36504) hydrogen bonds : bond 0.03430 / 1.69 ( 1096) hydrogen bonds : angle 3.79638 / 2.50 ( 3017) metal coordination : bond 0.00292 / 0.16 ( 8) metal coordination : angle 2.02853 / 1.35 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 308 time to evaluate : 1.078 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: G 25 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.7968 (mtmt) REVERT: G 127 GLN cc_start: 0.7259 (OUTLIER) cc_final: 0.7011 (mp10) REVERT: G 143 ARG cc_start: 0.7084 (mmm-85) cc_final: 0.6750 (mtm180) REVERT: G 145 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7902 (tttm) REVERT: H 200 LYS cc_start: 0.8760 (ttpp) cc_final: 0.8522 (tttp) REVERT: I 88 ARG cc_start: 0.7486 (ttm110) cc_final: 0.7240 (mtt-85) REVERT: I 434 ASP cc_start: 0.7162 (m-30) cc_final: 0.6934 (m-30) REVERT: I 452 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7948 (mtp-110) REVERT: I 697 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.7292 (pmtt) REVERT: I 719 LYS cc_start: 0.7959 (mttt) cc_final: 0.7756 (mttt) REVERT: I 1114 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7565 (tt0) REVERT: J 137 ARG cc_start: 0.7361 (mtt180) cc_final: 0.7043 (mmt90) REVERT: J 227 PHE cc_start: 0.8556 (OUTLIER) cc_final: 0.7682 (t80) REVERT: J 244 VAL cc_start: 0.8154 (m) cc_final: 0.7842 (t) REVERT: J 497 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7232 (mp0) REVERT: J 737 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8208 (mp) REVERT: J 773 PHE cc_start: 0.6875 (OUTLIER) cc_final: 0.5978 (m-80) REVERT: J 802 ASP cc_start: 0.6637 (m-30) cc_final: 0.6437 (m-30) REVERT: J 842 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.8115 (mmt180) REVERT: J 848 VAL cc_start: 0.8054 (OUTLIER) cc_final: 0.7741 (t) REVERT: J 925 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7811 (tm-30) REVERT: J 1138 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8127 (tt) outliers start: 85 outliers final: 41 residues processed: 368 average time/residue: 0.7260 time to fit residues: 307.9153 Evaluate side-chains 351 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 297 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 25 LYS Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 145 LYS Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 229 GLU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 118 LYS Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 452 ARG Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 631 GLU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 772 SER Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1114 GLU Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 773 PHE Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 842 ARG Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 864 LEU Chi-restraints excluded: chain J residue 925 GLU Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 994 SER Chi-restraints excluded: chain J residue 1011 VAL Chi-restraints excluded: chain J residue 1028 ILE Chi-restraints excluded: chain J residue 1060 VAL Chi-restraints excluded: chain J residue 1106 ILE Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain J residue 1138 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1239 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 294 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 175 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 134 optimal weight: 0.2980 chunk 317 optimal weight: 0.0980 chunk 144 optimal weight: 9.9990 chunk 316 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 437 ASN J 229 GLN J 430 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.198156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.152521 restraints weight = 28753.561| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 3.55 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26823 Z= 0.130 Angle : 0.548 13.019 36516 Z= 0.284 Chirality : 0.042 0.175 4187 Planarity : 0.004 0.056 4547 Dihedral : 12.964 172.421 4403 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.70 % Allowed : 18.62 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.36 (0.15), residues: 3174 helix: 1.72 (0.16), residues: 1087 sheet: 0.20 (0.24), residues: 444 loop : -0.78 (0.14), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG J1123 TYR 0.014 0.001 TYR J 457 PHE 0.012 0.001 PHE I 514 TRP 0.005 0.001 TRP J 686 HIS 0.004 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (26815) covalent geometry : angle 0.54663 / 0.28 (36504) hydrogen bonds : bond 0.04278 / 2.11 ( 1096) hydrogen bonds : angle 3.87082 / 2.55 ( 3017) metal coordination : bond 0.00397 / 0.22 ( 8) metal coordination : angle 1.97035 / 1.31 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 299 time to evaluate : 0.995 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: G 25 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8002 (mtmt) REVERT: G 127 GLN cc_start: 0.7286 (OUTLIER) cc_final: 0.7035 (mp10) REVERT: G 145 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7898 (tttm) REVERT: I 434 ASP cc_start: 0.7185 (m-30) cc_final: 0.6968 (m-30) REVERT: I 451 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.7812 (mtt180) REVERT: I 452 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.8053 (mtp-110) REVERT: I 697 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.7462 (pmtt) REVERT: I 1114 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7185 (tm-30) REVERT: I 1156 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7242 (ptt180) REVERT: J 137 ARG cc_start: 0.7416 (mtt180) cc_final: 0.7087 (mmt90) REVERT: J 227 PHE cc_start: 0.8599 (OUTLIER) cc_final: 0.7683 (t80) REVERT: J 244 VAL cc_start: 0.8233 (m) cc_final: 0.7894 (t) REVERT: J 282 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7631 (tt) REVERT: J 413 ASP cc_start: 0.6685 (OUTLIER) cc_final: 0.6440 (m-30) REVERT: J 497 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7253 (mp0) REVERT: J 737 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8254 (mp) REVERT: J 802 ASP cc_start: 0.6635 (m-30) cc_final: 0.6418 (m-30) REVERT: J 848 VAL cc_start: 0.8061 (OUTLIER) cc_final: 0.7782 (t) REVERT: J 925 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7960 (tm-30) REVERT: J 1138 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8195 (tt) outliers start: 73 outliers final: 48 residues processed: 352 average time/residue: 0.7354 time to fit residues: 298.3232 Evaluate side-chains 352 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 289 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 25 LYS Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 145 LYS Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 229 GLU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 118 LYS Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 451 ARG Chi-restraints excluded: chain I residue 452 ARG Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 601 ASP Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 631 GLU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 772 SER Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1114 GLU Chi-restraints excluded: chain I residue 1135 GLN Chi-restraints excluded: chain I residue 1156 ARG Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain J residue 413 ASP Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 864 LEU Chi-restraints excluded: chain J residue 925 GLU Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 994 SER Chi-restraints excluded: chain J residue 1011 VAL Chi-restraints excluded: chain J residue 1028 ILE Chi-restraints excluded: chain J residue 1060 VAL Chi-restraints excluded: chain J residue 1106 ILE Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain J residue 1138 LEU Chi-restraints excluded: chain J residue 1163 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 22 optimal weight: 5.9990 chunk 228 optimal weight: 4.9990 chunk 166 optimal weight: 0.0170 chunk 95 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 219 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 169 optimal weight: 0.0980 overall best weight: 1.3822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 430 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.196975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.152823 restraints weight = 28658.883| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 3.37 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26823 Z= 0.127 Angle : 0.553 16.340 36516 Z= 0.286 Chirality : 0.042 0.176 4187 Planarity : 0.004 0.090 4547 Dihedral : 12.972 172.815 4401 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.66 % Allowed : 18.73 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.34 (0.15), residues: 3174 helix: 1.71 (0.16), residues: 1087 sheet: 0.17 (0.24), residues: 449 loop : -0.79 (0.14), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.000 ARG J 60 TYR 0.013 0.001 TYR J 457 PHE 0.016 0.001 PHE I 195 TRP 0.005 0.001 TRP J 409 HIS 0.004 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (26815) covalent geometry : angle 0.55197 / 0.29 (36504) hydrogen bonds : bond 0.04236 / 2.08 ( 1096) hydrogen bonds : angle 3.87411 / 2.55 ( 3017) metal coordination : bond 0.00382 / 0.21 ( 8) metal coordination : angle 2.00947 / 1.34 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 291 time to evaluate : 1.116 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: G 25 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.7992 (mtmt) REVERT: G 127 GLN cc_start: 0.7304 (OUTLIER) cc_final: 0.7049 (mp10) REVERT: G 145 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7878 (tttm) REVERT: I 88 ARG cc_start: 0.7568 (ttm110) cc_final: 0.7245 (mtt-85) REVERT: I 451 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.7822 (mtt180) REVERT: I 452 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.8025 (mtp-110) REVERT: I 697 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.7442 (pmtt) REVERT: I 1114 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7264 (tm-30) REVERT: I 1156 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7250 (ptt180) REVERT: J 29 MET cc_start: 0.7490 (ttp) cc_final: 0.7178 (ptm) REVERT: J 137 ARG cc_start: 0.7442 (mtt180) cc_final: 0.7124 (mmt90) REVERT: J 227 PHE cc_start: 0.8628 (OUTLIER) cc_final: 0.7753 (t80) REVERT: J 244 VAL cc_start: 0.8270 (m) cc_final: 0.7944 (t) REVERT: J 282 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7625 (tt) REVERT: J 497 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7235 (mp0) REVERT: J 737 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8213 (mp) REVERT: J 802 ASP cc_start: 0.6659 (m-30) cc_final: 0.6422 (m-30) REVERT: J 848 VAL cc_start: 0.8002 (OUTLIER) cc_final: 0.7783 (t) REVERT: J 925 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7948 (tm-30) REVERT: J 1123 ARG cc_start: 0.7306 (mtm110) cc_final: 0.6964 (ptt-90) REVERT: J 1138 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8179 (tt) outliers start: 72 outliers final: 48 residues processed: 346 average time/residue: 0.7352 time to fit residues: 291.7087 Evaluate side-chains 346 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 284 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 25 LYS Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 145 LYS Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 229 GLU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 118 LYS Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 451 ARG Chi-restraints excluded: chain I residue 452 ARG Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 601 ASP Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 631 GLU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 772 SER Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1114 GLU Chi-restraints excluded: chain I residue 1156 ARG Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 693 VAL Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 864 LEU Chi-restraints excluded: chain J residue 886 VAL Chi-restraints excluded: chain J residue 925 GLU Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 994 SER Chi-restraints excluded: chain J residue 1011 VAL Chi-restraints excluded: chain J residue 1028 ILE Chi-restraints excluded: chain J residue 1060 VAL Chi-restraints excluded: chain J residue 1106 ILE Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain J residue 1138 LEU Chi-restraints excluded: chain J residue 1163 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 57 optimal weight: 5.9990 chunk 209 optimal weight: 0.0370 chunk 149 optimal weight: 7.9990 chunk 144 optimal weight: 0.6980 chunk 312 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 318 optimal weight: 6.9990 chunk 278 optimal weight: 1.9990 chunk 73 optimal weight: 50.0000 chunk 102 optimal weight: 2.9990 chunk 299 optimal weight: 1.9990 overall best weight: 1.1464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 430 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.198728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.153241 restraints weight = 28515.865| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 3.46 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26823 Z= 0.116 Angle : 0.535 15.709 36516 Z= 0.277 Chirality : 0.041 0.171 4187 Planarity : 0.004 0.082 4547 Dihedral : 12.942 172.647 4401 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.66 % Allowed : 18.95 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.39 (0.15), residues: 3174 helix: 1.76 (0.16), residues: 1087 sheet: 0.21 (0.24), residues: 449 loop : -0.77 (0.14), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG I 88 TYR 0.014 0.001 TYR I 70 PHE 0.018 0.001 PHE I 195 TRP 0.005 0.001 TRP J 409 HIS 0.004 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (26815) covalent geometry : angle 0.53400 / 0.28 (36504) hydrogen bonds : bond 0.04008 / 1.97 ( 1096) hydrogen bonds : angle 3.84976 / 2.54 ( 3017) metal coordination : bond 0.00356 / 0.19 ( 8) metal coordination : angle 1.90344 / 1.27 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9527.98 seconds wall clock time: 162 minutes 35.60 seconds (9755.60 seconds total)