Starting phenix.real_space_refine on Tue Feb 20 00:06:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eh8_28143/02_2024/8eh8_28143_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eh8_28143/02_2024/8eh8_28143.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eh8_28143/02_2024/8eh8_28143.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eh8_28143/02_2024/8eh8_28143.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eh8_28143/02_2024/8eh8_28143_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eh8_28143/02_2024/8eh8_28143_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 16257 2.51 5 N 4640 2.21 5 O 5177 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G GLU 58": "OE1" <-> "OE2" Residue "G GLU 76": "OE1" <-> "OE2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "I GLU 44": "OE1" <-> "OE2" Residue "I GLU 461": "OE1" <-> "OE2" Residue "I GLU 472": "OE1" <-> "OE2" Residue "I GLU 631": "OE1" <-> "OE2" Residue "I GLU 641": "OE1" <-> "OE2" Residue "I GLU 1143": "OE1" <-> "OE2" Residue "J GLU 100": "OE1" <-> "OE2" Residue "J GLU 195": "OE1" <-> "OE2" Residue "J GLU 199": "OE1" <-> "OE2" Residue "J GLU 402": "OE1" <-> "OE2" Residue "J GLU 418": "OE1" <-> "OE2" Residue "J GLU 497": "OE1" <-> "OE2" Residue "J GLU 532": "OE1" <-> "OE2" Residue "J GLU 658": "OE1" <-> "OE2" Residue "J GLU 811": "OE1" <-> "OE2" Residue "J GLU 833": "OE1" <-> "OE2" Residue "J GLU 981": "OE1" <-> "OE2" Residue "J GLU 1158": "OE1" <-> "OE2" Residue "J GLU 1205": "OE1" <-> "OE2" Residue "J GLU 1254": "OE1" <-> "OE2" Residue "J GLU 1276": "OE1" <-> "OE2" Residue "J GLU 1334": "OE1" <-> "OE2" Residue "K GLU 42": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26246 Number of models: 1 Model: "" Number of chains: 11 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: "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: "G" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1679 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1689 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 10375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1316, 10375 Classifications: {'peptide': 1316} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1260} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 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: {'GLN:plan1': 1, 'GLU:plan': 2} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15505 SG CYS J 70 103.836 100.483 90.419 1.00 70.37 S ATOM 15519 SG CYS J 72 104.023 104.237 91.029 1.00 75.80 S ATOM 15627 SG CYS J 85 106.007 101.835 93.174 1.00 70.92 S ATOM 15651 SG CYS J 88 102.184 102.000 93.480 1.00 68.44 S ATOM 21331 SG CYS J 814 86.797 35.957 86.865 1.00 40.60 S ATOM 21896 SG CYS J 888 85.189 39.298 87.381 1.00 32.63 S ATOM 21947 SG CYS J 895 85.991 38.080 83.828 1.00 30.88 S ATOM 21968 SG CYS J 898 83.206 36.455 85.725 1.00 30.20 S Time building chain proxies: 13.35, per 1000 atoms: 0.51 Number of scatterers: 26246 At special positions: 0 Unit cell: (137.8, 145.6, 165.1, 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 5177 8.00 N 4640 7.00 C 16257 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 - 3.50 Amino acid : False - 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: 10.66 Conformation dependent library (CDL) restraints added in 5.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1501 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 88 " pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 888 " 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... running ksdssp... Secondary structure from input PDB file: 100 helices and 35 sheets defined 31.6% alpha, 11.6% beta 28 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 13.30 Creating SS restraints... Processing helix chain 'G' and resid 35 through 49 Processing helix chain 'G' and resid 78 through 86 Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'G' and resid 213 through 230 removed outlier: 4.219A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 49 Processing helix chain 'H' and resid 78 through 86 Processing helix chain 'H' and resid 112 through 114 No H-bonds generated for 'chain 'H' and resid 112 through 114' Processing helix chain 'H' and resid 213 through 229 removed outlier: 3.889A pdb=" N GLU H 229 " --> pdb=" O ALA H 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 31 through 39 Processing helix chain 'I' and resid 50 through 53 No H-bonds generated for 'chain 'I' and resid 50 through 53' Processing helix chain 'I' and resid 82 through 88 Processing helix chain 'I' and resid 206 through 212 Processing helix chain 'I' and resid 217 through 224 Processing helix chain 'I' and resid 243 through 246 Processing helix chain 'I' and resid 271 through 280 Processing helix chain 'I' and resid 289 through 294 removed outlier: 3.706A pdb=" N GLY I 294 " --> pdb=" O TYR I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 319 through 326 Processing helix chain 'I' and resid 346 through 353 Processing helix chain 'I' and resid 359 through 370 Processing helix chain 'I' and resid 378 through 389 removed outlier: 4.185A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 399 through 408 Processing helix chain 'I' and resid 422 through 437 Processing helix chain 'I' and resid 448 through 450 No H-bonds generated for 'chain 'I' and resid 448 through 450' Processing helix chain 'I' and resid 456 through 481 removed outlier: 4.177A pdb=" N SER I 480 " --> pdb=" O LYS I 476 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU I 481 " --> pdb=" O GLU I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 507 Processing helix chain 'I' and resid 520 through 527 Processing helix chain 'I' and resid 552 through 554 No H-bonds generated for 'chain 'I' and resid 552 through 554' Processing helix chain 'I' and resid 657 through 659 No H-bonds generated for 'chain 'I' and resid 657 through 659' Processing helix chain 'I' and resid 665 through 667 No H-bonds generated for 'chain 'I' and resid 665 through 667' Processing helix chain 'I' and resid 671 through 673 No H-bonds generated for 'chain 'I' and resid 671 through 673' Processing helix chain 'I' and resid 676 through 687 Processing helix chain 'I' and resid 705 through 712 Processing helix chain 'I' and resid 820 through 824 Processing helix chain 'I' and resid 943 through 979 removed outlier: 3.520A pdb=" N LEU I 960 " --> pdb=" O ALA I 956 " (cutoff:3.500A) Processing helix chain 'I' and resid 986 through 991 removed outlier: 3.938A pdb=" N ASP I 990 " --> pdb=" O ALA I 986 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LYS I 991 " --> pdb=" O GLU I 987 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 986 through 991' Processing helix chain 'I' and resid 1006 through 1036 Processing helix chain 'I' and resid 1082 through 1084 No H-bonds generated for 'chain 'I' and resid 1082 through 1084' Processing helix chain 'I' and resid 1100 through 1105 Proline residue: I1104 - end of helix Processing helix chain 'I' and resid 1109 through 1133 removed outlier: 3.523A pdb=" N LEU I1113 " --> pdb=" O GLY I1110 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS I1133 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1138 through 1149 Processing helix chain 'I' and resid 1161 through 1163 No H-bonds generated for 'chain 'I' and resid 1161 through 1163' Processing helix chain 'I' and resid 1168 through 1176 Processing helix chain 'I' and resid 1192 through 1201 Processing helix chain 'I' and resid 1239 through 1241 No H-bonds generated for 'chain 'I' and resid 1239 through 1241' Processing helix chain 'I' and resid 1272 through 1281 removed outlier: 3.617A pdb=" N TRP I1276 " --> pdb=" O GLU I1272 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA I1277 " --> pdb=" O MET I1273 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU I1278 " --> pdb=" O GLU I1274 " (cutoff:3.500A) Processing helix chain 'I' and resid 1284 through 1291 Processing helix chain 'I' and resid 1299 through 1310 Processing helix chain 'I' and resid 1321 through 1331 Processing helix chain 'J' and resid 27 through 33 Processing helix chain 'J' and resid 78 through 80 No H-bonds generated for 'chain 'J' and resid 78 through 80' Processing helix chain 'J' and resid 95 through 99 removed outlier: 3.852A pdb=" N ARG J 99 " --> pdb=" O LYS J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 115 through 118 No H-bonds generated for 'chain 'J' and resid 115 through 118' Processing helix chain 'J' and resid 123 through 127 Processing helix chain 'J' and resid 132 through 139 Processing helix chain 'J' and resid 162 through 171 Processing helix chain 'J' and resid 182 through 190 Processing helix chain 'J' and resid 194 through 207 Processing helix chain 'J' and resid 211 through 229 Processing helix chain 'J' and resid 234 through 237 Processing helix chain 'J' and resid 247 through 249 No H-bonds generated for 'chain 'J' and resid 247 through 249' Processing helix chain 'J' and resid 264 through 284 removed outlier: 3.520A pdb=" N ASP J 284 " --> pdb=" O LYS J 280 " (cutoff:3.500A) Processing helix chain 'J' and resid 289 through 307 Processing helix chain 'J' and resid 370 through 376 removed outlier: 3.711A pdb=" N LEU J 374 " --> pdb=" O LYS J 370 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU J 375 " --> pdb=" O LYS J 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 378 through 388 Processing helix chain 'J' and resid 394 through 403 Processing helix chain 'J' and resid 406 through 415 removed outlier: 4.266A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 431 through 433 No H-bonds generated for 'chain 'J' and resid 431 through 433' Processing helix chain 'J' and resid 454 through 457 No H-bonds generated for 'chain 'J' and resid 454 through 457' Processing helix chain 'J' and resid 474 through 482 Processing helix chain 'J' and resid 486 through 488 No H-bonds generated for 'chain 'J' and resid 486 through 488' Processing helix chain 'J' and resid 506 through 513 Processing helix chain 'J' and resid 530 through 539 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.789A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 599 through 611 Processing helix chain 'J' and resid 614 through 635 removed outlier: 3.890A pdb=" N SER J 635 " --> pdb=" O TYR J 631 " (cutoff:3.500A) Processing helix chain 'J' and resid 650 through 670 Processing helix chain 'J' and resid 675 through 702 removed outlier: 4.027A pdb=" N TYR J 679 " --> pdb=" O ALA J 675 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASN J 680 " --> pdb=" O GLY J 676 " (cutoff:3.500A) Processing helix chain 'J' and resid 721 through 727 Processing helix chain 'J' and resid 734 through 741 Processing helix chain 'J' and resid 771 through 789 removed outlier: 3.793A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR J 786 " --> pdb=" O GLY J 782 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA J 787 " --> pdb=" O LEU J 783 " (cutoff:3.500A) Processing helix chain 'J' and resid 791 through 801 removed outlier: 4.169A pdb=" N LEU J 796 " --> pdb=" O ASN J 792 " (cutoff:3.500A) Processing helix chain 'J' and resid 835 through 839 Processing helix chain 'J' and resid 866 through 875 Processing helix chain 'J' and resid 896 through 899 No H-bonds generated for 'chain 'J' and resid 896 through 899' Processing helix chain 'J' and resid 915 through 924 Processing helix chain 'J' and resid 927 through 931 Processing helix chain 'J' and resid 1070 through 1073 removed outlier: 4.430A pdb=" N ASP J1073 " --> pdb=" O GLY J1070 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 1070 through 1073' Processing helix chain 'J' and resid 1140 through 1146 Processing helix chain 'J' and resid 1219 through 1244 removed outlier: 7.919A pdb=" N VAL J1226 " --> pdb=" O ARG J1222 " (cutoff:3.500A) removed outlier: 8.899A pdb=" N HIS J1227 " --> pdb=" O LEU J1223 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA J1228 " --> pdb=" O ARG J1224 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1260 Processing helix chain 'J' and resid 1282 through 1294 Processing helix chain 'J' and resid 1311 through 1314 No H-bonds generated for 'chain 'J' and resid 1311 through 1314' Processing helix chain 'J' and resid 1319 through 1325 Processing helix chain 'J' and resid 1328 through 1338 Processing helix chain 'J' and resid 1348 through 1353 Processing helix chain 'J' and resid 1363 through 1372 Processing helix chain 'K' and resid 7 through 12 Processing helix chain 'K' and resid 18 through 31 Processing helix chain 'K' and resid 46 through 56 Processing helix chain 'K' and resid 61 through 79 Processing sheet with id= A, first strand: chain 'G' and resid 12 through 17 removed outlier: 6.901A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'G' and resid 97 through 99 removed outlier: 3.870A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N GLY G 149 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N CYS G 54 " --> pdb=" O GLY G 149 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'G' and resid 102 through 105 removed outlier: 3.617A pdb=" N LYS G 104 " --> pdb=" O ILE G 140 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'G' and resid 151 through 153 Processing sheet with id= E, first strand: chain 'G' and resid 187 through 189 Processing sheet with id= F, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.553A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 12 through 15 removed outlier: 3.509A pdb=" N GLU H 29 " --> pdb=" O ARG H 12 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N THR H 27 " --> pdb=" O VAL H 14 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 97 through 101 removed outlier: 6.087A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 108 through 111 Processing sheet with id= J, first strand: chain 'I' and resid 93 through 95 Processing sheet with id= K, first strand: chain 'I' and resid 143 through 145 Processing sheet with id= L, first strand: chain 'I' and resid 148 through 151 removed outlier: 3.531A pdb=" N HIS I 150 " --> pdb=" O ARG I 452 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'I' and resid 154 through 158 removed outlier: 3.580A pdb=" N ASN I 173 " --> pdb=" O ASP I 158 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'I' and resid 184 through 188 Processing sheet with id= O, first strand: chain 'I' and resid 227 through 231 Processing sheet with id= P, first strand: chain 'I' and resid 603 through 607 Processing sheet with id= Q, first strand: chain 'I' and resid 633 through 637 Processing sheet with id= R, first strand: chain 'I' and resid 749 through 752 removed outlier: 3.651A pdb=" N ASP I 749 " --> pdb=" O ILE I 734 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 1226 through 1233 removed outlier: 4.516A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE I1096 " --> pdb=" O ALA I 803 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 930 through 935 removed outlier: 3.839A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N SER I 840 " --> pdb=" O LEU I1047 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ILE I1049 " --> pdb=" O CYS I 838 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N CYS I 838 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LYS I1051 " --> pdb=" O LEU I 836 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N LEU I 836 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TYR I1053 " --> pdb=" O GLN I 834 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLN I 834 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA I1055 " --> pdb=" O HIS I 832 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N HIS I 832 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYS I1057 " --> pdb=" O THR I 830 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N THR I 830 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 66 through 75 removed outlier: 6.809A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL I 98 " --> pdb=" O VAL I 122 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS I 118 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE I 104 " --> pdb=" O ASP I 116 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'I' and resid 816 through 819 removed outlier: 7.695A pdb=" N VAL I 818 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ILE I1079 " --> pdb=" O VAL I 818 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'J' and resid 103 through 106 removed outlier: 3.713A pdb=" N GLY J 103 " --> pdb=" O VAL J 244 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'J' and resid 350 through 354 Processing sheet with id= Y, first strand: chain 'J' and resid 365 through 369 removed outlier: 6.247A pdb=" N GLU J 438 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU J 368 " --> pdb=" O GLU J 438 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N VAL J 440 " --> pdb=" O LEU J 368 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'J' and resid 548 through 556 removed outlier: 3.710A pdb=" N GLU J 554 " --> pdb=" O LYS J 566 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'J' and resid 706 through 708 Processing sheet with id= AB, first strand: chain 'J' and resid 820 through 822 Processing sheet with id= AC, first strand: chain 'J' and resid 957 through 961 Processing sheet with id= AD, first strand: chain 'J' and resid 965 through 967 Processing sheet with id= AE, first strand: chain 'J' and resid 1034 through 1038 removed outlier: 3.575A pdb=" N LYS J1079 " --> pdb=" O ARG J1036 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR J1038 " --> pdb=" O ALA J1077 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'J' and resid 1046 through 1051 removed outlier: 3.810A pdb=" N GLN J1049 " --> pdb=" O SER J1058 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU J1056 " --> pdb=" O ASP J1051 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU J1059 " --> pdb=" O VAL J1107 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL J1107 " --> pdb=" O LEU J1059 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA J1105 " --> pdb=" O VAL J1061 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'J' and resid 1162 through 1165 removed outlier: 3.525A pdb=" N ILE J1177 " --> pdb=" O TYR J1186 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N TYR J1186 " --> pdb=" O ILE J1177 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 3.778A pdb=" N VAL J1280 " --> pdb=" O ALA J1264 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'J' and resid 949 through 952 removed outlier: 4.042A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL J 952 " --> pdb=" O THR J1016 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR J1016 " --> pdb=" O VAL J 952 " (cutoff:3.500A) 769 hydrogen bonds defined for protein. 2160 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 71 hydrogen bonds 142 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 11.75 Time building geometry restraints manager: 11.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8688 1.34 - 1.46: 4857 1.46 - 1.58: 12911 1.58 - 1.70: 126 1.70 - 1.82: 187 Bond restraints: 26769 Sorted by residual: bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.824 -0.292 2.00e-02 2.50e+03 2.13e+02 bond pdb=" C3 1N7 I1401 " pdb=" C4 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.729 -0.197 2.00e-02 2.50e+03 9.74e+01 bond pdb=" C7 1N7 I1401 " pdb=" C8 1N7 I1401 " ideal model delta sigma weight residual 1.542 1.705 -0.163 2.00e-02 2.50e+03 6.64e+01 bond pdb=" C19 1N7 I1401 " pdb=" C2 1N7 I1401 " ideal model delta sigma weight residual 1.551 1.403 0.148 2.00e-02 2.50e+03 5.48e+01 bond pdb=" C4 1N7 I1401 " pdb=" C5 1N7 I1401 " ideal model delta sigma weight residual 1.534 1.396 0.138 2.00e-02 2.50e+03 4.76e+01 ... (remaining 26764 not shown) Histogram of bond angle deviations from ideal: 98.64 - 105.73: 855 105.73 - 112.82: 14509 112.82 - 119.91: 9068 119.91 - 127.00: 11658 127.00 - 134.09: 347 Bond angle restraints: 36437 Sorted by residual: angle pdb=" N ILE J 331 " pdb=" CA ILE J 331 " pdb=" C ILE J 331 " ideal model delta sigma weight residual 113.53 108.67 4.86 9.80e-01 1.04e+00 2.46e+01 angle pdb=" N VAL J 769 " pdb=" CA VAL J 769 " pdb=" C VAL J 769 " ideal model delta sigma weight residual 113.00 108.09 4.91 1.30e+00 5.92e-01 1.43e+01 angle pdb=" C GLY J 924 " pdb=" N GLU J 925 " pdb=" CA GLU J 925 " ideal model delta sigma weight residual 121.80 113.14 8.66 2.44e+00 1.68e-01 1.26e+01 angle pdb=" C ARG J 709 " pdb=" N ASP J 710 " pdb=" CA ASP J 710 " ideal model delta sigma weight residual 126.45 132.56 -6.11 1.77e+00 3.19e-01 1.19e+01 angle pdb=" N GLU J 925 " pdb=" CA GLU J 925 " pdb=" C GLU J 925 " ideal model delta sigma weight residual 109.81 117.05 -7.24 2.21e+00 2.05e-01 1.07e+01 ... (remaining 36432 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 15863 35.83 - 71.65: 507 71.65 - 107.48: 27 107.48 - 143.30: 1 143.30 - 179.13: 1 Dihedral angle restraints: 16399 sinusoidal: 7248 harmonic: 9151 Sorted by residual: dihedral pdb=" CA LEU J1138 " pdb=" C LEU J1138 " pdb=" N PRO J1139 " pdb=" CA PRO J1139 " ideal model delta harmonic sigma weight residual 180.00 145.39 34.61 0 5.00e+00 4.00e-02 4.79e+01 dihedral pdb=" CA GLU J 925 " pdb=" C GLU J 925 " pdb=" N PRO J 926 " pdb=" CA PRO J 926 " ideal model delta harmonic sigma weight residual 180.00 147.14 32.86 0 5.00e+00 4.00e-02 4.32e+01 dihedral pdb=" CA GLY J 852 " pdb=" C GLY J 852 " pdb=" N THR J 853 " pdb=" CA THR J 853 " ideal model delta harmonic sigma weight residual -180.00 -155.47 -24.53 0 5.00e+00 4.00e-02 2.41e+01 ... (remaining 16396 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 3875 0.082 - 0.164: 295 0.164 - 0.247: 3 0.247 - 0.329: 2 0.329 - 0.411: 1 Chirality restraints: 4176 Sorted by residual: chirality pdb=" C19 1N7 I1401 " pdb=" C18 1N7 I1401 " pdb=" C2 1N7 I1401 " pdb=" C3 1N7 I1401 " both_signs ideal model delta sigma weight residual False -2.53 -2.94 0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" C15 1N7 I1401 " pdb=" C14 1N7 I1401 " pdb=" C16 1N7 I1401 " pdb=" C2 1N7 I1401 " both_signs ideal model delta sigma weight residual False -2.47 -2.75 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C5 1N7 I1401 " pdb=" C4 1N7 I1401 " pdb=" C6 1N7 I1401 " pdb=" C9 1N7 I1401 " both_signs ideal model delta sigma weight residual False -2.85 -2.60 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 4173 not shown) Planarity restraints: 4544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU J 925 " -0.056 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO J 926 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO J 926 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO J 926 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU J1138 " 0.052 5.00e-02 4.00e+02 7.96e-02 1.02e+01 pdb=" N PRO J1139 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO J1139 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO J1139 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS J 850 " 0.032 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO J 851 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO J 851 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO J 851 " 0.027 5.00e-02 4.00e+02 ... (remaining 4541 not shown) Histogram of nonbonded interaction distances: 1.20 - 1.94: 1 1.94 - 2.68: 626 2.68 - 3.42: 36009 3.42 - 4.16: 63038 4.16 - 4.90: 114197 Nonbonded interactions: 213871 Sorted by model distance: nonbonded pdb=" CG2 ILE J 664 " pdb=" NZ LYS J 681 " model vdw 1.203 3.540 nonbonded pdb=" O3' C R 18 " pdb="MG MG R 101 " model vdw 2.066 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG R 101 " model vdw 2.164 2.170 nonbonded pdb=" O ILE I 11 " pdb=" OH TYR I1149 " model vdw 2.197 2.440 nonbonded pdb=" OG SER J1318 " pdb=" OD2 ASP J1342 " model vdw 2.215 2.440 ... (remaining 213866 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'G' and (resid 8 through 135 or (resid 136 and (name N or name CA or name \ C or name O or name CB )) or resid 137 through 158 or resid 170 through 231)) selection = (chain 'H' and (resid 8 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 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: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 5.460 Check model and map are aligned: 0.440 Set scattering table: 0.250 Process input model: 81.870 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.090 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 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 0.292 26769 Z= 0.293 Angle : 0.593 11.095 36437 Z= 0.334 Chirality : 0.043 0.411 4176 Planarity : 0.004 0.084 4544 Dihedral : 15.425 179.130 10515 Min Nonbonded Distance : 1.203 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.77 % Allowed : 8.65 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.14), residues: 3174 helix: 0.12 (0.15), residues: 1094 sheet: -1.45 (0.25), residues: 410 loop : -1.74 (0.14), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 580 HIS 0.005 0.001 HIS J 430 PHE 0.009 0.001 PHE I1025 TYR 0.011 0.001 TYR I1018 ARG 0.003 0.000 ARG K 28 *********************** 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 564 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 462 time to evaluate : 2.846 Fit side-chains revert: symmetry clash REVERT: I 70 TYR cc_start: 0.8481 (t80) cc_final: 0.8206 (t80) REVERT: I 207 THR cc_start: 0.8596 (p) cc_final: 0.8304 (p) REVERT: I 573 ASN cc_start: 0.7851 (m110) cc_final: 0.7594 (m110) REVERT: I 686 GLN cc_start: 0.8475 (tt0) cc_final: 0.8246 (tt0) REVERT: I 814 ASP cc_start: 0.8319 (m-30) cc_final: 0.8063 (m-30) REVERT: I 1027 LYS cc_start: 0.8042 (ptpt) cc_final: 0.7608 (ptpt) REVERT: I 1180 MET cc_start: 0.8741 (ttm) cc_final: 0.8413 (ttm) REVERT: I 1243 MET cc_start: 0.8089 (ttp) cc_final: 0.7857 (ttt) REVERT: J 48 THR cc_start: 0.7019 (OUTLIER) cc_final: 0.6815 (t) REVERT: J 56 LEU cc_start: 0.8995 (mt) cc_final: 0.8748 (mt) REVERT: J 135 ILE cc_start: 0.8611 (pt) cc_final: 0.8395 (mm) REVERT: J 324 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8883 (pp) REVERT: J 626 TYR cc_start: 0.8327 (m-10) cc_final: 0.8091 (m-10) REVERT: J 864 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8579 (pp) REVERT: J 892 PHE cc_start: 0.8390 (m-80) cc_final: 0.7995 (m-10) REVERT: J 1107 VAL cc_start: 0.7639 (OUTLIER) cc_final: 0.7438 (p) REVERT: J 1349 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6972 (mt-10) outliers start: 102 outliers final: 48 residues processed: 540 average time/residue: 0.3885 time to fit residues: 328.1342 Evaluate side-chains 415 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 363 time to evaluate : 3.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 979 LEU Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 331 ILE Chi-restraints excluded: chain J residue 500 ILE Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 831 VAL Chi-restraints excluded: chain J residue 864 LEU Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 991 THR Chi-restraints excluded: chain J residue 1023 HIS Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1060 VAL Chi-restraints excluded: chain J residue 1061 VAL Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1366 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 271 optimal weight: 8.9990 chunk 243 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 251 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 152 optimal weight: 4.9990 chunk 187 optimal weight: 7.9990 chunk 291 optimal weight: 3.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 103 ASN G 117 HIS ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 490 GLN I 965 GLN ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 951 GLN ** J1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1218 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 26769 Z= 0.458 Angle : 0.651 11.204 36437 Z= 0.338 Chirality : 0.046 0.206 4176 Planarity : 0.005 0.084 4544 Dihedral : 14.650 177.913 4379 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 4.77 % Allowed : 13.24 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.14), residues: 3174 helix: 0.24 (0.15), residues: 1100 sheet: -1.72 (0.24), residues: 449 loop : -1.67 (0.14), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 409 HIS 0.008 0.001 HIS H 66 PHE 0.016 0.002 PHE J 116 TYR 0.017 0.002 TYR J 457 ARG 0.008 0.001 ARG I 352 *********************** 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 492 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 363 time to evaluate : 2.676 Fit side-chains revert: symmetry clash REVERT: H 97 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8404 (pt0) REVERT: I 207 THR cc_start: 0.8668 (p) cc_final: 0.8417 (p) REVERT: I 341 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8187 (pt) REVERT: I 490 GLN cc_start: 0.7838 (tp40) cc_final: 0.7561 (tp-100) REVERT: I 685 MET cc_start: 0.8478 (mtt) cc_final: 0.8243 (mtm) REVERT: I 1027 LYS cc_start: 0.8038 (ptpt) cc_final: 0.7703 (ptpt) REVERT: I 1180 MET cc_start: 0.8790 (ttm) cc_final: 0.8498 (ttm) REVERT: I 1243 MET cc_start: 0.8365 (ttp) cc_final: 0.8129 (ttt) REVERT: J 48 THR cc_start: 0.7604 (OUTLIER) cc_final: 0.7358 (t) REVERT: J 267 ASP cc_start: 0.8337 (t70) cc_final: 0.8125 (t0) REVERT: J 324 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.9010 (pp) REVERT: J 532 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7226 (tt0) REVERT: J 821 MET cc_start: 0.8348 (tpp) cc_final: 0.8125 (mmm) REVERT: J 864 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8646 (pp) REVERT: J 1260 MET cc_start: 0.8771 (mtp) cc_final: 0.8540 (mtm) REVERT: J 1349 GLU cc_start: 0.7340 (mt-10) cc_final: 0.7109 (mt-10) outliers start: 129 outliers final: 83 residues processed: 460 average time/residue: 0.3917 time to fit residues: 288.3412 Evaluate side-chains 421 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 332 time to evaluate : 2.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 71 LYS Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 341 LEU Chi-restraints excluded: chain I residue 446 ASP Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 631 GLU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 644 LEU Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 739 ASP Chi-restraints excluded: chain I residue 741 MET Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 778 GLU Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1140 LYS Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 331 ILE Chi-restraints excluded: chain J residue 532 GLU Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 831 VAL Chi-restraints excluded: chain J residue 864 LEU Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 991 THR Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1061 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1208 ASP Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1329 THR Chi-restraints excluded: chain J residue 1366 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 162 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 242 optimal weight: 4.9990 chunk 198 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 292 optimal weight: 0.9990 chunk 315 optimal weight: 2.9990 chunk 260 optimal weight: 6.9990 chunk 289 optimal weight: 20.0000 chunk 99 optimal weight: 0.7980 chunk 234 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 103 ASN G 117 HIS ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1010 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 26769 Z= 0.251 Angle : 0.546 8.933 36437 Z= 0.285 Chirality : 0.042 0.164 4176 Planarity : 0.004 0.086 4544 Dihedral : 14.364 178.282 4365 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 4.70 % Allowed : 14.76 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.15), residues: 3174 helix: 0.54 (0.16), residues: 1097 sheet: -1.61 (0.24), residues: 450 loop : -1.57 (0.15), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 807 HIS 0.009 0.001 HIS H 66 PHE 0.009 0.001 PHE J 116 TYR 0.012 0.001 TYR G 177 ARG 0.003 0.000 ARG J 99 *********************** 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 498 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 371 time to evaluate : 3.137 Fit side-chains revert: symmetry clash REVERT: G 95 LYS cc_start: 0.9447 (mtmm) cc_final: 0.8805 (pttt) REVERT: H 28 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8601 (pt) REVERT: H 97 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8309 (pt0) REVERT: I 47 TYR cc_start: 0.7583 (OUTLIER) cc_final: 0.6806 (p90) REVERT: I 207 THR cc_start: 0.8586 (p) cc_final: 0.8347 (p) REVERT: I 341 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8175 (pt) REVERT: I 427 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7825 (m-30) REVERT: I 490 GLN cc_start: 0.7848 (tp40) cc_final: 0.7512 (tp-100) REVERT: I 1027 LYS cc_start: 0.8106 (ptpt) cc_final: 0.7755 (ptpt) REVERT: I 1151 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8498 (tt) REVERT: I 1180 MET cc_start: 0.8771 (ttm) cc_final: 0.8491 (ttm) REVERT: I 1243 MET cc_start: 0.8353 (ttp) cc_final: 0.8080 (ttt) REVERT: J 48 THR cc_start: 0.7585 (OUTLIER) cc_final: 0.7343 (t) REVERT: J 56 LEU cc_start: 0.9039 (mt) cc_final: 0.8816 (mt) REVERT: J 500 ILE cc_start: 0.9536 (OUTLIER) cc_final: 0.9241 (pp) REVERT: J 1260 MET cc_start: 0.8738 (mtp) cc_final: 0.8445 (mtm) REVERT: J 1349 GLU cc_start: 0.7272 (mt-10) cc_final: 0.7020 (mt-10) outliers start: 127 outliers final: 87 residues processed: 467 average time/residue: 0.3848 time to fit residues: 286.6331 Evaluate side-chains 445 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 350 time to evaluate : 2.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 71 LYS Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 197 ASP Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 341 LEU Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 423 ASP Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 446 ASP Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 631 GLU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 739 ASP Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 778 GLU Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 853 ASP Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 979 LEU Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1140 LYS Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 331 ILE Chi-restraints excluded: chain J residue 500 ILE Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 831 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 991 THR Chi-restraints excluded: chain J residue 1023 HIS Chi-restraints excluded: chain J residue 1061 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1219 ASP Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1329 THR Chi-restraints excluded: chain J residue 1366 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 288 optimal weight: 7.9990 chunk 219 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 293 optimal weight: 0.9990 chunk 310 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 277 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 103 ASN G 117 HIS ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1010 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 26769 Z= 0.229 Angle : 0.533 9.555 36437 Z= 0.277 Chirality : 0.041 0.149 4176 Planarity : 0.004 0.080 4544 Dihedral : 14.240 179.025 4358 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 5.36 % Allowed : 15.05 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.15), residues: 3174 helix: 0.71 (0.16), residues: 1099 sheet: -1.49 (0.25), residues: 424 loop : -1.48 (0.15), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 807 HIS 0.009 0.001 HIS H 66 PHE 0.019 0.001 PHE J 172 TYR 0.014 0.001 TYR J 995 ARG 0.006 0.000 ARG I 352 *********************** 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 520 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 375 time to evaluate : 3.127 Fit side-chains revert: symmetry clash REVERT: G 95 LYS cc_start: 0.9371 (mtmm) cc_final: 0.8708 (pttt) REVERT: H 28 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8578 (pt) REVERT: I 47 TYR cc_start: 0.7717 (OUTLIER) cc_final: 0.7017 (p90) REVERT: I 207 THR cc_start: 0.8593 (p) cc_final: 0.8340 (p) REVERT: I 341 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8195 (pt) REVERT: I 427 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7802 (m-30) REVERT: I 490 GLN cc_start: 0.7826 (tp40) cc_final: 0.7436 (tp-100) REVERT: I 580 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7629 (mt0) REVERT: I 1010 GLN cc_start: 0.6784 (mt0) cc_final: 0.6564 (mt0) REVERT: I 1027 LYS cc_start: 0.8093 (ptpt) cc_final: 0.7792 (ptpt) REVERT: I 1151 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8489 (tt) REVERT: I 1180 MET cc_start: 0.8729 (ttm) cc_final: 0.8452 (ttm) REVERT: I 1243 MET cc_start: 0.8352 (ttp) cc_final: 0.8068 (ttt) REVERT: J 48 THR cc_start: 0.7490 (OUTLIER) cc_final: 0.7219 (t) REVERT: J 56 LEU cc_start: 0.9052 (mt) cc_final: 0.8801 (mt) REVERT: J 500 ILE cc_start: 0.9504 (OUTLIER) cc_final: 0.9233 (pp) REVERT: J 898 CYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7827 (m) REVERT: J 1260 MET cc_start: 0.8650 (mtp) cc_final: 0.8319 (mtm) outliers start: 145 outliers final: 100 residues processed: 486 average time/residue: 0.3713 time to fit residues: 287.3215 Evaluate side-chains 464 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 355 time to evaluate : 3.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 71 LYS Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 341 LEU Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 423 ASP Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 446 ASP Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 580 GLN Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 631 GLU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 739 ASP Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 853 ASP Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 979 LEU Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1140 LYS Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 331 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 500 ILE Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 831 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 898 CYS Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 991 THR Chi-restraints excluded: chain J residue 1023 HIS Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1061 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1329 THR Chi-restraints excluded: chain J residue 1366 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 258 optimal weight: 0.0040 chunk 176 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 231 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 264 optimal weight: 0.9990 chunk 214 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 158 optimal weight: 0.9990 chunk 278 optimal weight: 20.0000 chunk 78 optimal weight: 4.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 117 HIS ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 965 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 26769 Z= 0.233 Angle : 0.531 9.556 36437 Z= 0.275 Chirality : 0.041 0.190 4176 Planarity : 0.004 0.081 4544 Dihedral : 14.188 179.608 4357 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 5.25 % Allowed : 15.90 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.15), residues: 3174 helix: 0.79 (0.16), residues: 1099 sheet: -1.28 (0.26), residues: 402 loop : -1.47 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J1020 HIS 0.009 0.001 HIS H 66 PHE 0.009 0.001 PHE J 116 TYR 0.011 0.001 TYR J 995 ARG 0.003 0.000 ARG J 81 *********************** 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 510 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 368 time to evaluate : 2.839 Fit side-chains revert: symmetry clash REVERT: G 95 LYS cc_start: 0.9353 (mtmm) cc_final: 0.8716 (pttt) REVERT: H 28 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8569 (pt) REVERT: H 188 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7615 (mt-10) REVERT: I 47 TYR cc_start: 0.7751 (OUTLIER) cc_final: 0.6980 (p90) REVERT: I 207 THR cc_start: 0.8459 (p) cc_final: 0.8185 (p) REVERT: I 341 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8183 (pt) REVERT: I 370 MET cc_start: 0.8609 (mmm) cc_final: 0.8403 (mmm) REVERT: I 427 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7804 (m-30) REVERT: I 490 GLN cc_start: 0.7779 (tp40) cc_final: 0.7417 (tp-100) REVERT: I 580 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7629 (mt0) REVERT: I 953 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8431 (mp) REVERT: I 1027 LYS cc_start: 0.8086 (ptpt) cc_final: 0.7767 (ptpt) REVERT: I 1151 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8477 (tt) REVERT: I 1180 MET cc_start: 0.8732 (ttm) cc_final: 0.8456 (ttm) REVERT: I 1243 MET cc_start: 0.8365 (ttp) cc_final: 0.8082 (ttt) REVERT: J 48 THR cc_start: 0.7498 (OUTLIER) cc_final: 0.7223 (t) REVERT: J 56 LEU cc_start: 0.9061 (mt) cc_final: 0.8820 (mt) REVERT: J 500 ILE cc_start: 0.9503 (OUTLIER) cc_final: 0.9250 (pp) REVERT: J 898 CYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7844 (m) outliers start: 142 outliers final: 107 residues processed: 473 average time/residue: 0.3615 time to fit residues: 273.1192 Evaluate side-chains 467 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 349 time to evaluate : 2.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 71 LYS Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 341 LEU Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 423 ASP Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 446 ASP Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 580 GLN Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 631 GLU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 739 ASP Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 778 GLU Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 853 ASP Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 979 LEU Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 194 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 331 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 500 ILE Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 831 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 898 CYS Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 991 THR Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1023 HIS Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1061 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1219 ASP Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1329 THR Chi-restraints excluded: chain J residue 1366 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 104 optimal weight: 0.9990 chunk 279 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 182 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 310 optimal weight: 1.9990 chunk 257 optimal weight: 2.9990 chunk 143 optimal weight: 8.9990 chunk 25 optimal weight: 0.3980 chunk 102 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 117 HIS I 965 GLN I1010 GLN J 504 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26769 Z= 0.200 Angle : 0.526 14.027 36437 Z= 0.270 Chirality : 0.041 0.178 4176 Planarity : 0.004 0.078 4544 Dihedral : 14.089 179.581 4357 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 5.25 % Allowed : 16.79 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.15), residues: 3174 helix: 0.93 (0.16), residues: 1090 sheet: -1.20 (0.26), residues: 416 loop : -1.47 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 807 HIS 0.005 0.001 HIS G 117 PHE 0.018 0.001 PHE J 172 TYR 0.010 0.001 TYR G 177 ARG 0.006 0.000 ARG I 352 *********************** 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 508 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 366 time to evaluate : 2.952 Fit side-chains revert: symmetry clash REVERT: G 95 LYS cc_start: 0.9331 (mtmm) cc_final: 0.8739 (pttt) REVERT: H 28 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8554 (pt) REVERT: H 188 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7605 (mt-10) REVERT: I 47 TYR cc_start: 0.7767 (OUTLIER) cc_final: 0.6990 (p90) REVERT: I 207 THR cc_start: 0.8450 (p) cc_final: 0.8183 (p) REVERT: I 341 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8212 (pt) REVERT: I 427 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7782 (m-30) REVERT: I 490 GLN cc_start: 0.7701 (tp40) cc_final: 0.7317 (tp-100) REVERT: I 580 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7644 (mt0) REVERT: I 953 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8485 (mp) REVERT: I 1027 LYS cc_start: 0.8071 (ptpt) cc_final: 0.7774 (ptpt) REVERT: I 1151 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8484 (tt) REVERT: I 1180 MET cc_start: 0.8706 (ttm) cc_final: 0.8312 (ttm) REVERT: I 1243 MET cc_start: 0.8386 (ttp) cc_final: 0.8095 (ttt) REVERT: J 48 THR cc_start: 0.7401 (OUTLIER) cc_final: 0.7118 (t) REVERT: J 56 LEU cc_start: 0.9049 (mt) cc_final: 0.8806 (mt) REVERT: J 500 ILE cc_start: 0.9487 (OUTLIER) cc_final: 0.9255 (pp) REVERT: J 898 CYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7855 (m) outliers start: 142 outliers final: 108 residues processed: 474 average time/residue: 0.3842 time to fit residues: 288.9230 Evaluate side-chains 468 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 349 time to evaluate : 3.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 71 LYS Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 341 LEU Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 423 ASP Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 446 ASP Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 580 GLN Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 644 LEU Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 739 ASP Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 778 GLU Chi-restraints excluded: chain I residue 853 ASP Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 979 LEU Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 194 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 331 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 500 ILE Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 831 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 898 CYS Chi-restraints excluded: chain J residue 967 VAL Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 991 THR Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1023 HIS Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1061 VAL Chi-restraints excluded: chain J residue 1062 LEU Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1167 LYS Chi-restraints excluded: chain J residue 1219 ASP Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1329 THR Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 56 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 299 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 chunk 226 optimal weight: 2.9990 chunk 175 optimal weight: 0.9980 chunk 261 optimal weight: 0.9990 chunk 173 optimal weight: 1.9990 chunk 309 optimal weight: 1.9990 chunk 193 optimal weight: 0.0870 chunk 188 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 117 HIS I 684 ASN I 965 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 26769 Z= 0.156 Angle : 0.505 13.177 36437 Z= 0.260 Chirality : 0.040 0.150 4176 Planarity : 0.004 0.078 4544 Dihedral : 13.960 178.167 4357 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 4.47 % Allowed : 17.86 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.15), residues: 3174 helix: 1.12 (0.16), residues: 1080 sheet: -1.12 (0.26), residues: 418 loop : -1.39 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 807 HIS 0.005 0.001 HIS G 117 PHE 0.007 0.001 PHE J 437 TYR 0.009 0.001 TYR H 177 ARG 0.006 0.000 ARG I 352 *********************** 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 493 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 372 time to evaluate : 3.215 Fit side-chains revert: symmetry clash REVERT: G 95 LYS cc_start: 0.9267 (mtmm) cc_final: 0.8733 (pttt) REVERT: H 28 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8450 (pt) REVERT: I 47 TYR cc_start: 0.7734 (OUTLIER) cc_final: 0.6962 (p90) REVERT: I 207 THR cc_start: 0.8403 (p) cc_final: 0.8144 (p) REVERT: I 341 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8193 (pt) REVERT: I 370 MET cc_start: 0.8540 (mmm) cc_final: 0.8256 (mmm) REVERT: I 427 ASP cc_start: 0.7972 (OUTLIER) cc_final: 0.7716 (m-30) REVERT: I 490 GLN cc_start: 0.7833 (tp40) cc_final: 0.7422 (tp-100) REVERT: I 580 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7610 (mt0) REVERT: I 953 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8479 (mp) REVERT: I 968 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7005 (mm-30) REVERT: I 1027 LYS cc_start: 0.8049 (ptpt) cc_final: 0.7754 (ptpt) REVERT: I 1151 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8508 (tt) REVERT: I 1180 MET cc_start: 0.8730 (ttm) cc_final: 0.8336 (ttm) REVERT: I 1243 MET cc_start: 0.8336 (ttp) cc_final: 0.8042 (ttt) REVERT: J 48 THR cc_start: 0.7315 (OUTLIER) cc_final: 0.7111 (t) REVERT: J 56 LEU cc_start: 0.9040 (mt) cc_final: 0.8805 (mt) REVERT: J 375 GLU cc_start: 0.8202 (tp30) cc_final: 0.7980 (tp30) REVERT: J 500 ILE cc_start: 0.9471 (OUTLIER) cc_final: 0.9267 (pp) REVERT: J 898 CYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7879 (m) REVERT: J 1135 THR cc_start: 0.8762 (m) cc_final: 0.8491 (p) REVERT: K 8 ASP cc_start: 0.7595 (OUTLIER) cc_final: 0.6825 (t0) REVERT: K 56 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.6836 (mp0) outliers start: 121 outliers final: 90 residues processed: 464 average time/residue: 0.3814 time to fit residues: 282.1219 Evaluate side-chains 451 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 348 time to evaluate : 3.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 71 LYS Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 341 LEU Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 446 ASP Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 580 GLN Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 739 ASP Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 778 GLU Chi-restraints excluded: chain I residue 853 ASP Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 979 LEU Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 194 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 331 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 500 ILE Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 831 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 898 CYS Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 991 THR Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1023 HIS Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1167 LYS Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1219 ASP Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 56 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 191 optimal weight: 0.7980 chunk 123 optimal weight: 5.9990 chunk 184 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 196 optimal weight: 1.9990 chunk 210 optimal weight: 7.9990 chunk 152 optimal weight: 2.9990 chunk 28 optimal weight: 0.0980 chunk 243 optimal weight: 6.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 103 ASN G 117 HIS J 504 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 26769 Z= 0.150 Angle : 0.507 14.889 36437 Z= 0.261 Chirality : 0.040 0.206 4176 Planarity : 0.004 0.075 4544 Dihedral : 13.899 177.457 4354 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 4.47 % Allowed : 17.97 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.15), residues: 3174 helix: 1.17 (0.16), residues: 1080 sheet: -0.99 (0.26), residues: 398 loop : -1.37 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 807 HIS 0.005 0.001 HIS G 117 PHE 0.019 0.001 PHE J 172 TYR 0.014 0.001 TYR J 995 ARG 0.006 0.000 ARG I 352 *********************** 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 484 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 363 time to evaluate : 2.724 Fit side-chains revert: symmetry clash REVERT: G 95 LYS cc_start: 0.9225 (mtmm) cc_final: 0.8712 (pttt) REVERT: H 28 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8414 (pt) REVERT: I 47 TYR cc_start: 0.7724 (OUTLIER) cc_final: 0.6948 (p90) REVERT: I 207 THR cc_start: 0.8407 (p) cc_final: 0.8162 (p) REVERT: I 341 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8075 (pt) REVERT: I 370 MET cc_start: 0.8533 (mmm) cc_final: 0.8086 (mmm) REVERT: I 490 GLN cc_start: 0.7820 (tp40) cc_final: 0.7413 (tp-100) REVERT: I 580 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7582 (mt0) REVERT: I 778 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6481 (mt-10) REVERT: I 953 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8487 (mp) REVERT: I 1027 LYS cc_start: 0.8032 (ptpt) cc_final: 0.7744 (ptpt) REVERT: I 1151 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8517 (tt) REVERT: I 1180 MET cc_start: 0.8720 (ttm) cc_final: 0.8300 (ttm) REVERT: I 1243 MET cc_start: 0.8338 (ttp) cc_final: 0.8032 (ttt) REVERT: J 48 THR cc_start: 0.7233 (OUTLIER) cc_final: 0.6996 (t) REVERT: J 56 LEU cc_start: 0.9042 (mt) cc_final: 0.8816 (mt) REVERT: J 898 CYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7869 (m) REVERT: J 1135 THR cc_start: 0.8709 (m) cc_final: 0.8458 (p) REVERT: K 8 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.6817 (t0) outliers start: 121 outliers final: 93 residues processed: 458 average time/residue: 0.3787 time to fit residues: 276.5575 Evaluate side-chains 454 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 351 time to evaluate : 2.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 71 LYS Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 341 LEU Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 423 ASP Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 580 GLN Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 644 LEU Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 739 ASP Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 778 GLU Chi-restraints excluded: chain I residue 853 ASP Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 979 LEU Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 194 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 331 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 831 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 898 CYS Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 991 THR Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1023 HIS Chi-restraints excluded: chain J residue 1062 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1167 LYS Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 42 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 281 optimal weight: 20.0000 chunk 296 optimal weight: 0.4980 chunk 270 optimal weight: 1.9990 chunk 288 optimal weight: 0.6980 chunk 173 optimal weight: 0.0170 chunk 125 optimal weight: 3.9990 chunk 226 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 260 optimal weight: 5.9990 chunk 272 optimal weight: 0.8980 chunk 287 optimal weight: 0.0570 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 26769 Z= 0.133 Angle : 0.503 15.039 36437 Z= 0.257 Chirality : 0.040 0.210 4176 Planarity : 0.004 0.075 4544 Dihedral : 13.807 176.088 4353 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.74 % Allowed : 18.34 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.15), residues: 3174 helix: 1.28 (0.16), residues: 1076 sheet: -0.98 (0.25), residues: 426 loop : -1.29 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 807 HIS 0.003 0.000 HIS G 23 PHE 0.007 0.001 PHE J 437 TYR 0.012 0.001 TYR J 995 ARG 0.008 0.000 ARG J1174 *********************** 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 485 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 384 time to evaluate : 2.924 Fit side-chains revert: symmetry clash REVERT: G 95 LYS cc_start: 0.9200 (mtmm) cc_final: 0.8639 (pttt) REVERT: H 83 LEU cc_start: 0.8698 (mp) cc_final: 0.8476 (mp) REVERT: I 47 TYR cc_start: 0.7700 (OUTLIER) cc_final: 0.6928 (p90) REVERT: I 70 TYR cc_start: 0.8291 (t80) cc_final: 0.7796 (t80) REVERT: I 207 THR cc_start: 0.8267 (p) cc_final: 0.8029 (p) REVERT: I 341 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8058 (pt) REVERT: I 370 MET cc_start: 0.8506 (mmm) cc_final: 0.8121 (mmm) REVERT: I 427 ASP cc_start: 0.7854 (m-30) cc_final: 0.7617 (m-30) REVERT: I 429 MET cc_start: 0.8409 (mtp) cc_final: 0.8120 (mtp) REVERT: I 490 GLN cc_start: 0.7783 (tp40) cc_final: 0.7374 (tp-100) REVERT: I 580 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7576 (mt0) REVERT: I 778 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6540 (mt-10) REVERT: I 1027 LYS cc_start: 0.7989 (ptpt) cc_final: 0.7733 (ptpt) REVERT: I 1108 ASN cc_start: 0.9029 (p0) cc_final: 0.8631 (p0) REVERT: I 1151 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8517 (tt) REVERT: I 1180 MET cc_start: 0.8730 (ttm) cc_final: 0.8331 (ttm) REVERT: I 1243 MET cc_start: 0.8322 (ttp) cc_final: 0.8034 (ttt) REVERT: J 48 THR cc_start: 0.7251 (OUTLIER) cc_final: 0.7023 (t) REVERT: J 56 LEU cc_start: 0.9009 (mt) cc_final: 0.8790 (mt) REVERT: J 898 CYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7876 (m) REVERT: J 1135 THR cc_start: 0.8618 (m) cc_final: 0.8381 (p) REVERT: K 8 ASP cc_start: 0.7539 (OUTLIER) cc_final: 0.6787 (t0) REVERT: K 56 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6822 (mp0) outliers start: 101 outliers final: 75 residues processed: 461 average time/residue: 0.3862 time to fit residues: 284.2446 Evaluate side-chains 449 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 365 time to evaluate : 2.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 71 LYS Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 341 LEU Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 580 GLN Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 644 LEU Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 739 ASP Chi-restraints excluded: chain I residue 778 GLU Chi-restraints excluded: chain I residue 853 ASP Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 831 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 898 CYS Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 991 THR Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1023 HIS Chi-restraints excluded: chain J residue 1062 LEU Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1167 LYS Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 56 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 189 optimal weight: 0.8980 chunk 304 optimal weight: 7.9990 chunk 186 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 319 optimal weight: 4.9990 chunk 294 optimal weight: 30.0000 chunk 254 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 196 optimal weight: 0.7980 chunk 156 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 387 ASN I 965 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26769 Z= 0.227 Angle : 0.539 14.756 36437 Z= 0.274 Chirality : 0.041 0.218 4176 Planarity : 0.004 0.073 4544 Dihedral : 13.836 176.654 4343 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.66 % Allowed : 18.60 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.15), residues: 3174 helix: 1.14 (0.16), residues: 1086 sheet: -0.95 (0.26), residues: 424 loop : -1.29 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 686 HIS 0.009 0.001 HIS J 80 PHE 0.020 0.001 PHE J 172 TYR 0.015 0.001 TYR J 165 ARG 0.010 0.000 ARG J1174 ********************** 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 462 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 363 time to evaluate : 2.889 Fit side-chains revert: symmetry clash REVERT: G 95 LYS cc_start: 0.9208 (mtmm) cc_final: 0.8643 (pttt) REVERT: I 47 TYR cc_start: 0.7930 (OUTLIER) cc_final: 0.7279 (p90) REVERT: I 207 THR cc_start: 0.8231 (p) cc_final: 0.8009 (p) REVERT: I 341 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8066 (pt) REVERT: I 368 ARG cc_start: 0.8711 (ttm-80) cc_final: 0.8313 (mtt-85) REVERT: I 370 MET cc_start: 0.8526 (mmm) cc_final: 0.8155 (mmm) REVERT: I 427 ASP cc_start: 0.7907 (m-30) cc_final: 0.7653 (m-30) REVERT: I 429 MET cc_start: 0.8532 (mtp) cc_final: 0.8233 (mtp) REVERT: I 490 GLN cc_start: 0.7673 (tp40) cc_final: 0.7290 (tp-100) REVERT: I 580 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7623 (mt0) REVERT: I 778 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6587 (mt-10) REVERT: I 964 LEU cc_start: 0.7823 (tt) cc_final: 0.7619 (tp) REVERT: I 1027 LYS cc_start: 0.8037 (ptpt) cc_final: 0.7742 (ptpt) REVERT: I 1151 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8571 (tt) REVERT: I 1180 MET cc_start: 0.8719 (ttm) cc_final: 0.8453 (ttm) REVERT: I 1243 MET cc_start: 0.8371 (ttp) cc_final: 0.8071 (ttt) REVERT: J 48 THR cc_start: 0.7284 (OUTLIER) cc_final: 0.7034 (t) REVERT: J 56 LEU cc_start: 0.9061 (mt) cc_final: 0.8814 (mt) REVERT: J 136 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7520 (tp30) REVERT: J 698 MET cc_start: 0.8855 (mmm) cc_final: 0.8427 (tpp) REVERT: J 898 CYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7846 (m) REVERT: J 1135 THR cc_start: 0.8665 (m) cc_final: 0.8408 (p) REVERT: K 56 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6868 (mp0) outliers start: 99 outliers final: 83 residues processed: 440 average time/residue: 0.3813 time to fit residues: 268.5951 Evaluate side-chains 444 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 352 time to evaluate : 2.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 71 LYS Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 341 LEU Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 423 ASP Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 580 GLN Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 644 LEU Chi-restraints excluded: chain I residue 650 VAL Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 739 ASP Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 778 GLU Chi-restraints excluded: chain I residue 853 ASP Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 979 LEU Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 831 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 898 CYS Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 991 THR Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1023 HIS Chi-restraints excluded: chain J residue 1062 LEU Chi-restraints excluded: chain J residue 1119 ASP Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1167 LYS Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 56 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 202 optimal weight: 0.0040 chunk 271 optimal weight: 3.9990 chunk 78 optimal weight: 20.0000 chunk 234 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 255 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 261 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 620 ASN ** I 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 157 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.157617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.118460 restraints weight = 32947.873| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.81 r_work: 0.3096 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 26769 Z= 0.151 Angle : 0.518 16.228 36437 Z= 0.263 Chirality : 0.040 0.215 4176 Planarity : 0.004 0.076 4544 Dihedral : 13.767 175.887 4343 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.37 % Allowed : 19.23 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.15), residues: 3174 helix: 1.21 (0.16), residues: 1083 sheet: -0.91 (0.26), residues: 424 loop : -1.27 (0.15), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 807 HIS 0.011 0.001 HIS J 80 PHE 0.007 0.001 PHE I 35 TYR 0.012 0.001 TYR J 995 ARG 0.009 0.000 ARG J1174 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6288.39 seconds wall clock time: 116 minutes 52.47 seconds (7012.47 seconds total)