Starting phenix.real_space_refine on Sat Aug 8 08:14:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8eg8_28110/08_2026/8eg8_28110.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eg8_28110/08_2026/8eg8_28110.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8eg8_28110/08_2026/8eg8_28110.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8eg8_28110/08_2026/8eg8_28110.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8eg8_28110/08_2026/8eg8_28110.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eg8_28110/08_2026/8eg8_28110.map" model { file = "/net/cci-nas-00/data/ceres_data/8eg8_28110/08_2026/8eg8_28110.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eg8_28110/08_2026/8eg8_28110.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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 67 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 16436 2.51 5 N 4686 2.21 5 O 5255 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26553 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 509 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain breaks: 1 Chain: "B" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 615 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "R" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 256 Classifications: {'RNAv2': 12} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna2p': 2, 'rna3p': 9} Chain: "G" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1670 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1687 Classifications: {'peptide': 219} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Chain: "I" Number of atoms: 10559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10559 Classifications: {'peptide': 1341} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "J" Number of atoms: 10545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1358, 10545 Classifications: {'peptide': 1358} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1302} Chain: "K" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 655 Classifications: {'peptide': 83} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 79} Chain: "I" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'1N7': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'1N7:plan-1': 2} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15745 SG CYS J 70 108.229 58.756 75.171 1.00 64.91 S ATOM 15759 SG CYS J 72 108.325 55.103 74.188 1.00 70.75 S ATOM 15867 SG CYS J 85 110.889 57.557 72.820 1.00 69.62 S ATOM 15891 SG CYS J 88 107.130 57.961 71.819 1.00 67.78 S ATOM 21579 SG CYS J 814 82.273 120.049 81.500 1.00 36.78 S ATOM 22144 SG CYS J 888 81.065 116.446 80.973 1.00 35.14 S ATOM 22195 SG CYS J 895 81.894 117.715 84.407 1.00 32.95 S ATOM 22216 SG CYS J 898 78.829 118.916 82.928 1.00 32.65 S Time building chain proxies: 5.56, per 1000 atoms: 0.21 Number of scatterers: 26553 At special positions: 0 Unit cell: (137.8, 150.8, 167.7, 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 67 15.00 Mg 1 11.99 O 5255 8.00 N 4686 7.00 C 16436 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " Number of angles added : 12 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5936 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 47 sheets defined 38.0% alpha, 16.0% beta 30 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 3.51 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.523A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 212 through 229 Processing helix chain 'G' and resid 230 through 232 No H-bonds generated for 'chain 'G' and resid 230 through 232' Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.700A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 Processing helix chain 'H' and resid 111 through 115 Processing helix chain 'H' and resid 212 through 228 Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.531A pdb=" N PHE I 38 " --> pdb=" O SER I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 57 removed outlier: 3.529A pdb=" N ALA I 51 " --> pdb=" O TYR I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.605A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 removed outlier: 4.036A pdb=" N ARG I 247 " --> pdb=" O GLU I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 290 through 294 removed outlier: 3.599A pdb=" N GLY I 294 " --> pdb=" O TYR I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 328 removed outlier: 3.847A pdb=" N GLN I 327 " --> pdb=" O ALA I 323 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER I 328 " --> pdb=" O LYS I 324 " (cutoff:3.500A) Processing helix chain 'I' and resid 345 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 3.996A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 455 through 481 removed outlier: 3.759A pdb=" N ARG I 470 " --> pdb=" O VAL I 466 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER I 480 " --> pdb=" O LYS I 476 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU I 481 " --> pdb=" O GLU I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 482 through 487 removed outlier: 6.028A pdb=" N ASP I 485 " --> pdb=" O GLY I 482 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU I 487 " --> pdb=" O LEU I 484 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 507 Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.656A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 608 through 613 removed outlier: 3.913A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) Processing helix chain 'I' and resid 664 through 668 removed outlier: 3.604A pdb=" N LEU I 667 " --> pdb=" O GLY I 664 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 687 Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 896 through 906 Processing helix chain 'I' and resid 942 through 980 Processing helix chain 'I' and resid 1005 through 1038 removed outlier: 4.018A pdb=" N ASN I1009 " --> pdb=" O GLU I1005 " (cutoff:3.500A) Processing helix chain 'I' and resid 1081 through 1085 Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 3.785A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 4.217A pdb=" N GLN I1134 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1150 Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 4.118A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1177 removed outlier: 3.615A pdb=" N ARG I1171 " --> pdb=" O GLU I1167 " (cutoff:3.500A) Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1242 Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1283 through 1292 Processing helix chain 'I' and resid 1297 through 1311 Processing helix chain 'I' and resid 1320 through 1332 removed outlier: 3.675A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 34 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 96 through 100 Processing helix chain 'J' and resid 113 through 118 Processing helix chain 'J' and resid 122 through 128 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 181 through 191 Processing helix chain 'J' and resid 193 through 207 Processing helix chain 'J' and resid 211 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 271 removed outlier: 3.872A pdb=" N ASP J 267 " --> pdb=" O SER J 263 " (cutoff:3.500A) Processing helix chain 'J' and resid 272 through 285 Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 326 through 332 Processing helix chain 'J' and resid 336 through 341 Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 405 through 417 removed outlier: 3.845A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG J 417 " --> pdb=" O ASP J 413 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 504 through 514 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.552A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 589 through 593 Processing helix chain 'J' and resid 597 through 612 Processing helix chain 'J' and resid 614 through 636 Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 703 removed outlier: 3.709A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 removed outlier: 3.510A pdb=" N SER J 728 " --> pdb=" O MET J 724 " (cutoff:3.500A) Processing helix chain 'J' and resid 733 through 742 Processing helix chain 'J' and resid 770 through 788 removed outlier: 4.237A pdb=" N THR J 776 " --> pdb=" O TYR J 772 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) Processing helix chain 'J' and resid 789 through 804 removed outlier: 4.091A pdb=" N SER J 793 " --> pdb=" O LYS J 789 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 839 Processing helix chain 'J' and resid 865 through 876 Processing helix chain 'J' and resid 884 through 888 Processing helix chain 'J' and resid 895 through 900 removed outlier: 3.513A pdb=" N TYR J 899 " --> pdb=" O CYS J 895 " (cutoff:3.500A) Processing helix chain 'J' and resid 914 through 934 removed outlier: 3.752A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Proline residue: J 926 - end of helix Processing helix chain 'J' and resid 935 through 938 removed outlier: 3.632A pdb=" N GLY J 938 " --> pdb=" O PHE J 935 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 935 through 938' Processing helix chain 'J' and resid 1133 through 1147 Proline residue: J1139 - end of helix Processing helix chain 'J' and resid 1216 through 1224 Processing helix chain 'J' and resid 1225 through 1244 Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.212A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1318 through 1325 removed outlier: 3.832A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1354 removed outlier: 3.801A pdb=" N ASN J1350 " --> pdb=" O GLY J1346 " (cutoff:3.500A) Processing helix chain 'J' and resid 1361 through 1372 removed outlier: 4.129A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 17 through 32 Processing helix chain 'K' and resid 45 through 56 Processing helix chain 'K' and resid 60 through 84 Processing sheet with id=AA1, first strand: chain 'G' and resid 12 through 18 removed outlier: 5.213A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N HIS G 23 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR G 207 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'G' and resid 97 through 105 removed outlier: 7.689A pdb=" N SER G 141 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ILE G 61 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AA5, first strand: chain 'G' and resid 108 through 111 removed outlier: 6.504A pdb=" N GLY G 108 " --> pdb=" O HIS G 132 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N HIS G 132 " --> pdb=" O GLY G 108 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL G 110 " --> pdb=" O ILE G 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 12 through 18 removed outlier: 5.846A pdb=" N LEU H 13 " --> pdb=" O GLU H 29 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N GLU H 29 " --> pdb=" O LEU H 13 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP H 15 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL H 202 " --> pdb=" O TYR H 185 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N TYR H 185 " --> pdb=" O VAL H 202 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLU H 204 " --> pdb=" O ILE H 183 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ILE H 183 " --> pdb=" O GLU H 204 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLU H 206 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 98 through 105 removed outlier: 7.943A pdb=" N SER H 141 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ILE H 61 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY H 53 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AA9, first strand: chain 'H' and resid 108 through 110 removed outlier: 3.765A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.504A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 59 through 60 removed outlier: 3.517A pdb=" N ARG I 101 " --> pdb=" O GLN I 69 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.714A 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: 4.387A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB5, first strand: chain 'I' and resid 147 through 148 removed outlier: 6.394A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'I' and resid 154 through 158 removed outlier: 3.706A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 284 through 285 removed outlier: 4.367A pdb=" N ILE I 229 " --> pdb=" O GLU I 240 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 255 through 257 removed outlier: 3.893A pdb=" N VAL I 263 " --> pdb=" O ILE I 255 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 296 through 297 removed outlier: 4.041A pdb=" N MET I 315 " --> pdb=" O VAL I 297 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 301 through 302 removed outlier: 3.733A pdb=" N CYS I 311 " --> pdb=" O TYR I 301 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC3, first strand: chain 'I' and resid 580 through 581 removed outlier: 3.590A pdb=" N ILE I 616 " --> pdb=" O ARG I 637 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.382A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 749 through 751 removed outlier: 6.834A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AC7, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC8, first strand: chain 'I' and resid 1066 through 1067 removed outlier: 4.440A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 9.393A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ILE I 816 " --> pdb=" O LYS I1078 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ASN I1080 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL I 818 " --> pdb=" O ASN I1080 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 1066 through 1067 Processing sheet with id=AD1, first strand: chain 'I' and resid 846 through 847 removed outlier: 3.524A pdb=" N THR I 843 " --> pdb=" O GLY I 846 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ASP I 842 " --> pdb=" O VAL I1046 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL I1046 " --> pdb=" O ASP I 842 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N LEU I1047 " --> pdb=" O THR I 935 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N THR I 935 " --> pdb=" O LEU I1047 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE I1049 " --> pdb=" O VAL I 933 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL I 933 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LYS I1051 " --> pdb=" O VAL I 931 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL I 931 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N TYR I1053 " --> pdb=" O ILE I 929 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR I 927 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 882 through 884 removed outlier: 7.414A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 887 through 888 Processing sheet with id=AD4, first strand: chain 'I' and resid 1087 through 1088 Processing sheet with id=AD5, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AD6, first strand: chain 'I' and resid 1268 through 1270 removed outlier: 3.702A pdb=" N GLN I1268 " --> pdb=" O VAL J 347 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 1335 through 1340 removed outlier: 4.466A pdb=" N ALA J 19 " --> pdb=" O GLU I1340 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 103 through 112 removed outlier: 9.767A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.720A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 159 through 160 removed outlier: 3.837A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AE2, first strand: chain 'J' and resid 706 through 707 removed outlier: 3.654A pdb=" N ILE J 707 " --> pdb=" O GLU J 714 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLU J 714 " --> pdb=" O ILE J 707 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'J' and resid 745 through 748 removed outlier: 7.857A pdb=" N GLY J 745 " --> pdb=" O THR J 757 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N THR J 757 " --> pdb=" O GLY J 745 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N MET J 747 " --> pdb=" O ILE J 755 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE5, first strand: chain 'J' and resid 848 through 849 removed outlier: 6.764A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 949 through 952 removed outlier: 6.659A pdb=" N ILE J 950 " --> pdb=" O VAL J1017 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU J1015 " --> pdb=" O VAL J 952 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 957 through 961 removed outlier: 4.027A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 1024 through 1026 Processing sheet with id=AE9, first strand: chain 'J' and resid 1098 through 1100 removed outlier: 3.770A pdb=" N GLY J1033 " --> pdb=" O ILE J1115 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 1187 through 1189 Processing sheet with id=AF2, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.641A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) 1062 hydrogen bonds defined for protein. 2970 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 75 hydrogen bonds 150 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 7.58 Time building geometry restraints manager: 3.22 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: 8829 1.34 - 1.46: 5285 1.46 - 1.58: 12648 1.58 - 1.70: 136 1.70 - 1.82: 190 Bond restraints: 27088 Sorted by residual: bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.825 -0.293 2.00e-02 2.50e+03 2.14e+02 bond pdb=" C19 1N7 I1402 " pdb=" C3 1N7 I1402 " ideal model delta sigma weight residual 1.532 1.820 -0.288 2.00e-02 2.50e+03 2.07e+02 bond pdb=" C3 1N7 I1401 " pdb=" C4 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.731 -0.199 2.00e-02 2.50e+03 9.93e+01 bond pdb=" C3 1N7 I1402 " pdb=" C4 1N7 I1402 " ideal model delta sigma weight residual 1.532 1.728 -0.196 2.00e-02 2.50e+03 9.62e+01 bond pdb=" C7 1N7 I1401 " pdb=" C8 1N7 I1401 " ideal model delta sigma weight residual 1.542 1.707 -0.165 2.00e-02 2.50e+03 6.78e+01 ... (remaining 27083 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 36107 1.83 - 3.65: 652 3.65 - 5.48: 115 5.48 - 7.30: 13 7.30 - 9.13: 4 Bond angle restraints: 36891 Sorted by residual: angle pdb=" N VAL J 272 " pdb=" CA VAL J 272 " pdb=" C VAL J 272 " ideal model delta sigma weight residual 111.81 107.13 4.68 8.60e-01 1.35e+00 2.96e+01 angle pdb=" O4' DA B 18 " pdb=" C4' DA B 18 " pdb=" C3' DA B 18 " ideal model delta sigma weight residual 106.00 102.98 3.02 6.00e-01 2.78e+00 2.53e+01 angle pdb=" O4' DA B 19 " pdb=" C4' DA B 19 " pdb=" C3' DA B 19 " ideal model delta sigma weight residual 106.00 103.45 2.55 6.00e-01 2.78e+00 1.80e+01 angle pdb=" N3 DT B 21 " pdb=" C4 DT B 21 " pdb=" O4 DT B 21 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 angle pdb=" N3 DT B 23 " pdb=" C4 DT B 23 " pdb=" O4 DT B 23 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.74e+01 ... (remaining 36886 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.51: 15904 32.51 - 65.02: 508 65.02 - 97.53: 39 97.53 - 130.03: 1 130.03 - 162.54: 1 Dihedral angle restraints: 16453 sinusoidal: 7220 harmonic: 9233 Sorted by residual: dihedral pdb=" C4' G R 7 " pdb=" C3' G R 7 " pdb=" C2' G R 7 " pdb=" C1' G R 7 " ideal model delta sinusoidal sigma weight residual 36.34 -36.55 72.90 1 3.10e+00 1.04e-01 7.05e+02 dihedral pdb=" C4' U R 6 " pdb=" C3' U R 6 " pdb=" C2' U R 6 " pdb=" C1' U R 6 " ideal model delta sinusoidal sigma weight residual 36.35 -36.12 72.47 1 3.10e+00 1.04e-01 6.98e+02 dihedral pdb=" O4' U R 6 " pdb=" C4' U R 6 " pdb=" C3' U R 6 " pdb=" C2' U R 6 " ideal model delta sinusoidal sigma weight residual -35.15 25.22 -60.37 1 4.00e+00 6.25e-02 3.03e+02 ... (remaining 16450 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 3849 0.083 - 0.166: 355 0.166 - 0.250: 20 0.250 - 0.333: 8 0.333 - 0.416: 3 Chirality restraints: 4235 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 -2.95 0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" C15 1N7 I1402 " pdb=" C14 1N7 I1402 " pdb=" C16 1N7 I1402 " pdb=" C2 1N7 I1402 " both_signs ideal model delta sigma weight residual False -2.47 -2.88 0.41 2.00e-01 2.50e+01 4.25e+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 -2.83 0.36 2.00e-01 2.50e+01 3.26e+00 ... (remaining 4232 not shown) Planarity restraints: 4588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY I 344 " -0.055 5.00e-02 4.00e+02 8.47e-02 1.15e+01 pdb=" N PRO I 345 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO I 345 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO I 345 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR I 742 " 0.050 5.00e-02 4.00e+02 7.44e-02 8.84e+00 pdb=" N PRO I 743 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO I 743 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO I 743 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS I 559 " -0.045 5.00e-02 4.00e+02 6.85e-02 7.51e+00 pdb=" N PRO I 560 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO I 560 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO I 560 " -0.038 5.00e-02 4.00e+02 ... (remaining 4585 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 241 2.57 - 3.16: 22113 3.16 - 3.74: 40753 3.74 - 4.32: 57871 4.32 - 4.90: 96761 Nonbonded interactions: 217739 Sorted by model distance: nonbonded pdb=" OG1 THR I 91 " pdb=" O ILE I 138 " model vdw 1.992 3.040 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1501 " model vdw 2.060 2.170 nonbonded pdb=" OP1 C R 17 " pdb="MG MG J1501 " model vdw 2.072 2.170 nonbonded pdb=" OD1 ASP J 464 " pdb="MG MG J1501 " model vdw 2.078 2.170 nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1501 " model vdw 2.080 2.170 ... (remaining 217734 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'G' and (resid 7 through 158 or resid 169 through 232)) selection = (chain 'H' and (resid 7 through 190 or (resid 191 through 192 and (name N or nam \ e CA or name C or name O or name CB )) or resid 193 or (resid 194 and (name N or \ name CA or name C or name O or name CB )) or resid 195 through 232)) } 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: 1.070 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: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 32.330 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 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 : 0.005 0.293 27096 Z= 0.286 Angle : 0.631 9.129 36903 Z= 0.371 Chirality : 0.049 0.416 4235 Planarity : 0.004 0.085 4588 Dihedral : 15.051 162.544 10517 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.15), residues: 3205 helix: 1.27 (0.16), residues: 1135 sheet: -0.92 (0.24), residues: 446 loop : -1.03 (0.16), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 3 TYR 0.014 0.001 TYR I1018 PHE 0.010 0.001 PHE I 337 TRP 0.006 0.001 TRP I 997 HIS 0.006 0.001 HIS J 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.29 (27088) covalent geometry : angle 0.62753 / 0.37 (36891) hydrogen bonds : bond 0.14954 / 15.85 ( 1133) hydrogen bonds : angle 5.95668 / 5.99 ( 3120) metal coordination : bond 0.00925 / 0.83 ( 8) metal coordination : angle 3.92903 / 7.06 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 1.036 Fit side-chains REVERT: G 10 LYS cc_start: 0.8371 (mptt) cc_final: 0.8150 (mptt) REVERT: G 103 ASN cc_start: 0.7863 (m-40) cc_final: 0.7588 (m-40) REVERT: G 141 SER cc_start: 0.7660 (t) cc_final: 0.7311 (t) REVERT: H 142 MET cc_start: 0.7984 (ptm) cc_final: 0.7659 (ptp) REVERT: I 600 THR cc_start: 0.8369 (m) cc_final: 0.8151 (p) REVERT: I 1158 LYS cc_start: 0.7904 (mmtp) cc_final: 0.7205 (tppt) REVERT: J 158 GLN cc_start: 0.7610 (tt0) cc_final: 0.7146 (tp40) REVERT: J 725 MET cc_start: 0.8196 (mtm) cc_final: 0.7979 (mtp) REVERT: J 873 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6895 (mt-10) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.2052 time to fit residues: 100.0867 Evaluate side-chains 269 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.3980 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.3980 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 3.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 132 HIS I 686 GLN ** I 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1111 GLN ** J 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 720 ASN J 875 ASN ** J 954 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.137695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.101898 restraints weight = 36548.291| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.98 r_work: 0.2968 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27096 Z= 0.153 Angle : 0.629 16.280 36903 Z= 0.319 Chirality : 0.050 1.077 4235 Planarity : 0.004 0.054 4588 Dihedral : 13.168 156.970 4260 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.81 % Allowed : 5.21 % Favored : 93.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.15), residues: 3205 helix: 1.36 (0.16), residues: 1154 sheet: -0.82 (0.25), residues: 433 loop : -1.04 (0.16), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 3 TYR 0.017 0.001 TYR J 631 PHE 0.022 0.001 PHE I 405 TRP 0.015 0.001 TRP J1193 HIS 0.010 0.001 HIS G 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (27088) covalent geometry : angle 0.62621 / 0.32 (36891) hydrogen bonds : bond 0.04210 / 4.60 ( 1133) hydrogen bonds : angle 4.81848 / 4.79 ( 3120) metal coordination : bond 0.00798 / 0.65 ( 8) metal coordination : angle 3.41287 / 6.45 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 288 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: G 10 LYS cc_start: 0.8443 (mptt) cc_final: 0.8240 (mptt) REVERT: G 141 SER cc_start: 0.8228 (t) cc_final: 0.7911 (t) REVERT: H 95 LYS cc_start: 0.6666 (ttpp) cc_final: 0.6235 (ttpt) REVERT: H 142 MET cc_start: 0.8417 (ptm) cc_final: 0.8041 (ptp) REVERT: I 23 ASP cc_start: 0.8649 (OUTLIER) cc_final: 0.8436 (t0) REVERT: I 83 GLN cc_start: 0.8618 (mp10) cc_final: 0.8130 (mp10) REVERT: I 473 ARG cc_start: 0.8003 (ttm-80) cc_final: 0.7796 (ttm110) REVERT: I 488 MET cc_start: 0.5814 (mmp) cc_final: 0.5439 (mmp) REVERT: I 1158 LYS cc_start: 0.8189 (mmtp) cc_final: 0.7125 (tppt) REVERT: J 158 GLN cc_start: 0.8201 (tt0) cc_final: 0.7651 (tp40) REVERT: J 308 ASP cc_start: 0.8668 (t0) cc_final: 0.8405 (t0) REVERT: J 591 ILE cc_start: 0.8525 (tt) cc_final: 0.8239 (mm) REVERT: J 873 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7626 (mt-10) REVERT: J 981 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7282 (mm-30) REVERT: J 1167 LYS cc_start: 0.7831 (mmmm) cc_final: 0.7073 (mmtp) REVERT: K 12 LYS cc_start: 0.8489 (tppt) cc_final: 0.8285 (ttmt) outliers start: 22 outliers final: 14 residues processed: 299 average time/residue: 0.1944 time to fit residues: 90.9425 Evaluate side-chains 270 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 255 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 394 ILE Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 703 THR Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1370 MET Chi-restraints excluded: chain K residue 58 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 115 optimal weight: 5.9990 chunk 213 optimal weight: 9.9990 chunk 297 optimal weight: 0.8980 chunk 315 optimal weight: 0.8980 chunk 32 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 chunk 292 optimal weight: 0.9990 chunk 146 optimal weight: 0.6980 chunk 22 optimal weight: 0.0270 chunk 177 optimal weight: 4.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 504 GLN J 708 ASN J 875 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.138971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.103179 restraints weight = 36504.721| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.83 r_work: 0.2978 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27096 Z= 0.118 Angle : 0.564 10.559 36903 Z= 0.289 Chirality : 0.045 0.553 4235 Planarity : 0.004 0.052 4588 Dihedral : 13.127 155.554 4260 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.99 % Allowed : 7.56 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.15), residues: 3205 helix: 1.44 (0.16), residues: 1161 sheet: -0.71 (0.25), residues: 425 loop : -1.08 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 3 TYR 0.016 0.001 TYR J 589 PHE 0.019 0.001 PHE I 405 TRP 0.009 0.001 TRP J1193 HIS 0.009 0.001 HIS G 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (27088) covalent geometry : angle 0.56128 / 0.29 (36891) hydrogen bonds : bond 0.03690 / 4.06 ( 1133) hydrogen bonds : angle 4.53873 / 4.58 ( 3120) metal coordination : bond 0.00605 / 0.49 ( 8) metal coordination : angle 2.88358 / 5.37 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 286 time to evaluate : 0.980 Fit side-chains revert: symmetry clash REVERT: G 10 LYS cc_start: 0.8466 (mptt) cc_final: 0.8106 (mptt) REVERT: G 80 GLU cc_start: 0.8341 (tt0) cc_final: 0.7892 (mm-30) REVERT: H 104 LYS cc_start: 0.7516 (ttmm) cc_final: 0.7254 (ttmt) REVERT: H 142 MET cc_start: 0.8385 (ptm) cc_final: 0.8063 (ptp) REVERT: I 23 ASP cc_start: 0.8716 (OUTLIER) cc_final: 0.8500 (t0) REVERT: I 80 PHE cc_start: 0.8155 (m-80) cc_final: 0.7882 (m-80) REVERT: I 83 GLN cc_start: 0.8687 (mp10) cc_final: 0.8123 (mp10) REVERT: I 286 GLU cc_start: 0.6245 (mt-10) cc_final: 0.5734 (pm20) REVERT: I 488 MET cc_start: 0.5827 (mmp) cc_final: 0.5516 (mmp) REVERT: I 600 THR cc_start: 0.8570 (m) cc_final: 0.8237 (p) REVERT: I 1158 LYS cc_start: 0.8178 (mmtp) cc_final: 0.7107 (tppt) REVERT: J 79 LYS cc_start: 0.7485 (ptmt) cc_final: 0.7248 (pttm) REVERT: J 158 GLN cc_start: 0.8235 (tt0) cc_final: 0.7569 (tp40) REVERT: J 591 ILE cc_start: 0.8547 (tt) cc_final: 0.8293 (mm) REVERT: J 873 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7586 (mt-10) REVERT: J 964 LYS cc_start: 0.8723 (ttpp) cc_final: 0.8109 (mttm) REVERT: J 1042 ASP cc_start: 0.6232 (t70) cc_final: 0.5525 (t70) REVERT: J 1167 LYS cc_start: 0.7782 (mmmm) cc_final: 0.7151 (mmtp) outliers start: 27 outliers final: 15 residues processed: 302 average time/residue: 0.1750 time to fit residues: 83.9566 Evaluate side-chains 278 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 262 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1090 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 190 optimal weight: 0.0980 chunk 6 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 301 optimal weight: 9.9990 chunk 294 optimal weight: 5.9990 chunk 263 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 278 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 224 optimal weight: 0.0770 chunk 289 optimal weight: 0.4980 overall best weight: 1.1340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 84 ASN ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 708 ASN J 875 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.138269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.102351 restraints weight = 36472.347| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.83 r_work: 0.2984 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27096 Z= 0.131 Angle : 0.560 12.507 36903 Z= 0.286 Chirality : 0.044 0.395 4235 Planarity : 0.004 0.052 4588 Dihedral : 13.115 157.153 4260 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.39 % Allowed : 9.35 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.15), residues: 3205 helix: 1.48 (0.16), residues: 1162 sheet: -0.73 (0.24), residues: 436 loop : -1.05 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J1258 TYR 0.016 0.001 TYR J 589 PHE 0.017 0.001 PHE I 405 TRP 0.008 0.001 TRP J1193 HIS 0.008 0.001 HIS G 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (27088) covalent geometry : angle 0.55732 / 0.29 (36891) hydrogen bonds : bond 0.03508 / 3.88 ( 1133) hydrogen bonds : angle 4.41146 / 4.50 ( 3120) metal coordination : bond 0.00656 / 0.52 ( 8) metal coordination : angle 2.99715 / 5.53 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 279 time to evaluate : 0.604 Fit side-chains revert: symmetry clash REVERT: G 80 GLU cc_start: 0.8400 (tt0) cc_final: 0.7897 (mm-30) REVERT: H 142 MET cc_start: 0.8406 (ptm) cc_final: 0.8027 (ptp) REVERT: I 23 ASP cc_start: 0.8728 (OUTLIER) cc_final: 0.8512 (t0) REVERT: I 80 PHE cc_start: 0.8186 (m-80) cc_final: 0.7953 (m-80) REVERT: I 83 GLN cc_start: 0.8721 (mp10) cc_final: 0.8145 (mp10) REVERT: I 286 GLU cc_start: 0.6148 (mt-10) cc_final: 0.5734 (pm20) REVERT: I 488 MET cc_start: 0.5818 (mmp) cc_final: 0.5544 (mmp) REVERT: I 600 THR cc_start: 0.8521 (m) cc_final: 0.8144 (p) REVERT: I 1034 ARG cc_start: 0.8567 (ttp80) cc_final: 0.7590 (ttm-80) REVERT: I 1158 LYS cc_start: 0.8202 (mmtp) cc_final: 0.7153 (tppt) REVERT: I 1180 MET cc_start: 0.9066 (ttm) cc_final: 0.8828 (ttt) REVERT: I 1319 MET cc_start: 0.8140 (ttp) cc_final: 0.7841 (ttp) REVERT: J 79 LYS cc_start: 0.7412 (ptmt) cc_final: 0.7192 (pttm) REVERT: J 158 GLN cc_start: 0.8263 (tt0) cc_final: 0.7628 (tp40) REVERT: J 591 ILE cc_start: 0.8520 (tt) cc_final: 0.8275 (mm) REVERT: J 873 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7446 (mt-10) REVERT: J 964 LYS cc_start: 0.8732 (ttpp) cc_final: 0.8143 (mttm) REVERT: J 1042 ASP cc_start: 0.5877 (t0) cc_final: 0.5224 (m-30) outliers start: 38 outliers final: 27 residues processed: 308 average time/residue: 0.1603 time to fit residues: 77.7509 Evaluate side-chains 289 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 261 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 857 VAL Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 703 THR Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1344 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 68 optimal weight: 0.5980 chunk 196 optimal weight: 0.6980 chunk 271 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 chunk 134 optimal weight: 6.9990 chunk 208 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 217 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 41 ASN ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 708 ASN J 875 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.138204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.102373 restraints weight = 36362.577| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.86 r_work: 0.2956 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27096 Z= 0.115 Angle : 0.544 12.210 36903 Z= 0.278 Chirality : 0.043 0.346 4235 Planarity : 0.004 0.061 4588 Dihedral : 13.082 158.613 4260 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.47 % Allowed : 10.05 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.15), residues: 3205 helix: 1.53 (0.16), residues: 1164 sheet: -0.71 (0.24), residues: 441 loop : -1.02 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 44 TYR 0.015 0.001 TYR J 589 PHE 0.016 0.001 PHE I 405 TRP 0.008 0.001 TRP J1193 HIS 0.008 0.001 HIS G 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (27088) covalent geometry : angle 0.54199 / 0.28 (36891) hydrogen bonds : bond 0.03341 / 3.69 ( 1133) hydrogen bonds : angle 4.33844 / 4.43 ( 3120) metal coordination : bond 0.00536 / 0.43 ( 8) metal coordination : angle 2.74156 / 5.05 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 274 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: G 80 GLU cc_start: 0.8365 (tt0) cc_final: 0.7852 (mm-30) REVERT: H 142 MET cc_start: 0.8393 (ptm) cc_final: 0.8182 (ptp) REVERT: I 80 PHE cc_start: 0.8193 (m-80) cc_final: 0.7982 (m-80) REVERT: I 83 GLN cc_start: 0.8713 (mp10) cc_final: 0.8169 (mp10) REVERT: I 286 GLU cc_start: 0.6129 (mt-10) cc_final: 0.5695 (pm20) REVERT: I 488 MET cc_start: 0.5838 (mmp) cc_final: 0.5602 (mmp) REVERT: I 600 THR cc_start: 0.8484 (m) cc_final: 0.8094 (p) REVERT: I 1034 ARG cc_start: 0.8561 (ttp80) cc_final: 0.7569 (ttm-80) REVERT: I 1158 LYS cc_start: 0.8171 (mmtp) cc_final: 0.7089 (tppt) REVERT: J 79 LYS cc_start: 0.7391 (ptmt) cc_final: 0.7163 (pttm) REVERT: J 158 GLN cc_start: 0.8283 (tt0) cc_final: 0.7638 (tp40) REVERT: J 189 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8242 (mp) REVERT: J 591 ILE cc_start: 0.8536 (tt) cc_final: 0.8271 (mm) REVERT: J 873 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7454 (mt-10) REVERT: J 964 LYS cc_start: 0.8728 (ttpp) cc_final: 0.8107 (mttm) REVERT: J 1042 ASP cc_start: 0.5851 (t0) cc_final: 0.5540 (m-30) REVERT: J 1167 LYS cc_start: 0.8049 (mmmm) cc_final: 0.7221 (mmtp) REVERT: K 70 GLN cc_start: 0.7197 (tm-30) cc_final: 0.6803 (mt0) outliers start: 40 outliers final: 30 residues processed: 305 average time/residue: 0.1859 time to fit residues: 90.2160 Evaluate side-chains 295 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 264 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain J residue 486 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 703 THR Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1035 VAL Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1344 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 96 optimal weight: 0.4980 chunk 158 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 267 optimal weight: 0.9990 chunk 298 optimal weight: 4.9990 chunk 224 optimal weight: 0.0970 chunk 295 optimal weight: 6.9990 chunk 304 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 278 optimal weight: 7.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 65 ASN ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 458 ASN J 708 ASN J 875 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.139305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.103870 restraints weight = 36363.150| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.95 r_work: 0.2994 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 27096 Z= 0.109 Angle : 0.533 11.383 36903 Z= 0.273 Chirality : 0.043 0.332 4235 Planarity : 0.004 0.065 4588 Dihedral : 13.054 159.628 4260 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.47 % Allowed : 11.01 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.15), residues: 3205 helix: 1.57 (0.16), residues: 1166 sheet: -0.69 (0.24), residues: 439 loop : -1.01 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 478 TYR 0.014 0.001 TYR J 589 PHE 0.015 0.001 PHE I 405 TRP 0.008 0.001 TRP J1193 HIS 0.008 0.001 HIS G 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (27088) covalent geometry : angle 0.53084 / 0.27 (36891) hydrogen bonds : bond 0.03213 / 3.55 ( 1133) hydrogen bonds : angle 4.24410 / 4.35 ( 3120) metal coordination : bond 0.00453 / 0.36 ( 8) metal coordination : angle 2.56648 / 4.71 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 277 time to evaluate : 0.998 Fit side-chains revert: symmetry clash REVERT: G 80 GLU cc_start: 0.8411 (tt0) cc_final: 0.8181 (tt0) REVERT: H 76 GLU cc_start: 0.8551 (mp0) cc_final: 0.7899 (mp0) REVERT: H 142 MET cc_start: 0.8410 (ptm) cc_final: 0.8064 (ptp) REVERT: I 83 GLN cc_start: 0.8710 (mp10) cc_final: 0.8111 (mp10) REVERT: I 286 GLU cc_start: 0.6269 (mt-10) cc_final: 0.5767 (pm20) REVERT: I 488 MET cc_start: 0.5798 (mmp) cc_final: 0.5584 (mmp) REVERT: I 600 THR cc_start: 0.8491 (m) cc_final: 0.8048 (p) REVERT: I 1158 LYS cc_start: 0.8150 (mmtp) cc_final: 0.7055 (tppt) REVERT: I 1319 MET cc_start: 0.8082 (ttp) cc_final: 0.7763 (ttp) REVERT: J 79 LYS cc_start: 0.7395 (ptmt) cc_final: 0.7169 (pttm) REVERT: J 158 GLN cc_start: 0.8283 (tt0) cc_final: 0.7592 (tp40) REVERT: J 189 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8222 (mp) REVERT: J 267 ASP cc_start: 0.8558 (m-30) cc_final: 0.8313 (m-30) REVERT: J 591 ILE cc_start: 0.8539 (tt) cc_final: 0.8268 (mm) REVERT: J 964 LYS cc_start: 0.8585 (ttpp) cc_final: 0.7992 (mttm) REVERT: J 1042 ASP cc_start: 0.5878 (t0) cc_final: 0.5567 (m-30) REVERT: J 1132 LYS cc_start: 0.7639 (mtpt) cc_final: 0.7354 (mmmm) REVERT: K 12 LYS cc_start: 0.8392 (tppt) cc_final: 0.8161 (ttmt) REVERT: K 55 GLU cc_start: 0.7269 (mt-10) cc_final: 0.6925 (mt-10) outliers start: 40 outliers final: 32 residues processed: 310 average time/residue: 0.1888 time to fit residues: 92.9021 Evaluate side-chains 290 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 257 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain J residue 486 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 703 THR Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1344 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 89 optimal weight: 10.0000 chunk 277 optimal weight: 8.9990 chunk 290 optimal weight: 2.9990 chunk 80 optimal weight: 0.3980 chunk 153 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 201 optimal weight: 6.9990 chunk 307 optimal weight: 0.0020 chunk 160 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 322 optimal weight: 7.9990 overall best weight: 1.2592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 41 ASN ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 HIS ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 708 ASN J 875 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.138493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.102845 restraints weight = 36264.912| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.89 r_work: 0.3018 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27096 Z= 0.131 Angle : 0.545 11.660 36903 Z= 0.278 Chirality : 0.043 0.337 4235 Planarity : 0.004 0.070 4588 Dihedral : 13.076 159.630 4260 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.65 % Allowed : 11.59 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.15), residues: 3205 helix: 1.60 (0.16), residues: 1164 sheet: -0.72 (0.25), residues: 423 loop : -0.97 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J1258 TYR 0.015 0.001 TYR J 589 PHE 0.014 0.001 PHE I 405 TRP 0.008 0.001 TRP J1193 HIS 0.008 0.001 HIS G 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (27088) covalent geometry : angle 0.54264 / 0.28 (36891) hydrogen bonds : bond 0.03244 / 3.59 ( 1133) hydrogen bonds : angle 4.19753 / 4.33 ( 3120) metal coordination : bond 0.00558 / 0.43 ( 8) metal coordination : angle 2.57232 / 4.82 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 268 time to evaluate : 1.048 Fit side-chains revert: symmetry clash REVERT: H 76 GLU cc_start: 0.8533 (mp0) cc_final: 0.7939 (mp0) REVERT: H 142 MET cc_start: 0.8408 (ptm) cc_final: 0.8055 (ptp) REVERT: I 83 GLN cc_start: 0.8682 (mp10) cc_final: 0.8173 (mp10) REVERT: I 286 GLU cc_start: 0.6221 (mt-10) cc_final: 0.5769 (pm20) REVERT: I 600 THR cc_start: 0.8550 (m) cc_final: 0.8087 (p) REVERT: I 685 MET cc_start: 0.9060 (mtm) cc_final: 0.8763 (mtp) REVERT: I 1158 LYS cc_start: 0.8168 (mmtp) cc_final: 0.7113 (tppt) REVERT: I 1319 MET cc_start: 0.8071 (ttp) cc_final: 0.7777 (ttp) REVERT: J 79 LYS cc_start: 0.7380 (ptmt) cc_final: 0.7169 (pttm) REVERT: J 158 GLN cc_start: 0.8278 (tt0) cc_final: 0.7698 (tp40) REVERT: J 189 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8302 (mp) REVERT: J 267 ASP cc_start: 0.8566 (m-30) cc_final: 0.8342 (m-30) REVERT: J 591 ILE cc_start: 0.8532 (tt) cc_final: 0.8284 (mm) REVERT: J 964 LYS cc_start: 0.8591 (ttpp) cc_final: 0.8019 (mttm) REVERT: J 1167 LYS cc_start: 0.7952 (mmmm) cc_final: 0.7444 (mmtt) REVERT: K 70 GLN cc_start: 0.7286 (tm-30) cc_final: 0.6827 (mt0) outliers start: 45 outliers final: 35 residues processed: 304 average time/residue: 0.1850 time to fit residues: 89.9297 Evaluate side-chains 295 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 259 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 486 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 703 THR Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1370 MET Chi-restraints excluded: chain K residue 21 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 35 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 201 optimal weight: 9.9990 chunk 149 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 287 optimal weight: 20.0000 chunk 2 optimal weight: 30.0000 chunk 179 optimal weight: 5.9990 chunk 272 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 HIS H 227 GLN I 330 HIS I 526 HIS I 856 ASN ** I 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1111 GLN ** J 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1126 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.133148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.097174 restraints weight = 36527.245| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.90 r_work: 0.2887 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 27096 Z= 0.282 Angle : 0.675 11.846 36903 Z= 0.343 Chirality : 0.048 0.347 4235 Planarity : 0.005 0.063 4588 Dihedral : 13.332 156.273 4260 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 1.54 % Allowed : 12.29 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.15), residues: 3205 helix: 1.28 (0.15), residues: 1161 sheet: -0.69 (0.25), residues: 444 loop : -1.10 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J1258 TYR 0.021 0.002 TYR J 631 PHE 0.015 0.002 PHE I 405 TRP 0.008 0.002 TRP I1276 HIS 0.013 0.001 HIS J 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00677 / 0.28 (27088) covalent geometry : angle 0.67174 / 0.34 (36891) hydrogen bonds : bond 0.04068 / 4.52 ( 1133) hydrogen bonds : angle 4.41339 / 4.59 ( 3120) metal coordination : bond 0.01168 / 0.87 ( 8) metal coordination : angle 3.57558 / 7.34 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 265 time to evaluate : 1.002 Fit side-chains REVERT: H 41 ASN cc_start: 0.9002 (t0) cc_final: 0.8751 (t0) REVERT: H 104 LYS cc_start: 0.8195 (ttmm) cc_final: 0.7935 (ttpt) REVERT: H 142 MET cc_start: 0.8594 (ptm) cc_final: 0.8249 (ptp) REVERT: I 83 GLN cc_start: 0.8788 (mp10) cc_final: 0.8243 (mp10) REVERT: I 286 GLU cc_start: 0.6366 (mt-10) cc_final: 0.5808 (pm20) REVERT: I 1158 LYS cc_start: 0.8325 (mmtp) cc_final: 0.7395 (tppt) REVERT: I 1327 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8734 (mp) REVERT: J 79 LYS cc_start: 0.7432 (ptmt) cc_final: 0.7207 (pttm) REVERT: J 151 MET cc_start: 0.5961 (ppp) cc_final: 0.5432 (mmp) REVERT: J 158 GLN cc_start: 0.8500 (tt0) cc_final: 0.7853 (tp40) REVERT: J 189 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8505 (mp) REVERT: J 591 ILE cc_start: 0.8619 (tt) cc_final: 0.8367 (mm) REVERT: J 964 LYS cc_start: 0.8653 (ttpp) cc_final: 0.8081 (mttm) REVERT: J 981 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7369 (mm-30) REVERT: K 55 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6971 (mt-10) outliers start: 42 outliers final: 35 residues processed: 299 average time/residue: 0.1884 time to fit residues: 89.4194 Evaluate side-chains 292 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 255 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain J residue 330 MET Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 486 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 703 THR Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1370 MET Chi-restraints excluded: chain K residue 21 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 172 optimal weight: 4.9990 chunk 324 optimal weight: 5.9990 chunk 319 optimal weight: 3.9990 chunk 142 optimal weight: 0.7980 chunk 16 optimal weight: 8.9990 chunk 136 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 309 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 284 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 132 HIS ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 HIS I 214 ASN ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 875 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.137233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.102510 restraints weight = 36272.669| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.99 r_work: 0.2984 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27096 Z= 0.122 Angle : 0.566 11.669 36903 Z= 0.288 Chirality : 0.043 0.334 4235 Planarity : 0.004 0.059 4588 Dihedral : 13.201 157.562 4260 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.25 % Allowed : 13.06 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.15), residues: 3205 helix: 1.50 (0.16), residues: 1164 sheet: -0.64 (0.25), residues: 440 loop : -1.07 (0.15), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 478 TYR 0.015 0.001 TYR J 589 PHE 0.016 0.001 PHE I 405 TRP 0.009 0.001 TRP J1193 HIS 0.009 0.001 HIS G 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (27088) covalent geometry : angle 0.56281 / 0.29 (36891) hydrogen bonds : bond 0.03306 / 3.67 ( 1133) hydrogen bonds : angle 4.26054 / 4.44 ( 3120) metal coordination : bond 0.00573 / 0.43 ( 8) metal coordination : angle 3.23121 / 6.42 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 270 time to evaluate : 0.987 Fit side-chains REVERT: G 18 GLN cc_start: 0.8879 (mm-40) cc_final: 0.8393 (mm-40) REVERT: H 76 GLU cc_start: 0.8514 (mp0) cc_final: 0.8040 (mp0) REVERT: H 104 LYS cc_start: 0.8227 (ttmm) cc_final: 0.7891 (ttmt) REVERT: H 142 MET cc_start: 0.8568 (ptm) cc_final: 0.8228 (ptp) REVERT: H 147 GLN cc_start: 0.8163 (mt0) cc_final: 0.7934 (mt0) REVERT: I 5 TYR cc_start: 0.8116 (t80) cc_final: 0.7908 (t80) REVERT: I 83 GLN cc_start: 0.8730 (mp10) cc_final: 0.8204 (mp10) REVERT: I 286 GLU cc_start: 0.6307 (mt-10) cc_final: 0.5695 (pm20) REVERT: I 332 ARG cc_start: 0.6480 (ttt180) cc_final: 0.6142 (ttt180) REVERT: I 685 MET cc_start: 0.9088 (mtm) cc_final: 0.8886 (mtp) REVERT: I 1158 LYS cc_start: 0.8129 (mmtp) cc_final: 0.7205 (tppt) REVERT: J 79 LYS cc_start: 0.7388 (ptmt) cc_final: 0.7184 (pttm) REVERT: J 151 MET cc_start: 0.5815 (ppp) cc_final: 0.5256 (mmt) REVERT: J 158 GLN cc_start: 0.8337 (tt0) cc_final: 0.7757 (tp40) REVERT: J 189 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8276 (mp) REVERT: J 267 ASP cc_start: 0.8535 (m-30) cc_final: 0.8330 (m-30) REVERT: J 591 ILE cc_start: 0.8580 (tt) cc_final: 0.8332 (mm) REVERT: J 964 LYS cc_start: 0.8615 (ttpp) cc_final: 0.8016 (mttm) REVERT: J 981 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7320 (mm-30) REVERT: J 1165 PHE cc_start: 0.8014 (m-80) cc_final: 0.7723 (m-10) REVERT: K 12 LYS cc_start: 0.8317 (tppt) cc_final: 0.8109 (ttmt) REVERT: K 55 GLU cc_start: 0.7269 (mt-10) cc_final: 0.6987 (mt-10) REVERT: K 70 GLN cc_start: 0.7210 (tm-30) cc_final: 0.6701 (mt0) outliers start: 34 outliers final: 30 residues processed: 297 average time/residue: 0.1947 time to fit residues: 91.9699 Evaluate side-chains 288 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 257 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 703 THR Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 36 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 207 optimal weight: 0.7980 chunk 288 optimal weight: 0.9980 chunk 159 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 276 optimal weight: 0.0060 chunk 188 optimal weight: 9.9990 chunk 318 optimal weight: 0.8980 chunk 180 optimal weight: 0.9990 chunk 203 optimal weight: 0.0060 chunk 112 optimal weight: 1.9990 chunk 211 optimal weight: 7.9990 overall best weight: 0.5012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 41 ASN G 66 HIS ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 ASN H 132 HIS ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1111 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.138997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.103726 restraints weight = 36195.527| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.92 r_work: 0.3026 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 27096 Z= 0.108 Angle : 0.548 11.399 36903 Z= 0.279 Chirality : 0.042 0.317 4235 Planarity : 0.004 0.058 4588 Dihedral : 13.112 158.718 4260 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.14 % Allowed : 13.32 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.15), residues: 3205 helix: 1.67 (0.16), residues: 1158 sheet: -0.75 (0.25), residues: 435 loop : -0.98 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 33 TYR 0.012 0.001 TYR J 589 PHE 0.015 0.001 PHE I 405 TRP 0.009 0.001 TRP J1193 HIS 0.009 0.001 HIS G 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (27088) covalent geometry : angle 0.54625 / 0.28 (36891) hydrogen bonds : bond 0.03096 / 3.44 ( 1133) hydrogen bonds : angle 4.14621 / 4.34 ( 3120) metal coordination : bond 0.00370 / 0.28 ( 8) metal coordination : angle 2.68583 / 5.03 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 277 time to evaluate : 1.042 Fit side-chains REVERT: G 141 SER cc_start: 0.8693 (t) cc_final: 0.7894 (t) REVERT: H 104 LYS cc_start: 0.8189 (ttmm) cc_final: 0.7912 (ttpt) REVERT: H 142 MET cc_start: 0.8541 (ptm) cc_final: 0.8206 (ptp) REVERT: H 147 GLN cc_start: 0.8169 (mt0) cc_final: 0.7940 (mt0) REVERT: I 5 TYR cc_start: 0.8092 (t80) cc_final: 0.7883 (t80) REVERT: I 83 GLN cc_start: 0.8785 (mp10) cc_final: 0.8250 (mp10) REVERT: I 286 GLU cc_start: 0.6308 (mt-10) cc_final: 0.5680 (pm20) REVERT: I 332 ARG cc_start: 0.6423 (ttt180) cc_final: 0.6129 (ttt180) REVERT: I 508 SER cc_start: 0.8894 (p) cc_final: 0.8688 (p) REVERT: I 1034 ARG cc_start: 0.8457 (ttp80) cc_final: 0.7616 (ttm-80) REVERT: I 1158 LYS cc_start: 0.8096 (mmtp) cc_final: 0.7184 (tppt) REVERT: I 1319 MET cc_start: 0.8089 (ttp) cc_final: 0.7743 (ttp) REVERT: J 151 MET cc_start: 0.5622 (ppp) cc_final: 0.5366 (ppp) REVERT: J 158 GLN cc_start: 0.8392 (tt0) cc_final: 0.7734 (tp40) REVERT: J 189 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8198 (mp) REVERT: J 267 ASP cc_start: 0.8562 (m-30) cc_final: 0.8336 (m-30) REVERT: J 591 ILE cc_start: 0.8563 (tt) cc_final: 0.8300 (mm) REVERT: J 644 MET cc_start: 0.8297 (mpp) cc_final: 0.8057 (mtm) REVERT: J 873 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7267 (mt-10) REVERT: J 964 LYS cc_start: 0.8594 (ttpp) cc_final: 0.8000 (mttm) REVERT: J 981 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7207 (mm-30) REVERT: J 1146 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7964 (mm-30) REVERT: J 1165 PHE cc_start: 0.7796 (m-80) cc_final: 0.7431 (m-10) REVERT: J 1167 LYS cc_start: 0.8004 (mmmm) cc_final: 0.7666 (mmtt) REVERT: K 55 GLU cc_start: 0.7242 (mt-10) cc_final: 0.7019 (mt-10) REVERT: K 70 GLN cc_start: 0.7237 (tm-30) cc_final: 0.6717 (mt0) outliers start: 31 outliers final: 25 residues processed: 305 average time/residue: 0.1828 time to fit residues: 88.8266 Evaluate side-chains 292 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 266 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 703 THR Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1344 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 193 optimal weight: 6.9990 chunk 255 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 263 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 181 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 221 optimal weight: 7.9990 chunk 229 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 41 ASN H 66 HIS H 132 HIS ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.137566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.101342 restraints weight = 36242.294| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.88 r_work: 0.2961 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27096 Z= 0.145 Angle : 0.570 11.143 36903 Z= 0.288 Chirality : 0.043 0.302 4235 Planarity : 0.004 0.056 4588 Dihedral : 13.171 157.555 4260 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.25 % Allowed : 13.46 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.15), residues: 3205 helix: 1.62 (0.16), residues: 1162 sheet: -0.72 (0.25), residues: 430 loop : -0.98 (0.15), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 478 TYR 0.015 0.001 TYR J 589 PHE 0.015 0.001 PHE I 405 TRP 0.007 0.001 TRP J1193 HIS 0.010 0.001 HIS G 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (27088) covalent geometry : angle 0.56742 / 0.29 (36891) hydrogen bonds : bond 0.03265 / 3.63 ( 1133) hydrogen bonds : angle 4.15894 / 4.35 ( 3120) metal coordination : bond 0.00569 / 0.42 ( 8) metal coordination : angle 2.80145 / 5.37 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6653.56 seconds wall clock time: 114 minutes 49.68 seconds (6889.68 seconds total)