Starting phenix.real_space_refine on Sat Aug 8 07:26:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8eg7_28109/08_2026/8eg7_28109.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eg7_28109/08_2026/8eg7_28109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8eg7_28109/08_2026/8eg7_28109.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eg7_28109/08_2026/8eg7_28109.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8eg7_28109/08_2026/8eg7_28109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eg7_28109/08_2026/8eg7_28109.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8eg7_28109/08_2026/8eg7_28109.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8eg7_28109/08_2026/8eg7_28109.cif" } resolution = 3.2 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 65 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 16229 2.51 5 N 4622 2.21 5 O 5175 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 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: 26200 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 487 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain breaks: 1 Chain: "B" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 637 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "R" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 216 Classifications: {'RNAv2': 10} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 8} 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: 10407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1319, 10407 Classifications: {'peptide': 1319} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 54, 'TRANS': 1262} Chain breaks: 1 Chain: "J" Number of atoms: 10384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10384 Classifications: {'peptide': 1335} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1279} Chain breaks: 2 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 15553 SG CYS J 70 53.029 119.153 59.080 1.00 86.99 S ATOM 15567 SG CYS J 72 54.601 122.596 59.656 1.00 88.75 S ATOM 15675 SG CYS J 85 52.546 121.989 56.573 1.00 89.70 S ATOM 15699 SG CYS J 88 55.890 120.173 56.949 1.00 87.25 S ATOM 21387 SG CYS J 814 47.420 53.415 48.194 1.00 45.00 S ATOM 21952 SG CYS J 888 49.889 56.203 49.052 1.00 39.19 S ATOM 22003 SG CYS J 895 47.509 54.773 51.686 1.00 35.31 S ATOM 22024 SG CYS J 898 50.362 52.689 50.469 1.00 37.07 S Time building chain proxies: 5.38, per 1000 atoms: 0.21 Number of scatterers: 26200 At special positions: 0 Unit cell: (148.2, 136.5, 145.6, 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 65 15.00 Mg 1 11.99 O 5175 8.00 N 4622 7.00 C 16229 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: 2.33 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " 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 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " Number of angles added : 12 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5858 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 46 sheets defined 37.1% alpha, 15.8% beta 29 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 2.66 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 Processing helix chain 'G' and resid 77 through 87 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 228 Processing helix chain 'G' and resid 229 through 232 removed outlier: 3.864A pdb=" N VAL G 232 " --> pdb=" O GLU G 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 229 through 232' Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.682A 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 227 Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.600A pdb=" N LYS I 37 " --> pdb=" O ASP I 33 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE I 38 " --> pdb=" O SER I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 57 removed outlier: 3.603A 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: 3.819A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 removed outlier: 3.664A pdb=" N LEU I 246 " --> pdb=" O PRO I 243 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG I 247 " --> pdb=" O GLU I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 280 Processing helix chain 'I' and resid 291 through 295 removed outlier: 3.924A pdb=" N GLY I 294 " --> pdb=" O TYR I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 329 removed outlier: 3.791A pdb=" N GLN I 327 " --> pdb=" O ALA I 323 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER I 328 " --> pdb=" O LYS I 324 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY I 329 " --> pdb=" O LEU I 325 " (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: 4.224A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE I 390 " --> pdb=" O GLU I 386 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 455 through 479 removed outlier: 3.743A pdb=" N ARG I 470 " --> pdb=" O VAL I 466 " (cutoff:3.500A) Processing helix chain 'I' and resid 483 through 487 removed outlier: 4.054A pdb=" N LEU I 487 " --> pdb=" O LEU I 484 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 508 Processing helix chain 'I' and resid 519 through 528 removed outlier: 3.644A pdb=" N ARG I 528 " --> pdb=" O ILE I 524 " (cutoff:3.500A) Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.998A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 608 through 613 removed outlier: 4.170A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (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 738 through 741 Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 858 through 863 removed outlier: 3.645A pdb=" N LEU I 862 " --> pdb=" O GLY I 858 " (cutoff:3.500A) Processing helix chain 'I' and resid 942 through 979 Processing helix chain 'I' and resid 1005 through 1038 removed outlier: 4.048A pdb=" N ASN I1009 " --> pdb=" O GLU I1005 " (cutoff:3.500A) Processing helix chain 'I' and resid 1081 through 1085 removed outlier: 3.750A pdb=" N MET I1085 " --> pdb=" O ILE I1082 " (cutoff:3.500A) Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 4.433A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG I1106 " --> pdb=" O GLY I1102 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1101 through 1106' Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.791A pdb=" N GLN I1134 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1150 removed outlier: 3.529A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1177 removed outlier: 3.536A pdb=" N ARG I1171 " --> pdb=" O GLU I1167 " (cutoff:3.500A) Processing helix chain 'I' and resid 1191 through 1202 removed outlier: 3.559A pdb=" N GLY I1202 " --> pdb=" O LEU I1198 " (cutoff:3.500A) Processing helix chain 'I' and resid 1238 through 1243 Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1283 through 1292 removed outlier: 3.580A pdb=" N LEU I1287 " --> pdb=" O ALA I1283 " (cutoff:3.500A) Processing helix chain 'I' and resid 1297 through 1311 Processing helix chain 'I' and resid 1320 through 1332 removed outlier: 3.603A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 77 through 81 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 180 through 191 removed outlier: 3.599A pdb=" N ALA J 184 " --> pdb=" O MET J 180 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 207 Processing helix chain 'J' and resid 210 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 265 through 285 removed outlier: 3.790A pdb=" N VAL J 272 " --> pdb=" O LEU J 268 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU J 285 " --> pdb=" O ARG J 281 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 326 through 332 Processing helix chain 'J' and resid 337 through 342 Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 393 through 404 removed outlier: 3.578A pdb=" N ALA J 397 " --> pdb=" O THR J 393 " (cutoff:3.500A) Processing helix chain 'J' and resid 407 through 417 removed outlier: 3.640A 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 450 through 452 No H-bonds generated for 'chain 'J' and resid 450 through 452' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 504 through 514 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 581 Processing helix chain 'J' and resid 588 through 593 removed outlier: 3.593A pdb=" N ASN J 593 " --> pdb=" O SER J 590 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 612 removed outlier: 3.631A pdb=" N ILE J 601 " --> pdb=" O GLY J 597 " (cutoff:3.500A) Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.584A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 703 Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 Processing helix chain 'J' and resid 768 through 804 removed outlier: 4.112A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 895 through 900 removed outlier: 3.553A pdb=" N TYR J 899 " --> pdb=" O CYS J 895 " (cutoff:3.500A) Processing helix chain 'J' and resid 914 through 925 removed outlier: 3.896A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 928 No H-bonds generated for 'chain 'J' and resid 926 through 928' Processing helix chain 'J' and resid 1137 through 1147 Processing helix chain 'J' and resid 1216 through 1224 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 3.639A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL J1240 " --> pdb=" O GLU J1236 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.377A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 removed outlier: 3.586A pdb=" N ASN J1295 " --> pdb=" O GLU J1291 " (cutoff:3.500A) Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1318 through 1325 removed outlier: 3.846A 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: 4.034A pdb=" N ASN J1350 " --> pdb=" O GLY J1346 " (cutoff:3.500A) Processing helix chain 'J' and resid 1361 through 1372 removed outlier: 4.283A 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 57 Processing helix chain 'K' and resid 60 through 84 Processing sheet with id=AA1, first strand: chain 'G' and resid 12 through 17 removed outlier: 5.522A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N HIS G 23 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR G 207 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LYS G 200 " --> pdb=" O VAL G 187 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL G 187 " --> pdb=" O LYS G 200 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL G 202 " --> pdb=" O TYR G 185 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TYR G 185 " --> pdb=" O VAL G 202 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLU G 204 " --> pdb=" O ILE G 183 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ILE G 183 " --> pdb=" O GLU G 204 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU G 206 " --> pdb=" O GLU G 181 " (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: 3.783A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (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: 6.556A pdb=" N GLY G 108 " --> pdb=" O HIS G 132 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N HIS G 132 " --> pdb=" O GLY G 108 " (cutoff:3.500A) removed outlier: 6.835A 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: 5.892A pdb=" N LEU H 13 " --> pdb=" O GLU H 29 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N GLU H 29 " --> pdb=" O LEU H 13 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASP H 15 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG H 182 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 98 through 105 removed outlier: 7.871A pdb=" N SER H 141 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ILE H 61 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 3.640A 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: 3.548A pdb=" N GLY H 108 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU H 133 " --> pdb=" O GLY H 108 " (cutoff:3.500A) removed outlier: 3.533A 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: 6.294A 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: 3.570A pdb=" N ARG I 101 " --> pdb=" O GLN I 69 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS I 118 " --> pdb=" O LEU I 102 " (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: 6.385A 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: 3.614A 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: 4.434A 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: 6.737A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 301 through 302 removed outlier: 7.313A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 580 through 581 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 748 through 752 removed outlier: 6.933A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AC5, first strand: chain 'I' and resid 768 through 769 Processing sheet with id=AC6, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC7, first strand: chain 'I' and resid 1066 through 1067 removed outlier: 4.163A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 9.038A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ILE I 816 " --> pdb=" O LYS I1078 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ASN I1080 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL I 818 " --> pdb=" O ASN I1080 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 1066 through 1067 removed outlier: 4.470A pdb=" N LEU I1212 " --> pdb=" O PHE I1221 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ARG I1223 " --> pdb=" O ILE I1210 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ILE I1210 " --> pdb=" O ARG I1223 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 830 through 841 removed outlier: 6.327A pdb=" N THR I 830 " --> pdb=" O LYS I1057 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LYS I1057 " --> pdb=" O THR I 830 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N HIS I 832 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ALA I1055 " --> pdb=" O HIS I 832 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLN I 834 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR I1053 " --> pdb=" O GLN I 834 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU I 836 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS I1051 " --> pdb=" O LEU I 836 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N CYS I 838 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE I1049 " --> pdb=" O CYS I 838 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N SER I 840 " --> pdb=" O LEU I1047 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 882 through 884 Processing sheet with id=AD2, first strand: chain 'I' and resid 887 through 888 Processing sheet with id=AD3, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AD4, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AD5, first strand: chain 'I' and resid 1335 through 1340 removed outlier: 4.500A pdb=" N ALA J 19 " --> pdb=" O GLU I1340 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.615A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 9.909A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.715A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 159 through 160 Processing sheet with id=AD8, first strand: chain 'J' and resid 547 through 556 Processing sheet with id=AD9, first strand: chain 'J' and resid 706 through 707 removed outlier: 3.873A pdb=" N ILE J 707 " --> pdb=" O GLU J 714 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU J 714 " --> pdb=" O ILE J 707 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE2, first strand: chain 'J' and resid 825 through 826 removed outlier: 7.049A pdb=" N VAL J 825 " --> pdb=" O LYS J 832 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 848 through 849 removed outlier: 7.036A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 957 through 961 Processing sheet with id=AE5, first strand: chain 'J' and resid 965 through 967 Processing sheet with id=AE6, first strand: chain 'J' and resid 1025 through 1026 Processing sheet with id=AE7, first strand: chain 'J' and resid 1098 through 1100 Processing sheet with id=AE8, first strand: chain 'J' and resid 1046 through 1049 removed outlier: 3.650A pdb=" N LEU J1059 " --> pdb=" O VAL J1107 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL J1107 " --> pdb=" O LEU J1059 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL J1061 " --> pdb=" O ALA J1105 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 1162 through 1165 Processing sheet with id=AF1, first strand: chain 'J' and resid 1279 through 1281 1005 hydrogen bonds defined for protein. 2832 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 72 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 6.53 Time building geometry restraints manager: 3.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8683 1.34 - 1.46: 5427 1.46 - 1.58: 12293 1.58 - 1.71: 134 1.71 - 1.83: 188 Bond restraints: 26725 Sorted by residual: bond pdb=" C19 1N7 I1402 " pdb=" C3 1N7 I1402 " ideal model delta sigma weight residual 1.532 1.829 -0.297 2.00e-02 2.50e+03 2.21e+02 bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.821 -0.289 2.00e-02 2.50e+03 2.09e+02 bond pdb=" C3 1N7 I1402 " pdb=" C4 1N7 I1402 " ideal model delta sigma weight residual 1.532 1.737 -0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C3 1N7 I1401 " pdb=" C4 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.726 -0.194 2.00e-02 2.50e+03 9.38e+01 bond pdb=" C7 1N7 I1401 " pdb=" C8 1N7 I1401 " ideal model delta sigma weight residual 1.542 1.706 -0.164 2.00e-02 2.50e+03 6.71e+01 ... (remaining 26720 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 35533 1.75 - 3.50: 758 3.50 - 5.25: 76 5.25 - 7.00: 15 7.00 - 8.75: 6 Bond angle restraints: 36388 Sorted by residual: angle pdb=" N TYR J 269 " pdb=" CA TYR J 269 " pdb=" C TYR J 269 " ideal model delta sigma weight residual 112.90 106.34 6.56 1.31e+00 5.83e-01 2.51e+01 angle pdb=" O4' DA B 18 " pdb=" C4' DA B 18 " pdb=" C3' DA B 18 " ideal model delta sigma weight residual 106.00 103.07 2.93 6.00e-01 2.78e+00 2.38e+01 angle pdb=" N3 DT B 23 " pdb=" C4 DT B 23 " pdb=" O4 DT B 23 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 angle pdb=" O4' DC B 17 " pdb=" C4' DC B 17 " pdb=" C3' DC B 17 " ideal model delta sigma weight residual 106.00 103.45 2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT A 27 " pdb=" C4 DT A 27 " pdb=" O4 DT A 27 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 ... (remaining 36383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.09: 15676 31.09 - 62.18: 516 62.18 - 93.27: 42 93.27 - 124.37: 0 124.37 - 155.46: 1 Dihedral angle restraints: 16235 sinusoidal: 7128 harmonic: 9107 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 -36.26 72.61 1 3.10e+00 1.04e-01 7.00e+02 dihedral pdb=" O4' G R 7 " pdb=" C4' G R 7 " pdb=" C3' G R 7 " pdb=" C2' G R 7 " ideal model delta sinusoidal sigma weight residual -35.15 24.81 -59.95 1 4.00e+00 6.25e-02 3.00e+02 dihedral pdb=" O4' G R 7 " pdb=" C2' G R 7 " pdb=" C1' G R 7 " pdb=" C3' G R 7 " ideal model delta sinusoidal sigma weight residual -94.41 -36.16 -58.25 3 3.80e+00 6.93e-02 1.47e+02 ... (remaining 16232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 3903 0.091 - 0.182: 251 0.182 - 0.273: 17 0.273 - 0.364: 3 0.364 - 0.455: 2 Chirality restraints: 4176 Sorted by residual: chirality pdb=" C19 1N7 I1402 " pdb=" C18 1N7 I1402 " pdb=" C2 1N7 I1402 " pdb=" C3 1N7 I1402 " both_signs ideal model delta sigma weight residual False -2.53 -2.99 0.45 2.00e-01 2.50e+01 5.17e+00 chirality pdb=" C19 1N7 I1401 " pdb=" C18 1N7 I1401 " pdb=" C2 1N7 I1401 " pdb=" C3 1N7 I1401 " both_signs ideal model delta sigma weight residual False -2.53 -2.92 0.39 2.00e-01 2.50e+01 3.76e+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 -2.77 0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 4173 not shown) Planarity restraints: 4525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS I 697 " 0.035 5.00e-02 4.00e+02 5.28e-02 4.47e+00 pdb=" N PRO I 698 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO I 698 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO I 698 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR I 589 " 0.027 5.00e-02 4.00e+02 4.05e-02 2.62e+00 pdb=" N PRO I 590 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO I 590 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO I 590 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS I 551 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO I 552 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO I 552 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO I 552 " -0.022 5.00e-02 4.00e+02 ... (remaining 4522 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 228 2.58 - 3.16: 21222 3.16 - 3.74: 40433 3.74 - 4.32: 56418 4.32 - 4.90: 94725 Nonbonded interactions: 213026 Sorted by model distance: nonbonded pdb=" O3' G R 16 " pdb="MG MG J1501 " model vdw 2.006 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1501 " model vdw 2.021 2.170 nonbonded pdb=" OD1 ASP J 464 " pdb="MG MG J1501 " model vdw 2.043 2.170 nonbonded pdb=" OH TYR J 795 " pdb=" OE1 GLN J1326 " model vdw 2.161 3.040 nonbonded pdb=" OG SER J 977 " pdb=" OG1 THR J 980 " model vdw 2.191 3.040 ... (remaining 213021 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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 29.980 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 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 : 0.006 0.297 26733 Z= 0.314 Angle : 0.628 8.746 36400 Z= 0.386 Chirality : 0.047 0.455 4176 Planarity : 0.004 0.053 4525 Dihedral : 14.408 155.456 10377 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.52 % Allowed : 7.97 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.07 % 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: -0.92 (0.15), residues: 3154 helix: 0.87 (0.16), residues: 1102 sheet: -0.87 (0.26), residues: 393 loop : -1.62 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I1223 TYR 0.018 0.001 TYR G 177 PHE 0.014 0.001 PHE I1221 TRP 0.009 0.001 TRP J 580 HIS 0.004 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.31 (26725) covalent geometry : angle 0.62744 / 0.39 (36388) hydrogen bonds : bond 0.13653 / 14.81 ( 1073) hydrogen bonds : angle 5.59507 / 5.85 ( 2972) metal coordination : bond 0.00684 / 0.69 ( 8) metal coordination : angle 1.80386 / 3.32 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 393 time to evaluate : 0.975 Fit side-chains REVERT: I 223 LEU cc_start: 0.8427 (tt) cc_final: 0.8160 (tp) REVERT: I 228 VAL cc_start: 0.7399 (t) cc_final: 0.7107 (t) REVERT: I 359 ARG cc_start: 0.6644 (ttt-90) cc_final: 0.6147 (ttt-90) REVERT: I 430 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8292 (mttp) REVERT: I 580 GLN cc_start: 0.7816 (mt0) cc_final: 0.7610 (mt0) REVERT: I 825 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7414 (mt-10) REVERT: I 842 ASP cc_start: 0.6772 (t70) cc_final: 0.6403 (t70) REVERT: I 930 ASP cc_start: 0.8229 (t70) cc_final: 0.7958 (t0) REVERT: I 1033 ARG cc_start: 0.7196 (ttm110) cc_final: 0.6390 (mtm180) REVERT: I 1085 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8469 (mmp) REVERT: I 1180 MET cc_start: 0.8532 (ttm) cc_final: 0.8130 (ttm) REVERT: I 1232 MET cc_start: 0.8751 (mmm) cc_final: 0.8494 (mmm) REVERT: J 267 ASP cc_start: 0.7968 (t0) cc_final: 0.7763 (m-30) REVERT: J 291 ILE cc_start: 0.8609 (mm) cc_final: 0.8170 (tt) REVERT: J 556 GLU cc_start: 0.7298 (tt0) cc_final: 0.7022 (tt0) REVERT: J 665 GLN cc_start: 0.7282 (tp40) cc_final: 0.6898 (tm-30) REVERT: J 667 GLN cc_start: 0.6967 (tt0) cc_final: 0.6592 (tt0) REVERT: J 827 GLU cc_start: 0.7259 (tp30) cc_final: 0.6744 (pm20) REVERT: J 913 GLU cc_start: 0.7787 (tt0) cc_final: 0.7552 (tt0) REVERT: J 1219 ASP cc_start: 0.7919 (m-30) cc_final: 0.7626 (m-30) REVERT: J 1275 LEU cc_start: 0.7835 (mm) cc_final: 0.7609 (mm) REVERT: J 1344 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8697 (pp) REVERT: K 42 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7504 (mt-10) REVERT: K 74 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7172 (mm-30) outliers start: 68 outliers final: 37 residues processed: 451 average time/residue: 0.1689 time to fit residues: 122.0583 Evaluate side-chains 351 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 311 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 430 LYS Chi-restraints excluded: chain I residue 446 ASP Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1085 MET Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1212 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 39 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 197 optimal weight: 0.3980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 137 ASN G 186 ASN I 214 ASN I 330 HIS I 490 GLN I 618 GLN J 777 HIS J1108 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.164642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.121272 restraints weight = 30956.522| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.27 r_work: 0.3020 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.0755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26733 Z= 0.131 Angle : 0.579 13.429 36400 Z= 0.301 Chirality : 0.045 0.861 4176 Planarity : 0.004 0.050 4525 Dihedral : 13.300 157.312 4250 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.04 % Allowed : 10.19 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.07 % 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: -0.71 (0.15), residues: 3154 helix: 1.12 (0.16), residues: 1114 sheet: -0.88 (0.25), residues: 405 loop : -1.53 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 33 TYR 0.016 0.001 TYR G 177 PHE 0.018 0.001 PHE I1025 TRP 0.010 0.001 TRP J1193 HIS 0.004 0.001 HIS I 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (26725) covalent geometry : angle 0.57760 / 0.30 (36388) hydrogen bonds : bond 0.04490 / 4.77 ( 1073) hydrogen bonds : angle 4.66439 / 4.89 ( 2972) metal coordination : bond 0.00557 / 0.54 ( 8) metal coordination : angle 1.93989 / 2.79 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 346 time to evaluate : 0.799 Fit side-chains REVERT: G 33 ARG cc_start: 0.7697 (ttm-80) cc_final: 0.7419 (ttm-80) REVERT: G 197 ASP cc_start: 0.5605 (t70) cc_final: 0.4644 (t0) REVERT: H 176 CYS cc_start: 0.9132 (p) cc_final: 0.8284 (t) REVERT: I 18 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.7445 (mtm-85) REVERT: I 81 ASP cc_start: 0.7760 (t70) cc_final: 0.7378 (t0) REVERT: I 223 LEU cc_start: 0.8103 (tt) cc_final: 0.7780 (tp) REVERT: I 239 MET cc_start: 0.5118 (OUTLIER) cc_final: 0.4715 (ttm) REVERT: I 386 GLU cc_start: 0.8249 (tm-30) cc_final: 0.8029 (tm-30) REVERT: I 430 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.7996 (mttp) REVERT: I 638 SER cc_start: 0.8800 (t) cc_final: 0.8525 (p) REVERT: I 805 MET cc_start: 0.9147 (ptm) cc_final: 0.8858 (ptp) REVERT: I 825 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8280 (mt-10) REVERT: I 842 ASP cc_start: 0.7126 (t70) cc_final: 0.6787 (t70) REVERT: I 930 ASP cc_start: 0.9088 (t70) cc_final: 0.8736 (t0) REVERT: I 1033 ARG cc_start: 0.7411 (ttm110) cc_final: 0.6555 (mtm180) REVERT: I 1085 MET cc_start: 0.9279 (OUTLIER) cc_final: 0.9067 (mmp) REVERT: I 1180 MET cc_start: 0.9024 (ttm) cc_final: 0.8715 (ttm) REVERT: I 1188 ASP cc_start: 0.8310 (t0) cc_final: 0.7953 (t0) REVERT: I 1232 MET cc_start: 0.9316 (mmm) cc_final: 0.9076 (mmm) REVERT: J 202 ARG cc_start: 0.8160 (ttm-80) cc_final: 0.7891 (ttm110) REVERT: J 291 ILE cc_start: 0.8497 (mm) cc_final: 0.8099 (tp) REVERT: J 556 GLU cc_start: 0.7965 (tt0) cc_final: 0.7690 (tt0) REVERT: J 665 GLN cc_start: 0.7324 (tp40) cc_final: 0.6693 (tm-30) REVERT: J 667 GLN cc_start: 0.7033 (tt0) cc_final: 0.6827 (tt0) REVERT: J 740 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8262 (mp) REVERT: J 827 GLU cc_start: 0.7378 (tp30) cc_final: 0.6470 (pm20) REVERT: J 913 GLU cc_start: 0.8654 (tt0) cc_final: 0.8444 (tt0) REVERT: J 1219 ASP cc_start: 0.8302 (m-30) cc_final: 0.8068 (m-30) REVERT: J 1275 LEU cc_start: 0.7768 (mm) cc_final: 0.7425 (mm) REVERT: J 1344 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8401 (pp) REVERT: K 76 GLU cc_start: 0.6592 (tm-30) cc_final: 0.5593 (mt-10) outliers start: 82 outliers final: 49 residues processed: 406 average time/residue: 0.1557 time to fit residues: 101.6238 Evaluate side-chains 367 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 312 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 430 LYS Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 492 MET Chi-restraints excluded: chain I residue 504 GLU Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 618 GLN Chi-restraints excluded: chain I residue 643 SER Chi-restraints excluded: chain I residue 739 ASP Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 1002 LEU Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1085 MET Chi-restraints excluded: chain I residue 1212 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1278 GLU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 39 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 94 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 74 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 chunk 121 optimal weight: 0.9980 chunk 118 optimal weight: 5.9990 chunk 263 optimal weight: 3.9990 chunk 180 optimal weight: 10.0000 chunk 152 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 276 optimal weight: 20.0000 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 75 GLN G 137 ASN I 214 ASN I 490 GLN I 513 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1116 HIS J 309 ASN J 777 HIS J1326 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.165248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.121895 restraints weight = 30969.067| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.12 r_work: 0.3020 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26733 Z= 0.143 Angle : 0.555 12.554 36400 Z= 0.289 Chirality : 0.044 0.397 4176 Planarity : 0.004 0.044 4525 Dihedral : 13.209 156.339 4238 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.93 % Allowed : 11.82 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.07 % 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: -0.66 (0.15), residues: 3154 helix: 1.18 (0.16), residues: 1116 sheet: -0.96 (0.25), residues: 419 loop : -1.50 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J1149 TYR 0.016 0.001 TYR G 177 PHE 0.015 0.001 PHE I 405 TRP 0.011 0.001 TRP J1193 HIS 0.004 0.001 HIS J 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (26725) covalent geometry : angle 0.55460 / 0.29 (36388) hydrogen bonds : bond 0.04282 / 4.47 ( 1073) hydrogen bonds : angle 4.50267 / 4.72 ( 2972) metal coordination : bond 0.00652 / 0.65 ( 8) metal coordination : angle 1.82736 / 2.52 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 326 time to evaluate : 0.850 Fit side-chains REVERT: G 197 ASP cc_start: 0.5763 (t70) cc_final: 0.4688 (t0) REVERT: H 176 CYS cc_start: 0.9085 (p) cc_final: 0.8692 (p) REVERT: I 18 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.7475 (mtm-85) REVERT: I 39 ILE cc_start: 0.8523 (pt) cc_final: 0.8255 (pt) REVERT: I 81 ASP cc_start: 0.7771 (t70) cc_final: 0.7390 (t0) REVERT: I 195 PHE cc_start: 0.8361 (m-80) cc_final: 0.7469 (m-80) REVERT: I 223 LEU cc_start: 0.8069 (tt) cc_final: 0.7862 (tp) REVERT: I 386 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7997 (tm-30) REVERT: I 477 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7319 (tp30) REVERT: I 487 LEU cc_start: 0.4273 (OUTLIER) cc_final: 0.4034 (pp) REVERT: I 638 SER cc_start: 0.8769 (t) cc_final: 0.8515 (p) REVERT: I 805 MET cc_start: 0.9109 (ptm) cc_final: 0.8828 (ptp) REVERT: I 842 ASP cc_start: 0.7168 (t70) cc_final: 0.6835 (t70) REVERT: I 930 ASP cc_start: 0.9055 (t70) cc_final: 0.8711 (t0) REVERT: I 962 GLU cc_start: 0.6867 (mt-10) cc_final: 0.6500 (mt-10) REVERT: I 1033 ARG cc_start: 0.7427 (ttm110) cc_final: 0.6535 (mtm180) REVERT: I 1085 MET cc_start: 0.9248 (OUTLIER) cc_final: 0.8998 (mmp) REVERT: I 1180 MET cc_start: 0.8995 (ttm) cc_final: 0.8661 (ttm) REVERT: I 1188 ASP cc_start: 0.8383 (t0) cc_final: 0.7912 (t0) REVERT: J 202 ARG cc_start: 0.8179 (ttm-80) cc_final: 0.7903 (ttm110) REVERT: J 227 PHE cc_start: 0.8079 (OUTLIER) cc_final: 0.7628 (m-80) REVERT: J 291 ILE cc_start: 0.8545 (mm) cc_final: 0.8146 (tp) REVERT: J 556 GLU cc_start: 0.8016 (tt0) cc_final: 0.7687 (tt0) REVERT: J 740 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8334 (mp) REVERT: J 805 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.7706 (pm20) REVERT: J 827 GLU cc_start: 0.7434 (tp30) cc_final: 0.6522 (pm20) REVERT: J 913 GLU cc_start: 0.8648 (tt0) cc_final: 0.8429 (tt0) REVERT: J 1040 MET cc_start: 0.4304 (ttp) cc_final: 0.2879 (tpp) REVERT: J 1149 ARG cc_start: 0.8558 (mtt90) cc_final: 0.8125 (mtp-110) REVERT: J 1275 LEU cc_start: 0.7796 (mm) cc_final: 0.7455 (mm) REVERT: J 1344 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8515 (pp) REVERT: K 76 GLU cc_start: 0.6611 (tm-30) cc_final: 0.5576 (mt-10) outliers start: 79 outliers final: 50 residues processed: 385 average time/residue: 0.1726 time to fit residues: 106.6241 Evaluate side-chains 363 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 306 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 430 LYS Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 492 MET Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 643 SER Chi-restraints excluded: chain I residue 739 ASP Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1085 MET Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 229 GLN Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 402 GLU Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1278 GLU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 39 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 121 optimal weight: 4.9990 chunk 143 optimal weight: 6.9990 chunk 139 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 286 optimal weight: 0.6980 chunk 34 optimal weight: 9.9990 chunk 188 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 141 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 245 optimal weight: 8.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 93 GLN G 137 ASN I 214 ASN I 618 GLN J 232 ASN J 777 HIS J1197 ASN K 31 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.161351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.116608 restraints weight = 31224.524| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.37 r_work: 0.2902 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 26733 Z= 0.239 Angle : 0.610 8.336 36400 Z= 0.318 Chirality : 0.046 0.209 4176 Planarity : 0.004 0.053 4525 Dihedral : 13.358 156.861 4235 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.52 % Allowed : 12.49 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.07 % 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: -0.78 (0.15), residues: 3154 helix: 0.99 (0.16), residues: 1122 sheet: -1.02 (0.25), residues: 427 loop : -1.50 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 33 TYR 0.018 0.002 TYR G 177 PHE 0.018 0.002 PHE I 645 TRP 0.012 0.001 TRP J1193 HIS 0.005 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.24 (26725) covalent geometry : angle 0.60872 / 0.32 (36388) hydrogen bonds : bond 0.04519 / 4.84 ( 1073) hydrogen bonds : angle 4.53920 / 4.78 ( 2972) metal coordination : bond 0.00999 / 0.98 ( 8) metal coordination : angle 2.11994 / 3.05 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 309 time to evaluate : 0.945 Fit side-chains REVERT: G 76 GLU cc_start: 0.8416 (mp0) cc_final: 0.7794 (mp0) REVERT: H 176 CYS cc_start: 0.9104 (p) cc_final: 0.8724 (p) REVERT: I 18 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.7219 (mtm-85) REVERT: I 39 ILE cc_start: 0.8522 (pt) cc_final: 0.8314 (pt) REVERT: I 81 ASP cc_start: 0.7752 (t70) cc_final: 0.7322 (t0) REVERT: I 223 LEU cc_start: 0.8169 (tt) cc_final: 0.7948 (tp) REVERT: I 319 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7146 (pt) REVERT: I 386 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7851 (tm-30) REVERT: I 487 LEU cc_start: 0.3981 (OUTLIER) cc_final: 0.3668 (pp) REVERT: I 638 SER cc_start: 0.8775 (t) cc_final: 0.8493 (p) REVERT: I 825 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8258 (mt-10) REVERT: I 842 ASP cc_start: 0.7295 (t70) cc_final: 0.6986 (t70) REVERT: I 930 ASP cc_start: 0.9101 (t70) cc_final: 0.8738 (t0) REVERT: I 962 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6532 (mt-10) REVERT: I 1033 ARG cc_start: 0.7413 (ttm110) cc_final: 0.6437 (mtm180) REVERT: I 1085 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.8856 (mmp) REVERT: I 1180 MET cc_start: 0.9073 (ttm) cc_final: 0.8764 (ttm) REVERT: I 1188 ASP cc_start: 0.8593 (t0) cc_final: 0.8115 (t0) REVERT: J 202 ARG cc_start: 0.8146 (ttm-80) cc_final: 0.7838 (ttm110) REVERT: J 227 PHE cc_start: 0.8125 (OUTLIER) cc_final: 0.7623 (m-80) REVERT: J 291 ILE cc_start: 0.8433 (mm) cc_final: 0.8033 (tp) REVERT: J 556 GLU cc_start: 0.8028 (tt0) cc_final: 0.7732 (tt0) REVERT: J 665 GLN cc_start: 0.7368 (tp40) cc_final: 0.6736 (tm-30) REVERT: J 805 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.7823 (pm20) REVERT: J 807 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8818 (tt) REVERT: J 827 GLU cc_start: 0.7475 (tp30) cc_final: 0.6552 (pm20) REVERT: J 1040 MET cc_start: 0.4214 (ttp) cc_final: 0.2931 (tpp) REVERT: J 1149 ARG cc_start: 0.8630 (mtt90) cc_final: 0.8135 (mtp-110) REVERT: J 1275 LEU cc_start: 0.7815 (mm) cc_final: 0.7502 (mm) REVERT: J 1344 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8551 (pp) REVERT: K 76 GLU cc_start: 0.6548 (tm-30) cc_final: 0.5528 (mt-10) outliers start: 95 outliers final: 68 residues processed: 387 average time/residue: 0.1653 time to fit residues: 102.9980 Evaluate side-chains 373 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 297 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 430 LYS Chi-restraints excluded: chain I residue 446 ASP Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 492 MET Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 643 SER Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1085 MET Chi-restraints excluded: chain I residue 1212 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 229 GLN Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 402 GLU Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 485 MET Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 958 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1273 ASP Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 39 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 171 optimal weight: 2.9990 chunk 248 optimal weight: 8.9990 chunk 303 optimal weight: 4.9990 chunk 183 optimal weight: 0.9980 chunk 175 optimal weight: 0.6980 chunk 304 optimal weight: 3.9990 chunk 202 optimal weight: 0.8980 chunk 187 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 233 optimal weight: 7.9990 chunk 114 optimal weight: 0.6980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 137 ASN ** I 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 777 HIS J1218 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.162903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.119279 restraints weight = 30905.077| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.23 r_work: 0.2963 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26733 Z= 0.141 Angle : 0.544 7.824 36400 Z= 0.285 Chirality : 0.043 0.166 4176 Planarity : 0.004 0.043 4525 Dihedral : 13.297 157.402 4235 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.82 % Allowed : 12.71 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.07 % 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: -0.65 (0.15), residues: 3154 helix: 1.14 (0.16), residues: 1121 sheet: -1.00 (0.25), residues: 421 loop : -1.45 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J1174 TYR 0.016 0.001 TYR G 177 PHE 0.013 0.001 PHE I 645 TRP 0.012 0.001 TRP J1193 HIS 0.004 0.001 HIS I 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (26725) covalent geometry : angle 0.54285 / 0.28 (36388) hydrogen bonds : bond 0.04061 / 4.31 ( 1073) hydrogen bonds : angle 4.40876 / 4.62 ( 2972) metal coordination : bond 0.00596 / 0.60 ( 8) metal coordination : angle 2.11538 / 3.01 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 312 time to evaluate : 0.786 Fit side-chains REVERT: G 76 GLU cc_start: 0.8423 (mp0) cc_final: 0.8027 (mp0) REVERT: H 176 CYS cc_start: 0.9042 (p) cc_final: 0.8662 (p) REVERT: I 18 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.7350 (mtm-85) REVERT: I 39 ILE cc_start: 0.8485 (pt) cc_final: 0.8197 (pt) REVERT: I 81 ASP cc_start: 0.7755 (t70) cc_final: 0.7374 (t0) REVERT: I 223 LEU cc_start: 0.8156 (tt) cc_final: 0.7927 (tp) REVERT: I 239 MET cc_start: 0.5152 (ttp) cc_final: 0.4733 (ttm) REVERT: I 386 GLU cc_start: 0.8299 (tm-30) cc_final: 0.7953 (tm-30) REVERT: I 477 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7408 (tp30) REVERT: I 638 SER cc_start: 0.8689 (t) cc_final: 0.8486 (p) REVERT: I 842 ASP cc_start: 0.7237 (t70) cc_final: 0.6938 (t70) REVERT: I 930 ASP cc_start: 0.9070 (t70) cc_final: 0.8719 (t0) REVERT: I 962 GLU cc_start: 0.6867 (mt-10) cc_final: 0.6493 (mt-10) REVERT: I 1033 ARG cc_start: 0.7401 (ttm110) cc_final: 0.6408 (mtm180) REVERT: I 1085 MET cc_start: 0.9250 (OUTLIER) cc_final: 0.8959 (mmp) REVERT: I 1180 MET cc_start: 0.9065 (ttm) cc_final: 0.8736 (ttm) REVERT: I 1188 ASP cc_start: 0.8466 (t0) cc_final: 0.8065 (t0) REVERT: I 1340 GLU cc_start: 0.7990 (pt0) cc_final: 0.7737 (pt0) REVERT: J 202 ARG cc_start: 0.8181 (ttm-80) cc_final: 0.7870 (ttm110) REVERT: J 227 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.7757 (m-80) REVERT: J 291 ILE cc_start: 0.8442 (mm) cc_final: 0.8046 (tp) REVERT: J 556 GLU cc_start: 0.7944 (tt0) cc_final: 0.7648 (tt0) REVERT: J 740 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8241 (mp) REVERT: J 805 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.7694 (pm20) REVERT: J 807 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8824 (tt) REVERT: J 827 GLU cc_start: 0.7443 (tp30) cc_final: 0.6535 (pm20) REVERT: J 1174 ARG cc_start: 0.6839 (ttp-110) cc_final: 0.6600 (ttp-110) REVERT: J 1275 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7412 (mm) REVERT: J 1326 GLN cc_start: 0.8644 (mt0) cc_final: 0.8386 (mt0) REVERT: J 1344 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8550 (pp) REVERT: K 76 GLU cc_start: 0.6618 (tm-30) cc_final: 0.5574 (mt-10) outliers start: 103 outliers final: 71 residues processed: 395 average time/residue: 0.1631 time to fit residues: 103.8987 Evaluate side-chains 385 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 306 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 430 LYS Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 492 MET Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 643 SER Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1085 MET Chi-restraints excluded: chain I residue 1212 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 229 GLN Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 402 GLU Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 790 THR Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 913 GLU Chi-restraints excluded: chain J residue 958 ILE Chi-restraints excluded: chain J residue 976 THR Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1275 LEU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 39 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 45 optimal weight: 4.9990 chunk 264 optimal weight: 0.9980 chunk 2 optimal weight: 40.0000 chunk 251 optimal weight: 0.6980 chunk 64 optimal weight: 0.1980 chunk 258 optimal weight: 0.9990 chunk 229 optimal weight: 0.1980 chunk 300 optimal weight: 0.9980 chunk 210 optimal weight: 6.9990 chunk 254 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 137 ASN I 513 GLN I 618 GLN J 232 ASN J 365 GLN J 777 HIS K 31 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.165646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.121502 restraints weight = 31204.383| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.31 r_work: 0.2959 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 26733 Z= 0.108 Angle : 0.516 8.610 36400 Z= 0.270 Chirality : 0.042 0.178 4176 Planarity : 0.004 0.041 4525 Dihedral : 13.172 155.491 4235 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.63 % Allowed : 13.16 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.07 % 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: -0.49 (0.15), residues: 3154 helix: 1.37 (0.16), residues: 1113 sheet: -0.89 (0.25), residues: 418 loop : -1.42 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 33 TYR 0.014 0.001 TYR I 73 PHE 0.012 0.001 PHE I 405 TRP 0.014 0.001 TRP J1193 HIS 0.005 0.001 HIS J 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (26725) covalent geometry : angle 0.51467 / 0.27 (36388) hydrogen bonds : bond 0.03713 / 3.92 ( 1073) hydrogen bonds : angle 4.23829 / 4.44 ( 2972) metal coordination : bond 0.00435 / 0.45 ( 8) metal coordination : angle 1.97410 / 2.80 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 348 time to evaluate : 0.960 Fit side-chains REVERT: G 76 GLU cc_start: 0.8336 (mp0) cc_final: 0.7882 (mp0) REVERT: G 181 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7080 (mm-30) REVERT: G 188 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8158 (mt-10) REVERT: H 95 LYS cc_start: 0.7025 (ptmt) cc_final: 0.6824 (pttp) REVERT: H 114 ASP cc_start: 0.7495 (m-30) cc_final: 0.7261 (m-30) REVERT: H 176 CYS cc_start: 0.9051 (p) cc_final: 0.8624 (p) REVERT: I 18 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.6974 (mtm-85) REVERT: I 39 ILE cc_start: 0.8297 (pt) cc_final: 0.7903 (pt) REVERT: I 81 ASP cc_start: 0.7693 (t70) cc_final: 0.7263 (t0) REVERT: I 195 PHE cc_start: 0.8250 (m-80) cc_final: 0.7345 (m-80) REVERT: I 223 LEU cc_start: 0.7961 (tt) cc_final: 0.7570 (tp) REVERT: I 239 MET cc_start: 0.5203 (ttp) cc_final: 0.4680 (ttm) REVERT: I 319 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7039 (pt) REVERT: I 386 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7882 (tm-30) REVERT: I 430 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.7936 (mttp) REVERT: I 477 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7339 (tp30) REVERT: I 490 GLN cc_start: 0.7509 (tp-100) cc_final: 0.7238 (tp40) REVERT: I 638 SER cc_start: 0.8496 (t) cc_final: 0.8248 (p) REVERT: I 842 ASP cc_start: 0.7189 (t70) cc_final: 0.6896 (t70) REVERT: I 930 ASP cc_start: 0.9042 (t70) cc_final: 0.8731 (t0) REVERT: I 962 GLU cc_start: 0.6776 (mt-10) cc_final: 0.6424 (mt-10) REVERT: I 1033 ARG cc_start: 0.7459 (ttm110) cc_final: 0.6462 (mtm180) REVERT: I 1085 MET cc_start: 0.9236 (OUTLIER) cc_final: 0.8940 (mmp) REVERT: I 1180 MET cc_start: 0.9069 (ttm) cc_final: 0.8747 (ttm) REVERT: I 1188 ASP cc_start: 0.8342 (t0) cc_final: 0.7912 (t0) REVERT: I 1297 ASP cc_start: 0.8429 (t70) cc_final: 0.8177 (t70) REVERT: I 1340 GLU cc_start: 0.7741 (pt0) cc_final: 0.7480 (pt0) REVERT: J 94 GLN cc_start: 0.8058 (mm-40) cc_final: 0.7728 (mt0) REVERT: J 202 ARG cc_start: 0.8177 (ttm-80) cc_final: 0.7843 (ttm110) REVERT: J 227 PHE cc_start: 0.8317 (OUTLIER) cc_final: 0.7723 (m-80) REVERT: J 291 ILE cc_start: 0.8471 (mm) cc_final: 0.8052 (tp) REVERT: J 556 GLU cc_start: 0.7800 (tt0) cc_final: 0.7563 (tt0) REVERT: J 740 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8263 (mp) REVERT: J 807 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8889 (tt) REVERT: J 827 GLU cc_start: 0.7383 (tp30) cc_final: 0.6545 (pm20) REVERT: J 1244 GLN cc_start: 0.7605 (mm-40) cc_final: 0.6962 (mm-40) REVERT: J 1275 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7376 (mm) REVERT: J 1344 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8265 (pp) REVERT: J 1357 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8351 (tt) REVERT: K 76 GLU cc_start: 0.6655 (tm-30) cc_final: 0.5621 (mt-10) outliers start: 98 outliers final: 62 residues processed: 425 average time/residue: 0.1611 time to fit residues: 110.9010 Evaluate side-chains 392 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 319 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 430 LYS Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 643 SER Chi-restraints excluded: chain I residue 739 ASP Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 949 GLU Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1085 MET Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 229 GLN Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 402 GLU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 485 MET Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1275 LEU Chi-restraints excluded: chain J residue 1278 GLU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain K residue 12 LYS Chi-restraints excluded: chain K residue 39 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 138 optimal weight: 5.9990 chunk 153 optimal weight: 0.9990 chunk 283 optimal weight: 30.0000 chunk 204 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 chunk 170 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 240 optimal weight: 0.8980 chunk 266 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 232 ASN J 365 GLN J 777 HIS J1326 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.162627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.118704 restraints weight = 30979.098| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.14 r_work: 0.2971 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26733 Z= 0.158 Angle : 0.546 7.984 36400 Z= 0.286 Chirality : 0.043 0.199 4176 Planarity : 0.004 0.042 4525 Dihedral : 13.200 155.727 4234 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.26 % Allowed : 13.83 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.07 % 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: -0.48 (0.15), residues: 3154 helix: 1.30 (0.16), residues: 1115 sheet: -0.84 (0.25), residues: 420 loop : -1.36 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J1174 TYR 0.015 0.001 TYR G 177 PHE 0.013 0.001 PHE J 176 TRP 0.013 0.001 TRP J1193 HIS 0.006 0.001 HIS H 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (26725) covalent geometry : angle 0.54439 / 0.29 (36388) hydrogen bonds : bond 0.03905 / 4.14 ( 1073) hydrogen bonds : angle 4.27072 / 4.49 ( 2972) metal coordination : bond 0.00568 / 0.59 ( 8) metal coordination : angle 2.00144 / 2.74 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 325 time to evaluate : 0.988 Fit side-chains REVERT: G 76 GLU cc_start: 0.8304 (mp0) cc_final: 0.7810 (mp0) REVERT: G 181 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7135 (mm-30) REVERT: G 188 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8127 (mt-10) REVERT: H 176 CYS cc_start: 0.9054 (p) cc_final: 0.8635 (p) REVERT: I 18 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.7224 (mtm-85) REVERT: I 39 ILE cc_start: 0.8436 (pt) cc_final: 0.8092 (pt) REVERT: I 81 ASP cc_start: 0.7701 (t70) cc_final: 0.7294 (t0) REVERT: I 195 PHE cc_start: 0.8405 (m-80) cc_final: 0.7395 (m-80) REVERT: I 223 LEU cc_start: 0.8007 (tt) cc_final: 0.7746 (tp) REVERT: I 319 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7045 (pt) REVERT: I 386 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7952 (tm-30) REVERT: I 477 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7439 (tp30) REVERT: I 800 MET cc_start: 0.8526 (mtm) cc_final: 0.8065 (ptp) REVERT: I 842 ASP cc_start: 0.7199 (t70) cc_final: 0.6907 (t70) REVERT: I 930 ASP cc_start: 0.9024 (t70) cc_final: 0.8706 (t0) REVERT: I 962 GLU cc_start: 0.6838 (mt-10) cc_final: 0.6493 (mt-10) REVERT: I 1033 ARG cc_start: 0.7455 (ttm110) cc_final: 0.6456 (mtm180) REVERT: I 1085 MET cc_start: 0.9220 (OUTLIER) cc_final: 0.8894 (mmp) REVERT: I 1180 MET cc_start: 0.9053 (ttm) cc_final: 0.8734 (ttm) REVERT: I 1188 ASP cc_start: 0.8413 (t0) cc_final: 0.7929 (t0) REVERT: I 1297 ASP cc_start: 0.8428 (t70) cc_final: 0.8059 (t70) REVERT: I 1340 GLU cc_start: 0.7776 (pt0) cc_final: 0.7518 (pt0) REVERT: J 94 GLN cc_start: 0.8135 (mm-40) cc_final: 0.7855 (mt0) REVERT: J 227 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.7759 (m-80) REVERT: J 291 ILE cc_start: 0.8493 (mm) cc_final: 0.8074 (tp) REVERT: J 556 GLU cc_start: 0.7781 (tt0) cc_final: 0.7476 (tt0) REVERT: J 665 GLN cc_start: 0.7311 (tp40) cc_final: 0.6708 (tm-30) REVERT: J 740 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8353 (mp) REVERT: J 747 MET cc_start: 0.7887 (mmm) cc_final: 0.6785 (mmm) REVERT: J 805 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.7741 (pm20) REVERT: J 807 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8825 (tt) REVERT: J 1040 MET cc_start: 0.3647 (ttp) cc_final: 0.2923 (tpp) REVERT: J 1244 GLN cc_start: 0.7684 (mm-40) cc_final: 0.7050 (mm-40) REVERT: J 1275 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7401 (mm) REVERT: K 76 GLU cc_start: 0.6686 (tm-30) cc_final: 0.5640 (mt-10) outliers start: 88 outliers final: 69 residues processed: 392 average time/residue: 0.1776 time to fit residues: 112.3764 Evaluate side-chains 396 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 318 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 430 LYS Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 643 SER Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1085 MET Chi-restraints excluded: chain I residue 1212 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 229 GLN Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 402 GLU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 485 MET Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 790 THR Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 958 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1275 LEU Chi-restraints excluded: chain J residue 1278 GLU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 12 LYS Chi-restraints excluded: chain K residue 39 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 104 optimal weight: 2.9990 chunk 227 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 283 optimal weight: 30.0000 chunk 306 optimal weight: 0.9980 chunk 256 optimal weight: 0.9980 chunk 258 optimal weight: 0.8980 chunk 242 optimal weight: 0.8980 chunk 293 optimal weight: 10.0000 chunk 43 optimal weight: 0.2980 chunk 166 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 232 ASN J 365 GLN ** J 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.165069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.121274 restraints weight = 31086.920| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.22 r_work: 0.3006 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 26733 Z= 0.111 Angle : 0.522 9.426 36400 Z= 0.272 Chirality : 0.042 0.187 4176 Planarity : 0.003 0.042 4525 Dihedral : 13.134 155.365 4233 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.26 % Allowed : 14.34 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.07 % 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: -0.42 (0.15), residues: 3154 helix: 1.41 (0.16), residues: 1114 sheet: -0.79 (0.25), residues: 410 loop : -1.38 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J1174 TYR 0.014 0.001 TYR G 177 PHE 0.012 0.001 PHE I 405 TRP 0.018 0.001 TRP J 868 HIS 0.007 0.001 HIS H 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (26725) covalent geometry : angle 0.52113 / 0.27 (36388) hydrogen bonds : bond 0.03653 / 3.86 ( 1073) hydrogen bonds : angle 4.17918 / 4.40 ( 2972) metal coordination : bond 0.00381 / 0.41 ( 8) metal coordination : angle 2.03193 / 2.86 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 335 time to evaluate : 1.012 Fit side-chains REVERT: G 76 GLU cc_start: 0.8247 (mp0) cc_final: 0.7871 (mp0) REVERT: G 181 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7097 (mm-30) REVERT: G 188 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8145 (mt-10) REVERT: H 95 LYS cc_start: 0.7168 (ptmt) cc_final: 0.6957 (pttp) REVERT: H 176 CYS cc_start: 0.9086 (p) cc_final: 0.8656 (p) REVERT: I 18 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.7064 (mtm-85) REVERT: I 39 ILE cc_start: 0.8407 (pt) cc_final: 0.8050 (pt) REVERT: I 81 ASP cc_start: 0.7729 (t70) cc_final: 0.7328 (t0) REVERT: I 195 PHE cc_start: 0.8378 (m-80) cc_final: 0.7346 (m-80) REVERT: I 223 LEU cc_start: 0.7995 (tt) cc_final: 0.7623 (tp) REVERT: I 239 MET cc_start: 0.5279 (ttp) cc_final: 0.4744 (ttm) REVERT: I 319 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7024 (pt) REVERT: I 386 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7882 (tm-30) REVERT: I 430 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8041 (mttp) REVERT: I 477 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7461 (tp30) REVERT: I 800 MET cc_start: 0.8420 (mtm) cc_final: 0.7740 (ptp) REVERT: I 842 ASP cc_start: 0.7237 (t70) cc_final: 0.6939 (t70) REVERT: I 930 ASP cc_start: 0.8992 (t70) cc_final: 0.8731 (t0) REVERT: I 962 GLU cc_start: 0.6835 (mt-10) cc_final: 0.6489 (mt-10) REVERT: I 1033 ARG cc_start: 0.7480 (ttm110) cc_final: 0.6471 (mtm180) REVERT: I 1085 MET cc_start: 0.9239 (OUTLIER) cc_final: 0.8950 (mmp) REVERT: I 1180 MET cc_start: 0.9037 (ttm) cc_final: 0.8715 (ttm) REVERT: I 1188 ASP cc_start: 0.8416 (t0) cc_final: 0.7988 (t0) REVERT: I 1297 ASP cc_start: 0.8357 (t70) cc_final: 0.8036 (t70) REVERT: I 1340 GLU cc_start: 0.7793 (pt0) cc_final: 0.7527 (pt0) REVERT: J 227 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.7689 (m-80) REVERT: J 291 ILE cc_start: 0.8504 (mm) cc_final: 0.7987 (tt) REVERT: J 556 GLU cc_start: 0.7714 (tt0) cc_final: 0.7386 (tt0) REVERT: J 740 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8249 (mp) REVERT: J 805 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.7645 (pm20) REVERT: J 807 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8858 (tt) REVERT: J 1244 GLN cc_start: 0.7602 (mm-40) cc_final: 0.6972 (mm-40) REVERT: J 1275 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7401 (mm) REVERT: J 1357 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8397 (tt) REVERT: K 76 GLU cc_start: 0.6703 (tm-30) cc_final: 0.5670 (mt-10) outliers start: 88 outliers final: 67 residues processed: 401 average time/residue: 0.1773 time to fit residues: 114.5130 Evaluate side-chains 393 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 315 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 430 LYS Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 643 SER Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 949 GLU Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1085 MET Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 229 GLN Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 402 GLU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 485 MET Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 790 THR Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 913 GLU Chi-restraints excluded: chain J residue 958 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1275 LEU Chi-restraints excluded: chain J residue 1278 GLU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain K residue 12 LYS Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 58 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 62 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 261 optimal weight: 6.9990 chunk 129 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 281 optimal weight: 7.9990 chunk 312 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 513 GLN J 232 ASN J 365 GLN J 777 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.165162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.122600 restraints weight = 31078.052| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.27 r_work: 0.2984 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26733 Z= 0.142 Angle : 0.535 7.913 36400 Z= 0.279 Chirality : 0.043 0.190 4176 Planarity : 0.004 0.041 4525 Dihedral : 13.138 154.619 4233 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.37 % Allowed : 14.46 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.07 % 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: -0.43 (0.15), residues: 3154 helix: 1.34 (0.16), residues: 1120 sheet: -0.78 (0.25), residues: 423 loop : -1.35 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J1174 TYR 0.015 0.001 TYR G 177 PHE 0.012 0.001 PHE I 405 TRP 0.016 0.001 TRP I 997 HIS 0.008 0.001 HIS J 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (26725) covalent geometry : angle 0.53388 / 0.28 (36388) hydrogen bonds : bond 0.03769 / 4.00 ( 1073) hydrogen bonds : angle 4.20202 / 4.44 ( 2972) metal coordination : bond 0.00495 / 0.51 ( 8) metal coordination : angle 2.08274 / 2.90 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 318 time to evaluate : 0.940 Fit side-chains REVERT: G 76 GLU cc_start: 0.8284 (mp0) cc_final: 0.7886 (mp0) REVERT: G 181 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7123 (mm-30) REVERT: G 188 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8161 (mt-10) REVERT: H 176 CYS cc_start: 0.9108 (p) cc_final: 0.8685 (p) REVERT: I 18 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.7279 (mtm-85) REVERT: I 39 ILE cc_start: 0.8476 (pt) cc_final: 0.8131 (pt) REVERT: I 81 ASP cc_start: 0.7741 (t70) cc_final: 0.7339 (t0) REVERT: I 195 PHE cc_start: 0.8337 (m-80) cc_final: 0.7325 (m-80) REVERT: I 239 MET cc_start: 0.5303 (ttp) cc_final: 0.4762 (ttm) REVERT: I 319 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7050 (pt) REVERT: I 360 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8323 (pp) REVERT: I 386 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7961 (tm-30) REVERT: I 477 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7453 (tp30) REVERT: I 842 ASP cc_start: 0.7284 (t70) cc_final: 0.6992 (t70) REVERT: I 930 ASP cc_start: 0.8997 (t70) cc_final: 0.8739 (t0) REVERT: I 962 GLU cc_start: 0.6851 (mt-10) cc_final: 0.6497 (mt-10) REVERT: I 1033 ARG cc_start: 0.7500 (ttm110) cc_final: 0.6502 (mtm180) REVERT: I 1085 MET cc_start: 0.9232 (OUTLIER) cc_final: 0.8921 (mmp) REVERT: I 1180 MET cc_start: 0.9053 (ttm) cc_final: 0.8742 (ttm) REVERT: I 1188 ASP cc_start: 0.8447 (t0) cc_final: 0.8004 (t0) REVERT: I 1297 ASP cc_start: 0.8401 (t70) cc_final: 0.8076 (t70) REVERT: I 1340 GLU cc_start: 0.7874 (pt0) cc_final: 0.7607 (pt0) REVERT: J 227 PHE cc_start: 0.8465 (OUTLIER) cc_final: 0.7750 (m-80) REVERT: J 291 ILE cc_start: 0.8504 (mm) cc_final: 0.7984 (tt) REVERT: J 556 GLU cc_start: 0.7717 (tt0) cc_final: 0.7411 (tt0) REVERT: J 740 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8358 (mp) REVERT: J 805 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.7724 (pm20) REVERT: J 807 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8837 (tt) REVERT: J 1040 MET cc_start: 0.4080 (ttp) cc_final: 0.2798 (mmt) REVERT: J 1244 GLN cc_start: 0.7652 (mm-40) cc_final: 0.7010 (mm-40) REVERT: J 1275 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7417 (mm) REVERT: J 1357 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8433 (tt) REVERT: K 76 GLU cc_start: 0.6671 (tm-30) cc_final: 0.5629 (mt-10) outliers start: 91 outliers final: 71 residues processed: 389 average time/residue: 0.1731 time to fit residues: 109.5416 Evaluate side-chains 394 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 312 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 430 LYS Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 643 SER Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 949 GLU Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1085 MET Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 229 GLN Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 402 GLU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 485 MET Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 790 THR Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 913 GLU Chi-restraints excluded: chain J residue 958 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1275 LEU Chi-restraints excluded: chain J residue 1278 GLU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain K residue 12 LYS Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 58 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 70 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 170 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 299 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 20 optimal weight: 0.1980 chunk 314 optimal weight: 0.7980 chunk 48 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 232 ASN J 365 GLN ** J 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.165052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.121737 restraints weight = 31008.371| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.23 r_work: 0.3028 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 26733 Z= 0.112 Angle : 0.525 8.030 36400 Z= 0.275 Chirality : 0.042 0.204 4176 Planarity : 0.003 0.042 4525 Dihedral : 13.102 154.626 4233 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.11 % Allowed : 14.79 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.07 % 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: -0.37 (0.15), residues: 3154 helix: 1.41 (0.16), residues: 1120 sheet: -0.76 (0.25), residues: 412 loop : -1.33 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J1174 TYR 0.014 0.001 TYR G 177 PHE 0.012 0.001 PHE I 405 TRP 0.017 0.001 TRP J1193 HIS 0.009 0.001 HIS J 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (26725) covalent geometry : angle 0.52346 / 0.27 (36388) hydrogen bonds : bond 0.03607 / 3.81 ( 1073) hydrogen bonds : angle 4.15992 / 4.39 ( 2972) metal coordination : bond 0.00375 / 0.40 ( 8) metal coordination : angle 2.02696 / 2.84 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6308 Ramachandran restraints generated. 3154 Oldfield, 0 Emsley, 3154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 318 time to evaluate : 0.996 Fit side-chains REVERT: G 76 GLU cc_start: 0.8239 (mp0) cc_final: 0.7873 (mp0) REVERT: G 181 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7103 (mm-30) REVERT: G 188 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8152 (mt-10) REVERT: H 95 LYS cc_start: 0.7094 (ptmt) cc_final: 0.6886 (pttp) REVERT: H 176 CYS cc_start: 0.9092 (p) cc_final: 0.8670 (p) REVERT: I 18 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.7199 (mtm-85) REVERT: I 39 ILE cc_start: 0.8416 (pt) cc_final: 0.8056 (pt) REVERT: I 81 ASP cc_start: 0.7751 (t70) cc_final: 0.7390 (t0) REVERT: I 195 PHE cc_start: 0.8347 (m-80) cc_final: 0.7338 (m-80) REVERT: I 239 MET cc_start: 0.5166 (ttp) cc_final: 0.4628 (ttm) REVERT: I 319 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7031 (pt) REVERT: I 360 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8325 (pp) REVERT: I 386 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7912 (tm-30) REVERT: I 430 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8187 (mttp) REVERT: I 477 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7324 (tp30) REVERT: I 842 ASP cc_start: 0.7289 (t70) cc_final: 0.6996 (t70) REVERT: I 962 GLU cc_start: 0.6896 (mt-10) cc_final: 0.6478 (mt-10) REVERT: I 1033 ARG cc_start: 0.7551 (ttm110) cc_final: 0.6560 (mtm180) REVERT: I 1085 MET cc_start: 0.9236 (OUTLIER) cc_final: 0.8943 (mmp) REVERT: I 1180 MET cc_start: 0.9038 (ttm) cc_final: 0.8727 (ttm) REVERT: I 1188 ASP cc_start: 0.8469 (t0) cc_final: 0.8061 (t0) REVERT: I 1297 ASP cc_start: 0.8344 (t70) cc_final: 0.8070 (t70) REVERT: I 1340 GLU cc_start: 0.7863 (pt0) cc_final: 0.7603 (pt0) REVERT: J 227 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.7772 (m-80) REVERT: J 291 ILE cc_start: 0.8523 (mm) cc_final: 0.8005 (tt) REVERT: J 556 GLU cc_start: 0.7691 (tt0) cc_final: 0.7388 (tt0) REVERT: J 740 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8267 (mp) REVERT: J 805 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.7706 (pm20) REVERT: J 807 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8873 (tt) REVERT: J 1040 MET cc_start: 0.4087 (ttp) cc_final: 0.2692 (mmt) REVERT: J 1244 GLN cc_start: 0.7613 (mm-40) cc_final: 0.6987 (mm-40) REVERT: J 1275 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7427 (mm) REVERT: J 1357 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8419 (tt) REVERT: K 74 GLU cc_start: 0.7379 (mm-30) cc_final: 0.7164 (mm-30) REVERT: K 76 GLU cc_start: 0.6704 (tm-30) cc_final: 0.5647 (mt-10) outliers start: 84 outliers final: 62 residues processed: 382 average time/residue: 0.1454 time to fit residues: 90.2255 Evaluate side-chains 388 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 314 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 430 LYS Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 499 SER Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 643 SER Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 949 GLU Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1085 MET Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 229 GLN Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 402 GLU Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 485 MET Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 790 THR Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 913 GLU Chi-restraints excluded: chain J residue 958 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1275 LEU Chi-restraints excluded: chain J residue 1278 GLU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain K residue 12 LYS Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 58 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 166 optimal weight: 0.0010 chunk 270 optimal weight: 0.4980 chunk 240 optimal weight: 0.9980 chunk 238 optimal weight: 1.9990 chunk 189 optimal weight: 0.9990 chunk 215 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 71 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 258 optimal weight: 0.2980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 232 ASN ** J 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.166843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.123907 restraints weight = 30819.065| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.03 r_work: 0.2960 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 26733 Z= 0.106 Angle : 0.518 7.907 36400 Z= 0.271 Chirality : 0.042 0.188 4176 Planarity : 0.003 0.042 4525 Dihedral : 13.030 153.494 4225 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.04 % Allowed : 14.71 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.15), residues: 3154 helix: 1.41 (0.16), residues: 1127 sheet: -0.70 (0.25), residues: 410 loop : -1.32 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J1174 TYR 0.013 0.001 TYR G 177 PHE 0.012 0.001 PHE I 405 TRP 0.017 0.001 TRP J1193 HIS 0.009 0.001 HIS J 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (26725) covalent geometry : angle 0.51634 / 0.27 (36388) hydrogen bonds : bond 0.03511 / 3.70 ( 1073) hydrogen bonds : angle 4.12166 / 4.35 ( 2972) metal coordination : bond 0.00325 / 0.35 ( 8) metal coordination : angle 2.03497 / 2.85 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7031.32 seconds wall clock time: 120 minutes 44.75 seconds (7244.75 seconds total)