Starting phenix.real_space_refine on Sun Aug 9 05:10:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k59_36898/08_2026/8k59_36898.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k59_36898/08_2026/8k59_36898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k59_36898/08_2026/8k59_36898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k59_36898/08_2026/8k59_36898.map" model { file = "/net/cci-nas-00/data/ceres_data/8k59_36898/08_2026/8k59_36898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k59_36898/08_2026/8k59_36898.cif" } resolution = 3.5 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= 0.002 sd= 0.026 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: 5 Type Number sf(0) Gaussians P 126 5.49 5 S 135 5.16 5 C 20101 2.51 5 N 5805 2.21 5 O 6573 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.04s 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: 32740 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 10570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10570 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1280} Chain: "D" Number of atoms: 10494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1352, 10494 Classifications: {'peptide': 1352} Modifications used: {'COO': 1} Link IDs: {'CIS': 7, 'PTRANS': 55, 'TRANS': 1289} Chain breaks: 1 Chain: "E" Number of atoms: 606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 606 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "F" Number of atoms: 3846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3846 Classifications: {'peptide': 472} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 457} Chain breaks: 2 Chain: "A" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1788 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 220} Chain: "B" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1767 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "G" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1031 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "I" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1248 Classifications: {'DNA': 61} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 60} Chain: "H" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1283 Classifications: {'DNA': 63} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 62} Chain: "J" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 107 Classifications: {'RNA': 5} Modifications used: {'5*END': 1, 'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna3p': 4} Time building chain proxies: 6.87, per 1000 atoms: 0.21 Number of scatterers: 32740 At special positions: 0 Unit cell: (154.98, 159.08, 164.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 135 16.00 P 126 15.00 O 6573 8.00 N 5805 7.00 C 20101 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: 3.00 Conformation dependent library (CDL) restraints added in 1.4 seconds 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7112 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 48 sheets defined 45.4% alpha, 15.5% beta 39 base pairs and 79 stacking pairs defined. Time for finding SS restraints: 3.92 Creating SS restraints... Processing helix chain 'C' and resid 4 through 10 Processing helix chain 'C' and resid 28 through 40 Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 removed outlier: 4.127A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 288 through 293 Processing helix chain 'C' and resid 318 through 329 removed outlier: 3.735A pdb=" N GLY C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 3.735A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 409 Processing helix chain 'C' and resid 421 through 437 Processing helix chain 'C' and resid 455 through 482 removed outlier: 3.782A pdb=" N SER C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 494 through 508 removed outlier: 4.617A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 544 through 549 removed outlier: 3.859A pdb=" N ARG C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.576A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 614 removed outlier: 3.764A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 667 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 removed outlier: 3.832A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 712 removed outlier: 4.564A pdb=" N ALA C 707 " --> pdb=" O GLY C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 741 removed outlier: 3.571A pdb=" N MET C 741 " --> pdb=" O GLU C 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 738 through 741' Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 864 removed outlier: 3.662A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 907 Processing helix chain 'C' and resid 942 through 981 Processing helix chain 'C' and resid 986 through 991 removed outlier: 3.506A pdb=" N ASP C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS C 991 " --> pdb=" O GLU C 987 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 986 through 991' Processing helix chain 'C' and resid 993 through 997 removed outlier: 3.625A pdb=" N TRP C 997 " --> pdb=" O ARG C 994 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1038 Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1102 through 1107 removed outlier: 3.527A pdb=" N ARG C1106 " --> pdb=" O GLY C1102 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1135 Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 3.503A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1166 through 1177 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 Processing helix chain 'C' and resid 1271 through 1281 removed outlier: 3.583A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1284 through 1292 Processing helix chain 'C' and resid 1297 through 1311 Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 3.563A pdb=" N LEU C1333 " --> pdb=" O GLU C1329 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 94 through 100 Processing helix chain 'D' and resid 114 through 119 removed outlier: 3.725A pdb=" N SER D 119 " --> pdb=" O TRP D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 192 Processing helix chain 'D' and resid 193 through 208 removed outlier: 3.773A pdb=" N GLU D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 285 Processing helix chain 'D' and resid 288 through 309 Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 419 removed outlier: 3.836A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE D 411 " --> pdb=" O VAL D 407 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLU D 418 " --> pdb=" O GLU D 414 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N HIS D 419 " --> pdb=" O VAL D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 486 through 490 removed outlier: 4.164A pdb=" N ILE D 490 " --> pdb=" O THR D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 515 Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.986A pdb=" N ALA D 533 " --> pdb=" O GLY D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 583 removed outlier: 3.735A pdb=" N ILE D 582 " --> pdb=" O ILE D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 614 through 636 Processing helix chain 'D' and resid 649 through 670 Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.628A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 removed outlier: 3.567A pdb=" N LEU D 740 " --> pdb=" O GLN D 736 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 753 removed outlier: 4.132A pdb=" N SER D 753 " --> pdb=" O PRO D 750 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.875A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.672A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.750A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 930 Processing helix chain 'D' and resid 1136 through 1147 removed outlier: 3.960A pdb=" N ARG D1140 " --> pdb=" O GLY D1136 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1225 removed outlier: 3.529A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.773A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.296A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1293 Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1326 removed outlier: 3.738A pdb=" N PHE D1325 " --> pdb=" O SER D1321 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN D1326 " --> pdb=" O ALA D1322 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1346 through 1354 Processing helix chain 'D' and resid 1360 through 1373 removed outlier: 4.024A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 17 through 32 Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.757A pdb=" N ILE E 49 " --> pdb=" O LYS E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 77 Processing helix chain 'F' and resid 96 through 108 removed outlier: 3.683A pdb=" N MET F 100 " --> pdb=" O ASP F 96 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL F 108 " --> pdb=" O GLU F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 137 Processing helix chain 'F' and resid 137 through 153 removed outlier: 3.955A pdb=" N ILE F 141 " --> pdb=" O TYR F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 160 Processing helix chain 'F' and resid 214 through 234 removed outlier: 3.740A pdb=" N THR F 234 " --> pdb=" O VAL F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 258 removed outlier: 3.845A pdb=" N GLN F 258 " --> pdb=" O GLU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 296 Processing helix chain 'F' and resid 298 through 307 removed outlier: 4.165A pdb=" N PHE F 302 " --> pdb=" O PRO F 298 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE F 303 " --> pdb=" O LYS F 299 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR F 304 " --> pdb=" O LYS F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 321 Processing helix chain 'F' and resid 324 through 330 Processing helix chain 'F' and resid 333 through 352 Processing helix chain 'F' and resid 354 through 383 Processing helix chain 'F' and resid 383 through 396 removed outlier: 3.614A pdb=" N VAL F 387 " --> pdb=" O ASN F 383 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS F 393 " --> pdb=" O SER F 389 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR F 394 " --> pdb=" O ILE F 390 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASN F 396 " --> pdb=" O LYS F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 419 Processing helix chain 'F' and resid 426 through 447 removed outlier: 3.754A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA F 447 " --> pdb=" O ILE F 443 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 475 Processing helix chain 'F' and resid 479 through 487 Processing helix chain 'F' and resid 491 through 502 removed outlier: 3.854A pdb=" N LYS F 502 " --> pdb=" O LEU F 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 523 Processing helix chain 'F' and resid 530 through 551 Processing helix chain 'F' and resid 552 through 564 removed outlier: 3.519A pdb=" N MET F 561 " --> pdb=" O LYS F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 580 Processing helix chain 'F' and resid 584 through 599 removed outlier: 4.549A pdb=" N ARG F 588 " --> pdb=" O ARG F 584 " (cutoff:3.500A) Processing helix chain 'F' and resid 603 through 609 removed outlier: 4.252A pdb=" N LEU F 607 " --> pdb=" O ARG F 603 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER F 609 " --> pdb=" O GLU F 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.678A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 212 through 233 removed outlier: 4.109A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.574A pdb=" N LYS B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 154 through 161 removed outlier: 3.651A pdb=" N HIS B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 229 Processing helix chain 'B' and resid 230 through 232 No H-bonds generated for 'chain 'B' and resid 230 through 232' Processing helix chain 'G' and resid 11 through 15 Processing helix chain 'G' and resid 31 through 39 Processing helix chain 'G' and resid 41 through 52 Processing helix chain 'G' and resid 54 through 87 Processing helix chain 'G' and resid 102 through 105 Processing helix chain 'G' and resid 107 through 128 removed outlier: 3.778A pdb=" N ARG G 111 " --> pdb=" O ASN G 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.581A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 66 through 75 removed outlier: 7.081A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY C 125 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL C 98 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N TYR C 123 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N LEU C 100 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLU C 121 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N LEU C 102 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N GLU C 119 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ILE C 104 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ILE C 117 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AA4, first strand: chain 'C' and resid 451 through 454 removed outlier: 3.606A pdb=" N SER C 147 " --> pdb=" O ARG C 529 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N SER C 574 " --> pdb=" O CYS C 559 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 154 through 160 removed outlier: 6.056A pdb=" N TYR C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 284 through 286 removed outlier: 4.805A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.709A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 301 through 302 Processing sheet with id=AA9, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.414A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AB2, first strand: chain 'C' and resid 623 through 624 Processing sheet with id=AB3, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.858A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.622A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AB6, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AB7, first strand: chain 'C' and resid 1066 through 1068 removed outlier: 4.520A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 9.078A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 1066 through 1068 Processing sheet with id=AB9, first strand: chain 'C' and resid 846 through 847 removed outlier: 3.507A pdb=" N THR C 843 " --> pdb=" O GLY C 846 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ASP C 842 " --> pdb=" O VAL C1046 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL C1046 " --> pdb=" O ASP C 842 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AC2, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.690A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 7.538A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 1335 through 1340 Processing sheet with id=AC5, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.650A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 10.038A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.645A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 44 through 45 Processing sheet with id=AC7, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AC8, first strand: chain 'D' and resid 261 through 262 Processing sheet with id=AC9, first strand: chain 'D' and resid 526 through 528 removed outlier: 6.987A pdb=" N LEU D 527 " --> pdb=" O ARG D 551 " (cutoff:3.500A) removed outlier: 8.855A pdb=" N THR D 553 " --> pdb=" O LEU D 527 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 809 through 811 removed outlier: 6.110A pdb=" N VAL D 894 " --> pdb=" O VAL D 809 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU D 811 " --> pdb=" O VAL D 894 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AD3, first strand: chain 'D' and resid 825 through 827 removed outlier: 3.832A pdb=" N GLU D 833 " --> pdb=" O VAL D 825 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLU D 827 " --> pdb=" O VAL D 831 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N VAL D 831 " --> pdb=" O GLU D 827 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 949 through 951 removed outlier: 6.500A pdb=" N ILE D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 995 through 997 removed outlier: 4.114A pdb=" N THR D 980 " --> pdb=" O VAL D 997 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY D 956 " --> pdb=" O VAL D1011 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL D1011 " --> pdb=" O GLY D 956 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 1024 through 1028 removed outlier: 6.285A pdb=" N MET D1025 " --> pdb=" O ARG D1123 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ARG D1123 " --> pdb=" O MET D1025 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL D1027 " --> pdb=" O LEU D1121 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N LEU D1121 " --> pdb=" O GLN D1108 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN D1108 " --> pdb=" O LEU D1121 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LEU D1109 " --> pdb=" O SER D1057 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N SER D1057 " --> pdb=" O LEU D1109 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL D1060 " --> pdb=" O THR D1047 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 1034 through 1038 Processing sheet with id=AD8, first strand: chain 'D' and resid 1186 through 1191 removed outlier: 3.540A pdb=" N ILE D1162 " --> pdb=" O THR D1178 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 1277 through 1279 removed outlier: 6.137A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 162 through 165 removed outlier: 5.070A pdb=" N ARG F 260 " --> pdb=" O THR F 163 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 13 through 17 removed outlier: 9.018A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N HIS A 23 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N THR A 207 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LYS A 25 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N MET A 205 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N THR A 27 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE A 203 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N GLU A 29 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N LEU A 201 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 97 through 105 removed outlier: 3.647A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AE5, first strand: chain 'A' and resid 108 through 111 removed outlier: 6.483A pdb=" N GLY A 108 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N HIS A 132 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AE7, first strand: chain 'B' and resid 12 through 19 removed outlier: 4.870A pdb=" N LEU B 13 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N GLU B 29 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N THR B 196 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VAL B 192 " --> pdb=" O THR B 196 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU B 198 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 97 through 105 removed outlier: 3.901A pdb=" N GLU B 58 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AF1, first strand: chain 'B' and resid 108 through 111 Processing sheet with id=AF2, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AF3, first strand: chain 'G' and resid 91 through 94 1431 hydrogen bonds defined for protein. 4074 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 90 hydrogen bonds 152 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 79 stacking parallelities Total time for adding SS restraints: 9.89 Time building geometry restraints manager: 4.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8150 1.33 - 1.45: 6361 1.45 - 1.57: 18496 1.57 - 1.69: 253 1.69 - 1.82: 237 Bond restraints: 33497 Sorted by residual: bond pdb=" C3' DG H 35 " pdb=" C2' DG H 35 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.96e+00 bond pdb=" C3' DT H 15 " pdb=" O3' DT H 15 " ideal model delta sigma weight residual 1.435 1.395 0.040 1.30e-02 5.92e+03 9.32e+00 bond pdb=" C3' DT I 49 " pdb=" C2' DT I 49 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.20e+00 bond pdb=" C3' DC H 22 " pdb=" C2' DC H 22 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.54e+00 bond pdb=" C3' DG I 42 " pdb=" C2' DG I 42 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.01e+00 ... (remaining 33492 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 45482 3.21 - 6.41: 276 6.41 - 9.62: 17 9.62 - 12.83: 6 12.83 - 16.03: 1 Bond angle restraints: 45782 Sorted by residual: angle pdb=" C LEU F 488 " pdb=" N MET F 489 " pdb=" CA MET F 489 " ideal model delta sigma weight residual 120.67 136.70 -16.03 1.34e+00 5.57e-01 1.43e+02 angle pdb=" N ILE C 445 " pdb=" CA ILE C 445 " pdb=" C ILE C 445 " ideal model delta sigma weight residual 112.29 106.92 5.37 9.40e-01 1.13e+00 3.27e+01 angle pdb=" N SER C1247 " pdb=" CA SER C1247 " pdb=" C SER C1247 " ideal model delta sigma weight residual 114.56 107.63 6.93 1.27e+00 6.20e-01 2.98e+01 angle pdb=" N ASP C 814 " pdb=" CA ASP C 814 " pdb=" C ASP C 814 " ideal model delta sigma weight residual 113.19 104.94 8.25 1.58e+00 4.01e-01 2.73e+01 angle pdb=" CA PRO D1191 " pdb=" N PRO D1191 " pdb=" CD PRO D1191 " ideal model delta sigma weight residual 112.00 104.88 7.12 1.40e+00 5.10e-01 2.59e+01 ... (remaining 45777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.40: 19307 34.40 - 68.79: 882 68.79 - 103.18: 127 103.18 - 137.58: 2 137.58 - 171.97: 2 Dihedral angle restraints: 20320 sinusoidal: 9291 harmonic: 11029 Sorted by residual: dihedral pdb=" CA GLN G 16 " pdb=" C GLN G 16 " pdb=" N PRO G 17 " pdb=" CA PRO G 17 " ideal model delta harmonic sigma weight residual -180.00 -142.46 -37.54 0 5.00e+00 4.00e-02 5.64e+01 dihedral pdb=" CA GLU B 60 " pdb=" C GLU B 60 " pdb=" N ILE B 61 " pdb=" CA ILE B 61 " ideal model delta harmonic sigma weight residual 180.00 152.99 27.01 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA MET C1243 " pdb=" C MET C1243 " pdb=" N HIS C1244 " pdb=" CA HIS C1244 " ideal model delta harmonic sigma weight residual 180.00 154.59 25.41 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 20317 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 4012 0.047 - 0.095: 942 0.095 - 0.142: 238 0.142 - 0.189: 15 0.189 - 0.236: 3 Chirality restraints: 5210 Sorted by residual: chirality pdb=" CA ARG E 69 " pdb=" N ARG E 69 " pdb=" C ARG E 69 " pdb=" CB ARG E 69 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA GLN E 73 " pdb=" N GLN E 73 " pdb=" C GLN E 73 " pdb=" CB GLN E 73 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA ARG D 314 " pdb=" N ARG D 314 " pdb=" C ARG D 314 " pdb=" CB ARG D 314 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 5207 not shown) Planarity restraints: 5542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D1190 " -0.066 5.00e-02 4.00e+02 9.66e-02 1.49e+01 pdb=" N PRO D1191 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO D1191 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO D1191 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D1184 " 0.061 5.00e-02 4.00e+02 9.01e-02 1.30e+01 pdb=" N PRO D1185 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO D1185 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO D1185 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR D1186 " 0.016 2.00e-02 2.50e+03 3.17e-02 1.01e+01 pdb=" C TYR D1186 " -0.055 2.00e-02 2.50e+03 pdb=" O TYR D1186 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU D1187 " 0.018 2.00e-02 2.50e+03 ... (remaining 5539 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 646 2.66 - 3.22: 31880 3.22 - 3.78: 53810 3.78 - 4.34: 72802 4.34 - 4.90: 116414 Nonbonded interactions: 275552 Sorted by model distance: nonbonded pdb=" O GLU C1329 " pdb=" OG SER C1332 " model vdw 2.102 3.040 nonbonded pdb=" OD2 ASP C 516 " pdb=" OG SER C 522 " model vdw 2.106 3.040 nonbonded pdb=" OE1 GLU D1158 " pdb=" OH TYR D1186 " model vdw 2.112 3.040 nonbonded pdb=" OE1 GLU C 562 " pdb=" OG SER C 662 " model vdw 2.117 3.040 nonbonded pdb=" OH TYR C 555 " pdb=" OD2 ASP C 654 " model vdw 2.143 3.040 ... (remaining 275547 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 'A' and resid 7 through 233) selection = (chain 'B' and resid 7 through 233) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 35.860 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.070 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 33497 Z= 0.264 Angle : 0.741 16.034 45782 Z= 0.484 Chirality : 0.043 0.236 5210 Planarity : 0.005 0.097 5542 Dihedral : 18.465 171.972 13208 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.28 % Favored : 95.43 % Rotamer: Outliers : 0.03 % Allowed : 0.31 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.27 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.14), residues: 3807 helix: 1.33 (0.13), residues: 1552 sheet: -0.47 (0.26), residues: 378 loop : -1.28 (0.14), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG E 67 TYR 0.027 0.002 TYR B 185 PHE 0.033 0.001 PHE F 256 TRP 0.011 0.001 TRP G 36 HIS 0.007 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.26 (33497) covalent geometry : angle 0.74136 / 0.48 (45782) hydrogen bonds : bond 0.15689 / 10.51 ( 1517) hydrogen bonds : angle 6.68737 / 4.66 ( 4226) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 809 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 74 ARG cc_start: 0.7959 (ttp-170) cc_final: 0.7715 (ttp80) REVERT: C 79 VAL cc_start: 0.8532 (m) cc_final: 0.8306 (p) REVERT: C 80 PHE cc_start: 0.7736 (m-80) cc_final: 0.7089 (m-10) REVERT: C 119 GLU cc_start: 0.7553 (tp30) cc_final: 0.6199 (tp30) REVERT: C 126 GLU cc_start: 0.7018 (mt-10) cc_final: 0.6345 (mm-30) REVERT: C 130 MET cc_start: 0.8349 (ttt) cc_final: 0.7854 (ttt) REVERT: C 199 ASP cc_start: 0.8542 (m-30) cc_final: 0.8035 (m-30) REVERT: C 200 ARG cc_start: 0.8091 (mmm160) cc_final: 0.7682 (mmm160) REVERT: C 546 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7269 (mt-10) REVERT: C 551 HIS cc_start: 0.7692 (t-90) cc_final: 0.7198 (t-90) REVERT: C 610 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7786 (mt-10) REVERT: C 626 GLU cc_start: 0.7188 (pm20) cc_final: 0.6956 (pm20) REVERT: C 672 GLU cc_start: 0.7721 (pt0) cc_final: 0.7394 (pm20) REVERT: C 705 GLU cc_start: 0.7576 (mp0) cc_final: 0.7303 (mp0) REVERT: C 737 ASN cc_start: 0.6967 (m-40) cc_final: 0.6380 (m-40) REVERT: C 754 THR cc_start: 0.8332 (m) cc_final: 0.7936 (p) REVERT: C 1026 GLU cc_start: 0.8539 (tp30) cc_final: 0.8139 (mp0) REVERT: C 1056 VAL cc_start: 0.8387 (t) cc_final: 0.7961 (m) REVERT: C 1066 MET cc_start: 0.7663 (ttm) cc_final: 0.7394 (ttm) REVERT: C 1085 MET cc_start: 0.8035 (mmp) cc_final: 0.7746 (mmp) REVERT: C 1107 MET cc_start: 0.8006 (mmt) cc_final: 0.7525 (mmt) REVERT: C 1154 ASP cc_start: 0.8271 (m-30) cc_final: 0.7811 (t0) REVERT: C 1178 LYS cc_start: 0.8236 (mmtt) cc_final: 0.7958 (mtpt) REVERT: C 1188 ASP cc_start: 0.7637 (t0) cc_final: 0.7254 (t0) REVERT: C 1210 ILE cc_start: 0.6949 (mt) cc_final: 0.6702 (tp) REVERT: C 1229 TYR cc_start: 0.8166 (m-80) cc_final: 0.7769 (m-80) REVERT: C 1230 MET cc_start: 0.7819 (ttt) cc_final: 0.7526 (ttm) REVERT: C 1250 SER cc_start: 0.7516 (t) cc_final: 0.7293 (t) REVERT: C 1259 LEU cc_start: 0.6059 (tp) cc_final: 0.5700 (tp) REVERT: D 60 ARG cc_start: 0.8547 (tmt170) cc_final: 0.8038 (tmt-80) REVERT: D 66 LYS cc_start: 0.7900 (ttpt) cc_final: 0.7697 (tptt) REVERT: D 84 ILE cc_start: 0.7574 (pt) cc_final: 0.7075 (pt) REVERT: D 130 MET cc_start: 0.8041 (ttp) cc_final: 0.7264 (ttp) REVERT: D 166 LEU cc_start: 0.9287 (tp) cc_final: 0.8751 (tp) REVERT: D 167 ASP cc_start: 0.9230 (t0) cc_final: 0.9028 (m-30) REVERT: D 170 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8814 (mm-30) REVERT: D 235 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7384 (mp0) REVERT: D 281 ARG cc_start: 0.8248 (ttp-110) cc_final: 0.7935 (mtp180) REVERT: D 490 ILE cc_start: 0.8623 (pt) cc_final: 0.8328 (tt) REVERT: D 599 LYS cc_start: 0.8015 (mppt) cc_final: 0.7678 (tptp) REVERT: D 642 ASP cc_start: 0.8250 (m-30) cc_final: 0.7889 (p0) REVERT: D 677 GLU cc_start: 0.7580 (tt0) cc_final: 0.7199 (tp30) REVERT: D 680 ASN cc_start: 0.7899 (t0) cc_final: 0.7584 (t0) REVERT: D 681 LYS cc_start: 0.8592 (tppt) cc_final: 0.8330 (tptt) REVERT: D 712 GLN cc_start: 0.7349 (mm-40) cc_final: 0.6906 (tm-30) REVERT: D 715 LYS cc_start: 0.8074 (mmtm) cc_final: 0.7862 (tptm) REVERT: D 727 ASP cc_start: 0.7905 (t0) cc_final: 0.7647 (t0) REVERT: D 777 HIS cc_start: 0.6765 (t70) cc_final: 0.6363 (m90) REVERT: D 790 THR cc_start: 0.8097 (m) cc_final: 0.7751 (p) REVERT: D 837 ASP cc_start: 0.8582 (m-30) cc_final: 0.8270 (t70) REVERT: D 871 LEU cc_start: 0.8223 (mt) cc_final: 0.7985 (tp) REVERT: D 922 SER cc_start: 0.8343 (m) cc_final: 0.8090 (p) REVERT: D 1195 GLN cc_start: 0.6612 (tt0) cc_final: 0.6353 (pm20) REVERT: D 1243 LEU cc_start: 0.8023 (tp) cc_final: 0.7701 (tp) REVERT: D 1244 GLN cc_start: 0.7955 (mm110) cc_final: 0.7676 (mp10) REVERT: D 1281 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8280 (mt-10) REVERT: D 1321 SER cc_start: 0.7921 (t) cc_final: 0.7652 (m) REVERT: D 1343 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7532 (mm-30) REVERT: E 11 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7478 (mm-30) REVERT: E 61 ASN cc_start: 0.6260 (p0) cc_final: 0.5387 (p0) REVERT: F 100 MET cc_start: 0.2939 (ppp) cc_final: 0.2184 (tpp) REVERT: F 288 MET cc_start: -0.0249 (mmm) cc_final: -0.0827 (ttt) REVERT: F 297 MET cc_start: 0.0372 (ppp) cc_final: -0.1711 (tpt) REVERT: F 322 MET cc_start: 0.2919 (mpp) cc_final: 0.2554 (mpp) REVERT: F 419 PHE cc_start: 0.5345 (t80) cc_final: 0.5141 (t80) REVERT: F 433 TRP cc_start: 0.5067 (m100) cc_final: 0.3989 (m100) REVERT: F 470 MET cc_start: 0.7000 (mmp) cc_final: 0.6501 (mtp) REVERT: F 492 ASP cc_start: 0.8110 (p0) cc_final: 0.7102 (t0) REVERT: F 507 MET cc_start: 0.5567 (mpp) cc_final: 0.5354 (mtm) REVERT: F 541 ARG cc_start: 0.6635 (mtt-85) cc_final: 0.6227 (tmt170) REVERT: F 555 GLU cc_start: 0.7215 (mt-10) cc_final: 0.6947 (tt0) REVERT: F 561 MET cc_start: 0.7873 (mpp) cc_final: 0.7650 (mpp) REVERT: F 611 LEU cc_start: 0.7562 (mt) cc_final: 0.6673 (pp) REVERT: A 50 SER cc_start: 0.8206 (t) cc_final: 0.7601 (t) REVERT: A 67 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8017 (mt-10) REVERT: A 185 TYR cc_start: 0.8390 (p90) cc_final: 0.7782 (p90) REVERT: A 229 GLU cc_start: 0.8824 (tt0) cc_final: 0.8529 (mm-30) REVERT: B 59 VAL cc_start: 0.8907 (t) cc_final: 0.8649 (p) REVERT: B 71 LYS cc_start: 0.8578 (tptp) cc_final: 0.8246 (tptp) REVERT: B 80 GLU cc_start: 0.7145 (pm20) cc_final: 0.6573 (tm-30) REVERT: B 129 VAL cc_start: 0.8615 (t) cc_final: 0.7820 (p) REVERT: B 143 ARG cc_start: 0.7201 (pmt170) cc_final: 0.6980 (mtm110) REVERT: B 145 LYS cc_start: 0.8384 (mmpt) cc_final: 0.8123 (mmmt) REVERT: B 171 LEU cc_start: 0.8956 (mt) cc_final: 0.8578 (mp) REVERT: B 200 LYS cc_start: 0.6366 (mtpp) cc_final: 0.5888 (mttt) REVERT: B 211 ILE cc_start: 0.8353 (tp) cc_final: 0.7996 (tp) REVERT: G 8 TYR cc_start: 0.8245 (t80) cc_final: 0.7999 (t80) REVERT: G 28 ASN cc_start: 0.8166 (t0) cc_final: 0.7964 (t0) REVERT: G 38 LEU cc_start: 0.8459 (mp) cc_final: 0.8036 (mp) REVERT: G 61 TYR cc_start: 0.8744 (t80) cc_final: 0.8520 (t80) REVERT: G 72 LYS cc_start: 0.8912 (ttmt) cc_final: 0.8686 (ptpp) REVERT: G 73 TRP cc_start: 0.7773 (t60) cc_final: 0.7429 (t60) REVERT: G 100 LEU cc_start: 0.4380 (mt) cc_final: 0.3897 (mt) REVERT: G 109 ASP cc_start: 0.8095 (m-30) cc_final: 0.7260 (t0) REVERT: G 117 GLN cc_start: 0.8303 (mt0) cc_final: 0.7781 (mm-40) outliers start: 1 outliers final: 0 residues processed: 810 average time/residue: 0.2470 time to fit residues: 306.3310 Evaluate side-chains 468 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 468 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 50.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 40.0000 chunk 183 optimal weight: 0.7980 overall best weight: 4.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 46 GLN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 HIS C 490 GLN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 688 GLN C 799 ASN C1288 GLN C1299 ASN ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 HIS D1279 GLN F 409 ASN B 41 ASN ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.182797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.136162 restraints weight = 52078.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.133505 restraints weight = 59310.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.135010 restraints weight = 57710.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.135064 restraints weight = 36053.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.138181 restraints weight = 31129.152| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.130 33497 Z= 0.314 Angle : 0.762 9.849 45782 Z= 0.406 Chirality : 0.049 0.264 5210 Planarity : 0.006 0.086 5542 Dihedral : 18.240 175.766 5628 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.96 % Favored : 94.75 % Rotamer: Outliers : 2.17 % Allowed : 9.65 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.27 % Twisted Proline : 0.68 % 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 (0.13), residues: 3807 helix: 0.97 (0.13), residues: 1554 sheet: -0.53 (0.26), residues: 379 loop : -1.41 (0.13), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C1246 TYR 0.049 0.002 TYR D 46 PHE 0.022 0.002 PHE C1144 TRP 0.012 0.002 TRP F 434 HIS 0.008 0.002 HIS C1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00735 / 0.31 (33497) covalent geometry : angle 0.76201 / 0.41 (45782) hydrogen bonds : bond 0.05981 / 3.99 ( 1517) hydrogen bonds : angle 5.33678 / 3.71 ( 4226) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 468 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 151 ARG cc_start: 0.8153 (mtp-110) cc_final: 0.7364 (mtm-85) REVERT: C 371 ARG cc_start: 0.7429 (mpt-90) cc_final: 0.6554 (mtm110) REVERT: C 478 ARG cc_start: 0.6925 (tpt90) cc_final: 0.6555 (tpt90) REVERT: C 949 GLU cc_start: 0.5821 (mt-10) cc_final: 0.5482 (mm-30) REVERT: C 1229 TYR cc_start: 0.8585 (m-80) cc_final: 0.8284 (m-80) REVERT: C 1243 MET cc_start: 0.7288 (mtm) cc_final: 0.7051 (mtp) REVERT: C 1259 LEU cc_start: 0.6830 (tp) cc_final: 0.6484 (tp) REVERT: C 1296 ASP cc_start: 0.7344 (m-30) cc_final: 0.7063 (m-30) REVERT: D 166 LEU cc_start: 0.9071 (tp) cc_final: 0.8402 (tp) REVERT: D 235 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7766 (mp0) REVERT: D 490 ILE cc_start: 0.9336 (pt) cc_final: 0.9090 (tt) REVERT: D 680 ASN cc_start: 0.8361 (t0) cc_final: 0.8053 (t0) REVERT: D 681 LYS cc_start: 0.8334 (tppt) cc_final: 0.8082 (mmtp) REVERT: D 727 ASP cc_start: 0.8373 (t0) cc_final: 0.8115 (t0) REVERT: D 790 THR cc_start: 0.9025 (m) cc_final: 0.8625 (p) REVERT: D 1243 LEU cc_start: 0.8689 (tp) cc_final: 0.8332 (tp) REVERT: D 1344 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8185 (mp) REVERT: D 1348 LYS cc_start: 0.8088 (mmtt) cc_final: 0.7768 (mmtm) REVERT: E 52 ARG cc_start: 0.8143 (mtp85) cc_final: 0.7834 (mtp180) REVERT: F 100 MET cc_start: 0.2896 (ppp) cc_final: 0.1946 (mtp) REVERT: F 288 MET cc_start: -0.1018 (mmm) cc_final: -0.1491 (mmm) REVERT: F 322 MET cc_start: 0.4146 (mpp) cc_final: 0.3768 (mpp) REVERT: F 419 PHE cc_start: 0.5306 (t80) cc_final: 0.4985 (t80) REVERT: F 433 TRP cc_start: 0.4864 (m100) cc_final: 0.4062 (m100) REVERT: F 492 ASP cc_start: 0.7297 (p0) cc_final: 0.6687 (t0) REVERT: F 507 MET cc_start: 0.7295 (mpp) cc_final: 0.6919 (mtm) REVERT: F 540 LEU cc_start: 0.7189 (tp) cc_final: 0.6812 (tp) REVERT: F 541 ARG cc_start: 0.7329 (mtt-85) cc_final: 0.7020 (tmt170) REVERT: F 611 LEU cc_start: 0.7645 (mt) cc_final: 0.7129 (pp) REVERT: A 67 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7546 (mt-10) REVERT: A 185 TYR cc_start: 0.8508 (p90) cc_final: 0.8068 (p90) REVERT: B 68 TYR cc_start: 0.7460 (p90) cc_final: 0.7066 (p90) REVERT: B 129 VAL cc_start: 0.8971 (t) cc_final: 0.8556 (p) REVERT: B 194 GLN cc_start: 0.6935 (pp30) cc_final: 0.6611 (pp30) REVERT: G 73 TRP cc_start: 0.7747 (t60) cc_final: 0.7049 (t60) REVERT: G 75 GLU cc_start: 0.7986 (pp20) cc_final: 0.7765 (pp20) outliers start: 71 outliers final: 49 residues processed: 519 average time/residue: 0.2232 time to fit residues: 183.9249 Evaluate side-chains 408 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 358 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 590 SER Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 887 SER Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 925 GLU Chi-restraints excluded: chain D residue 1148 ARG Chi-restraints excluded: chain D residue 1155 ILE Chi-restraints excluded: chain D residue 1215 GLU Chi-restraints excluded: chain D residue 1230 THR Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 506 SER Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 183 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 46 optimal weight: 0.9990 chunk 272 optimal weight: 9.9990 chunk 298 optimal weight: 50.0000 chunk 377 optimal weight: 0.0870 chunk 107 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 329 optimal weight: 6.9990 chunk 367 optimal weight: 4.9990 chunk 188 optimal weight: 0.9980 chunk 149 optimal weight: 8.9990 chunk 291 optimal weight: 4.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 133 ASN C 490 GLN C 519 ASN C 628 HIS C 677 ASN C 799 ASN C 834 GLN D 209 ASN ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 HIS ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 875 ASN D1259 GLN G 50 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.187444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.151042 restraints weight = 51250.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.153689 restraints weight = 112227.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.152552 restraints weight = 53858.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.152897 restraints weight = 42085.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.153161 restraints weight = 36156.813| |-----------------------------------------------------------------------------| r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33497 Z= 0.148 Angle : 0.627 8.988 45782 Z= 0.338 Chirality : 0.044 0.265 5210 Planarity : 0.005 0.079 5542 Dihedral : 18.163 173.973 5628 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.47 % Favored : 95.30 % Rotamer: Outliers : 2.66 % Allowed : 11.60 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.27 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.13), residues: 3807 helix: 1.07 (0.13), residues: 1562 sheet: -0.54 (0.26), residues: 358 loop : -1.33 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 297 TYR 0.034 0.002 TYR G 8 PHE 0.018 0.002 PHE C1164 TRP 0.008 0.001 TRP D 33 HIS 0.006 0.001 HIS G 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (33497) covalent geometry : angle 0.62740 / 0.34 (45782) hydrogen bonds : bond 0.05417 / 3.68 ( 1517) hydrogen bonds : angle 5.03671 / 3.50 ( 4226) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 427 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 371 ARG cc_start: 0.7278 (mpt-90) cc_final: 0.6942 (mtm110) REVERT: C 551 HIS cc_start: 0.7619 (t-90) cc_final: 0.7401 (t-90) REVERT: D 1095 MET cc_start: -0.0181 (tpp) cc_final: -0.1048 (tpp) REVERT: D 1243 LEU cc_start: 0.8458 (tp) cc_final: 0.7842 (mp) REVERT: F 100 MET cc_start: 0.2250 (ppp) cc_final: 0.1728 (mtp) REVERT: F 288 MET cc_start: -0.0859 (mmm) cc_final: -0.1503 (mmm) REVERT: F 433 TRP cc_start: 0.3985 (m100) cc_final: 0.3691 (m100) REVERT: F 540 LEU cc_start: 0.7372 (tp) cc_final: 0.6630 (tt) REVERT: A 185 TYR cc_start: 0.8095 (p90) cc_final: 0.7874 (p90) REVERT: B 68 TYR cc_start: 0.6032 (p90) cc_final: 0.5820 (p90) REVERT: B 129 VAL cc_start: 0.8577 (t) cc_final: 0.8370 (p) REVERT: G 1 MET cc_start: 0.2609 (OUTLIER) cc_final: 0.2327 (mmm) REVERT: G 36 TRP cc_start: 0.6059 (OUTLIER) cc_final: 0.5577 (p-90) REVERT: G 73 TRP cc_start: 0.6802 (t60) cc_final: 0.6246 (t60) outliers start: 87 outliers final: 46 residues processed: 484 average time/residue: 0.2126 time to fit residues: 166.8139 Evaluate side-chains 402 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 354 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 666 SER Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 845 LEU Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1250 SER Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 590 SER Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 925 GLU Chi-restraints excluded: chain D residue 1215 GLU Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 36 TRP Chi-restraints excluded: chain G residue 59 HIS Chi-restraints excluded: chain G residue 99 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 233 optimal weight: 10.0000 chunk 209 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 372 optimal weight: 6.9990 chunk 272 optimal weight: 10.0000 chunk 348 optimal weight: 5.9990 chunk 281 optimal weight: 50.0000 chunk 315 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 190 optimal weight: 0.8980 chunk 331 optimal weight: 8.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 510 GLN C 618 GLN C 649 GLN C 673 HIS C 799 ASN C 834 GLN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 ASN ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN D 651 HIS D 680 ASN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 875 ASN F 383 ASN F 464 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.183288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.139664 restraints weight = 51032.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.133140 restraints weight = 56234.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.135484 restraints weight = 67159.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.135383 restraints weight = 46876.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.136496 restraints weight = 39044.442| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.114 33497 Z= 0.268 Angle : 0.691 9.758 45782 Z= 0.368 Chirality : 0.046 0.269 5210 Planarity : 0.005 0.093 5542 Dihedral : 18.214 174.191 5628 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.31 % Favored : 94.48 % Rotamer: Outliers : 3.24 % Allowed : 13.37 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.27 % Twisted Proline : 0.68 % 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: -0.52 (0.13), residues: 3807 helix: 0.97 (0.13), residues: 1568 sheet: -0.61 (0.25), residues: 383 loop : -1.47 (0.13), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 69 TYR 0.027 0.002 TYR D 140 PHE 0.040 0.002 PHE C 906 TRP 0.010 0.001 TRP G 36 HIS 0.008 0.001 HIS G 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.27 (33497) covalent geometry : angle 0.69114 / 0.37 (45782) hydrogen bonds : bond 0.05303 / 3.55 ( 1517) hydrogen bonds : angle 5.04811 / 3.51 ( 4226) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 363 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 551 HIS cc_start: 0.7901 (t-90) cc_final: 0.7644 (t-90) REVERT: C 649 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7337 (pt0) REVERT: C 1119 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8422 (tpt) REVERT: C 1296 ASP cc_start: 0.7387 (m-30) cc_final: 0.7185 (m-30) REVERT: D 743 MET cc_start: 0.8666 (ppp) cc_final: 0.8435 (ptm) REVERT: D 1243 LEU cc_start: 0.8649 (tp) cc_final: 0.7962 (mp) REVERT: F 100 MET cc_start: 0.2899 (ppp) cc_final: 0.1914 (tpp) REVERT: F 113 ARG cc_start: 0.3753 (tpt90) cc_final: 0.3462 (tpm170) REVERT: F 288 MET cc_start: -0.0869 (mmm) cc_final: -0.1387 (mmm) REVERT: F 322 MET cc_start: 0.3715 (mpp) cc_final: 0.3315 (mpp) REVERT: F 433 TRP cc_start: 0.5071 (m100) cc_final: 0.4109 (m100) REVERT: F 482 GLU cc_start: 0.7808 (mp0) cc_final: 0.7347 (mp0) REVERT: A 185 TYR cc_start: 0.8285 (p90) cc_final: 0.7980 (p90) REVERT: B 68 TYR cc_start: 0.7247 (p90) cc_final: 0.6853 (p90) REVERT: B 104 LYS cc_start: 0.5978 (OUTLIER) cc_final: 0.5752 (ptmt) REVERT: B 129 VAL cc_start: 0.8940 (t) cc_final: 0.8691 (p) REVERT: G 36 TRP cc_start: 0.6813 (OUTLIER) cc_final: 0.5898 (p-90) REVERT: G 73 TRP cc_start: 0.7707 (t60) cc_final: 0.7006 (t60) REVERT: G 77 MET cc_start: 0.8099 (mtp) cc_final: 0.7777 (mtp) outliers start: 106 outliers final: 68 residues processed: 432 average time/residue: 0.1871 time to fit residues: 133.2821 Evaluate side-chains 400 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 328 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 649 GLN Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 666 SER Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 845 LEU Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1119 MET Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1250 SER Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 875 ASN Chi-restraints excluded: chain D residue 925 GLU Chi-restraints excluded: chain D residue 1215 GLU Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 36 TRP Chi-restraints excluded: chain G residue 59 HIS Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain G residue 119 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 1 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 185 optimal weight: 4.9990 chunk 243 optimal weight: 2.9990 chunk 264 optimal weight: 0.9980 chunk 360 optimal weight: 9.9990 chunk 31 optimal weight: 20.0000 chunk 155 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 145 optimal weight: 0.9990 chunk 251 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 649 GLN C 834 GLN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 HIS D 875 ASN G 50 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.184170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.146014 restraints weight = 51302.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.148417 restraints weight = 121966.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.149252 restraints weight = 62394.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.149759 restraints weight = 42887.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.150584 restraints weight = 37370.872| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 33497 Z= 0.188 Angle : 0.630 10.547 45782 Z= 0.337 Chirality : 0.044 0.270 5210 Planarity : 0.005 0.079 5542 Dihedral : 18.171 173.118 5628 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.83 % Favored : 94.98 % Rotamer: Outliers : 3.15 % Allowed : 14.14 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.27 % Twisted Proline : 0.68 % 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: -0.46 (0.13), residues: 3807 helix: 1.03 (0.13), residues: 1571 sheet: -0.53 (0.26), residues: 370 loop : -1.46 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 69 TYR 0.023 0.002 TYR D 46 PHE 0.017 0.002 PHE C1025 TRP 0.010 0.001 TRP G 36 HIS 0.006 0.001 HIS G 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 (33497) covalent geometry : angle 0.63017 / 0.34 (45782) hydrogen bonds : bond 0.05066 / 3.42 ( 1517) hydrogen bonds : angle 4.89602 / 3.41 ( 4226) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 362 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 369 MET cc_start: 0.8808 (ppp) cc_final: 0.8450 (ppp) REVERT: C 487 LEU cc_start: 0.6099 (OUTLIER) cc_final: 0.5727 (tp) REVERT: C 1146 GLN cc_start: 0.8057 (tp40) cc_final: 0.7810 (tp-100) REVERT: D 81 ARG cc_start: 0.7352 (ttp80) cc_final: 0.6992 (tmm-80) REVERT: D 727 ASP cc_start: 0.8127 (t0) cc_final: 0.7884 (t0) REVERT: D 743 MET cc_start: 0.8662 (ppp) cc_final: 0.8360 (ptm) REVERT: D 1095 MET cc_start: -0.0235 (tpp) cc_final: -0.1087 (tpp) REVERT: D 1243 LEU cc_start: 0.8614 (tp) cc_final: 0.7997 (mp) REVERT: F 100 MET cc_start: 0.2920 (ppp) cc_final: 0.1834 (mmt) REVERT: F 113 ARG cc_start: 0.4787 (tpt90) cc_final: 0.4196 (tpm170) REVERT: F 288 MET cc_start: -0.0574 (mmm) cc_final: -0.1295 (mmm) REVERT: F 322 MET cc_start: 0.4086 (mpp) cc_final: 0.3695 (mpp) REVERT: F 414 LYS cc_start: 0.7684 (mmmm) cc_final: 0.7383 (mttt) REVERT: F 433 TRP cc_start: 0.4339 (m100) cc_final: 0.3866 (m100) REVERT: A 185 TYR cc_start: 0.8246 (p90) cc_final: 0.7866 (p90) REVERT: B 68 TYR cc_start: 0.6115 (p90) cc_final: 0.5885 (p90) REVERT: G 36 TRP cc_start: 0.6071 (OUTLIER) cc_final: 0.5527 (p-90) REVERT: G 73 TRP cc_start: 0.6944 (t60) cc_final: 0.6317 (t60) outliers start: 103 outliers final: 68 residues processed: 432 average time/residue: 0.1926 time to fit residues: 137.5942 Evaluate side-chains 398 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 328 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 666 SER Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 845 LEU Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 925 GLU Chi-restraints excluded: chain D residue 1215 GLU Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 603 ARG Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 36 TRP Chi-restraints excluded: chain G residue 59 HIS Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 119 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 194 optimal weight: 0.7980 chunk 184 optimal weight: 5.9990 chunk 171 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 291 optimal weight: 0.3980 chunk 274 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 360 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 299 optimal weight: 30.0000 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 551 HIS C 834 GLN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 HIS D 651 HIS ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 406 GLN G 128 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.183331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.143522 restraints weight = 51018.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.145384 restraints weight = 119803.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.146573 restraints weight = 71676.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.147569 restraints weight = 44576.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.148148 restraints weight = 38434.797| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 33497 Z= 0.204 Angle : 0.643 14.297 45782 Z= 0.341 Chirality : 0.044 0.270 5210 Planarity : 0.005 0.074 5542 Dihedral : 18.141 172.817 5628 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.12 % Favored : 94.69 % Rotamer: Outliers : 3.21 % Allowed : 15.48 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.27 % Twisted Proline : 0.68 % 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 (0.13), residues: 3807 helix: 1.01 (0.13), residues: 1571 sheet: -0.58 (0.26), residues: 365 loop : -1.47 (0.13), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 60 TYR 0.022 0.001 TYR D 46 PHE 0.013 0.002 PHE F 306 TRP 0.010 0.001 TRP G 36 HIS 0.006 0.001 HIS G 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.20 (33497) covalent geometry : angle 0.64339 / 0.34 (45782) hydrogen bonds : bond 0.05038 / 3.38 ( 1517) hydrogen bonds : angle 4.84148 / 3.37 ( 4226) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 344 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 487 LEU cc_start: 0.6179 (OUTLIER) cc_final: 0.5824 (tp) REVERT: C 1329 GLU cc_start: 0.6719 (mt-10) cc_final: 0.6408 (mt-10) REVERT: D 81 ARG cc_start: 0.7406 (ttp80) cc_final: 0.7079 (tmm-80) REVERT: D 727 ASP cc_start: 0.8210 (t0) cc_final: 0.7948 (t0) REVERT: D 743 MET cc_start: 0.8693 (ppp) cc_final: 0.8418 (ptm) REVERT: D 1095 MET cc_start: -0.0129 (tpp) cc_final: -0.0951 (tpp) REVERT: D 1243 LEU cc_start: 0.8612 (tp) cc_final: 0.8020 (mp) REVERT: D 1290 ARG cc_start: 0.6962 (ttt-90) cc_final: 0.6506 (tmt-80) REVERT: F 100 MET cc_start: 0.3189 (ppp) cc_final: 0.1791 (mmm) REVERT: F 113 ARG cc_start: 0.4777 (tpt90) cc_final: 0.4186 (tpm170) REVERT: F 288 MET cc_start: -0.0293 (mmm) cc_final: -0.1063 (mmm) REVERT: F 433 TRP cc_start: 0.4495 (m100) cc_final: 0.3937 (m100) REVERT: A 185 TYR cc_start: 0.8327 (p90) cc_final: 0.8064 (p90) REVERT: B 68 TYR cc_start: 0.6218 (p90) cc_final: 0.5971 (p90) REVERT: G 36 TRP cc_start: 0.6110 (OUTLIER) cc_final: 0.5519 (p-90) REVERT: G 73 TRP cc_start: 0.7098 (t60) cc_final: 0.6522 (t60) outliers start: 105 outliers final: 78 residues processed: 420 average time/residue: 0.1833 time to fit residues: 126.9193 Evaluate side-chains 406 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 326 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 666 SER Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 845 LEU Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 190 LYS Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 925 GLU Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 603 ARG Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 36 TRP Chi-restraints excluded: chain G residue 59 HIS Chi-restraints excluded: chain G residue 109 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 101 optimal weight: 30.0000 chunk 304 optimal weight: 10.0000 chunk 212 optimal weight: 0.8980 chunk 91 optimal weight: 8.9990 chunk 42 optimal weight: 8.9990 chunk 26 optimal weight: 0.1980 chunk 124 optimal weight: 6.9990 chunk 109 optimal weight: 0.4980 chunk 357 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 HIS D 669 GLN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.183883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.145331 restraints weight = 51236.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.147142 restraints weight = 127037.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.148316 restraints weight = 66605.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.148650 restraints weight = 44131.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.149907 restraints weight = 38237.907| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 33497 Z= 0.196 Angle : 0.638 13.066 45782 Z= 0.339 Chirality : 0.044 0.269 5210 Planarity : 0.005 0.069 5542 Dihedral : 18.089 173.184 5628 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.23 % Favored : 94.59 % Rotamer: Outliers : 3.18 % Allowed : 15.88 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.27 % Twisted Proline : 0.68 % 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: -0.47 (0.13), residues: 3807 helix: 1.03 (0.13), residues: 1572 sheet: -0.66 (0.25), residues: 384 loop : -1.45 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 69 TYR 0.022 0.001 TYR D 46 PHE 0.020 0.002 PHE C1025 TRP 0.010 0.001 TRP G 36 HIS 0.006 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.20 (33497) covalent geometry : angle 0.63765 / 0.34 (45782) hydrogen bonds : bond 0.04980 / 3.34 ( 1517) hydrogen bonds : angle 4.82839 / 3.36 ( 4226) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 351 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 487 LEU cc_start: 0.6102 (OUTLIER) cc_final: 0.5760 (tp) REVERT: D 81 ARG cc_start: 0.7322 (ttp80) cc_final: 0.7021 (tmm-80) REVERT: D 727 ASP cc_start: 0.8263 (t0) cc_final: 0.7962 (t0) REVERT: D 1095 MET cc_start: -0.0127 (tpp) cc_final: -0.0898 (tpp) REVERT: D 1243 LEU cc_start: 0.8605 (tp) cc_final: 0.8067 (mp) REVERT: D 1290 ARG cc_start: 0.6947 (ttt-90) cc_final: 0.6615 (tmt-80) REVERT: F 100 MET cc_start: 0.3324 (ppp) cc_final: 0.1891 (tpt) REVERT: F 113 ARG cc_start: 0.4772 (tpt90) cc_final: 0.4196 (tpm170) REVERT: F 288 MET cc_start: -0.0291 (mmm) cc_final: -0.1031 (mmm) REVERT: F 433 TRP cc_start: 0.4407 (m100) cc_final: 0.3923 (m100) REVERT: B 68 TYR cc_start: 0.6022 (p90) cc_final: 0.5796 (p90) REVERT: G 36 TRP cc_start: 0.6074 (OUTLIER) cc_final: 0.5498 (p-90) REVERT: G 73 TRP cc_start: 0.7035 (t60) cc_final: 0.6333 (t60) outliers start: 104 outliers final: 87 residues processed: 425 average time/residue: 0.1927 time to fit residues: 135.2808 Evaluate side-chains 418 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 329 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 666 SER Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 845 LEU Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1026 GLU Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 190 LYS Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 720 ASN Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 603 ARG Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 36 TRP Chi-restraints excluded: chain G residue 59 HIS Chi-restraints excluded: chain G residue 109 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 310 optimal weight: 9.9990 chunk 182 optimal weight: 0.0970 chunk 206 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 205 optimal weight: 0.7980 chunk 60 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 276 optimal weight: 9.9990 chunk 287 optimal weight: 9.9990 chunk 233 optimal weight: 0.8980 overall best weight: 1.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 HIS ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.184801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.147092 restraints weight = 51174.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.149945 restraints weight = 115827.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.150267 restraints weight = 55626.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.150540 restraints weight = 41268.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.151112 restraints weight = 36216.044| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 33497 Z= 0.161 Angle : 0.622 13.001 45782 Z= 0.331 Chirality : 0.043 0.271 5210 Planarity : 0.004 0.068 5542 Dihedral : 18.021 172.834 5628 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.99 % Favored : 94.83 % Rotamer: Outliers : 2.90 % Allowed : 16.64 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.27 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.13), residues: 3807 helix: 1.07 (0.13), residues: 1584 sheet: -0.59 (0.25), residues: 380 loop : -1.40 (0.14), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 69 TYR 0.023 0.001 TYR D 46 PHE 0.024 0.002 PHE G 127 TRP 0.010 0.001 TRP G 36 HIS 0.007 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (33497) covalent geometry : angle 0.62229 / 0.33 (45782) hydrogen bonds : bond 0.04876 / 3.28 ( 1517) hydrogen bonds : angle 4.77366 / 3.32 ( 4226) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 351 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 239 MET cc_start: 0.5104 (tmm) cc_final: 0.4865 (tmm) REVERT: C 551 HIS cc_start: 0.7910 (t-90) cc_final: 0.7482 (t-90) REVERT: D 81 ARG cc_start: 0.7296 (ttp80) cc_final: 0.7020 (tmm-80) REVERT: D 180 MET cc_start: 0.7722 (ttp) cc_final: 0.7372 (ptt) REVERT: D 727 ASP cc_start: 0.8144 (t0) cc_final: 0.7889 (t0) REVERT: D 1095 MET cc_start: -0.0079 (tpp) cc_final: -0.0822 (tpp) REVERT: D 1243 LEU cc_start: 0.8611 (tp) cc_final: 0.8059 (mp) REVERT: D 1290 ARG cc_start: 0.6851 (ttt-90) cc_final: 0.6586 (tmt-80) REVERT: F 100 MET cc_start: 0.3359 (ppp) cc_final: 0.1722 (tpt) REVERT: F 105 MET cc_start: 0.5201 (ppp) cc_final: 0.4294 (ppp) REVERT: F 113 ARG cc_start: 0.4862 (tpt90) cc_final: 0.4541 (tpm170) REVERT: F 288 MET cc_start: -0.0252 (mmm) cc_final: -0.1016 (mmm) REVERT: F 433 TRP cc_start: 0.4336 (m100) cc_final: 0.3905 (m100) REVERT: F 540 LEU cc_start: 0.7378 (tp) cc_final: 0.6918 (tp) REVERT: A 185 TYR cc_start: 0.8078 (p90) cc_final: 0.7703 (p90) REVERT: B 68 TYR cc_start: 0.5938 (p90) cc_final: 0.5690 (p90) REVERT: G 36 TRP cc_start: 0.6011 (OUTLIER) cc_final: 0.5490 (p-90) REVERT: G 73 TRP cc_start: 0.6966 (t60) cc_final: 0.6277 (t60) outliers start: 95 outliers final: 77 residues processed: 420 average time/residue: 0.1880 time to fit residues: 129.5166 Evaluate side-chains 402 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 324 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 666 SER Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 845 LEU Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1026 GLU Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 190 LYS Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 720 ASN Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 603 ARG Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain G residue 36 TRP Chi-restraints excluded: chain G residue 59 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 144 optimal weight: 4.9990 chunk 288 optimal weight: 0.1980 chunk 338 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 328 optimal weight: 0.3980 chunk 310 optimal weight: 10.0000 chunk 176 optimal weight: 0.5980 chunk 312 optimal weight: 0.1980 chunk 207 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 219 optimal weight: 9.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 65 ASN C 330 HIS C 462 ASN ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 ASN D 340 GLN ** D 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 HIS ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 50 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.186819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.150412 restraints weight = 51165.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.153134 restraints weight = 113565.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.153089 restraints weight = 51186.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.153274 restraints weight = 42216.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.153985 restraints weight = 35399.013| |-----------------------------------------------------------------------------| r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 33497 Z= 0.130 Angle : 0.624 14.914 45782 Z= 0.329 Chirality : 0.043 0.275 5210 Planarity : 0.004 0.070 5542 Dihedral : 17.947 173.075 5628 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.70 % Favored : 95.11 % Rotamer: Outliers : 2.38 % Allowed : 17.22 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.27 % Twisted Proline : 0.68 % 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: -0.28 (0.13), residues: 3807 helix: 1.14 (0.13), residues: 1580 sheet: -0.52 (0.26), residues: 368 loop : -1.31 (0.14), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 69 TYR 0.036 0.001 TYR B 177 PHE 0.049 0.002 PHE D1325 TRP 0.011 0.001 TRP G 36 HIS 0.005 0.001 HIS C1244 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (33497) covalent geometry : angle 0.62357 / 0.33 (45782) hydrogen bonds : bond 0.04794 / 3.24 ( 1517) hydrogen bonds : angle 4.71614 / 3.29 ( 4226) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 352 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 487 LEU cc_start: 0.6234 (OUTLIER) cc_final: 0.5822 (tp) REVERT: C 551 HIS cc_start: 0.7819 (t-90) cc_final: 0.7464 (t-90) REVERT: C 1231 TYR cc_start: 0.8883 (t80) cc_final: 0.8390 (t80) REVERT: C 1308 ILE cc_start: 0.9096 (mm) cc_final: 0.8862 (mm) REVERT: D 180 MET cc_start: 0.7637 (ttp) cc_final: 0.7322 (ptt) REVERT: D 727 ASP cc_start: 0.8063 (t0) cc_final: 0.7826 (t0) REVERT: D 1095 MET cc_start: -0.0134 (tpp) cc_final: -0.0838 (tpp) REVERT: D 1243 LEU cc_start: 0.8586 (tp) cc_final: 0.8043 (mp) REVERT: D 1314 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7536 (mt) REVERT: D 1326 GLN cc_start: 0.6812 (mp10) cc_final: 0.6423 (mp10) REVERT: E 42 GLU cc_start: 0.5676 (mp0) cc_final: 0.5211 (mp0) REVERT: F 100 MET cc_start: 0.3129 (ppp) cc_final: 0.1707 (tpt) REVERT: F 102 MET cc_start: 0.4502 (mmm) cc_final: 0.3383 (mmm) REVERT: F 105 MET cc_start: 0.5076 (ppp) cc_final: 0.4338 (ppp) REVERT: F 113 ARG cc_start: 0.4840 (tpt90) cc_final: 0.4580 (tpm170) REVERT: F 288 MET cc_start: -0.0235 (mmm) cc_final: -0.1444 (ppp) REVERT: F 297 MET cc_start: 0.1092 (ppp) cc_final: -0.1809 (tpt) REVERT: F 433 TRP cc_start: 0.4174 (m100) cc_final: 0.3848 (m100) REVERT: A 185 TYR cc_start: 0.8073 (p90) cc_final: 0.7704 (p90) REVERT: G 36 TRP cc_start: 0.6041 (OUTLIER) cc_final: 0.5528 (p-90) REVERT: G 73 TRP cc_start: 0.6910 (t60) cc_final: 0.6253 (t60) outliers start: 78 outliers final: 60 residues processed: 406 average time/residue: 0.1881 time to fit residues: 125.3724 Evaluate side-chains 382 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 319 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 845 LEU Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1026 GLU Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 720 ASN Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain E residue 72 GLN Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 603 ARG Chi-restraints excluded: chain F residue 611 LEU Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain G residue 36 TRP Chi-restraints excluded: chain G residue 59 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 62 optimal weight: 0.9990 chunk 326 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 160 optimal weight: 7.9990 chunk 389 optimal weight: 50.0000 chunk 103 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 356 optimal weight: 7.9990 chunk 380 optimal weight: 50.0000 chunk 123 optimal weight: 0.5980 chunk 98 optimal weight: 0.3980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 462 ASN ** C 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 HIS B 227 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.183684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.143928 restraints weight = 51374.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.145867 restraints weight = 118957.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.146778 restraints weight = 70634.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.147694 restraints weight = 44657.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.148372 restraints weight = 39168.413| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 33497 Z= 0.210 Angle : 0.668 12.193 45782 Z= 0.351 Chirality : 0.045 0.275 5210 Planarity : 0.005 0.073 5542 Dihedral : 17.967 173.227 5628 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.17 % Favored : 94.64 % Rotamer: Outliers : 2.38 % Allowed : 17.68 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.27 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.13), residues: 3807 helix: 1.09 (0.13), residues: 1577 sheet: -0.51 (0.24), residues: 410 loop : -1.39 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG G 111 TYR 0.038 0.002 TYR B 177 PHE 0.032 0.002 PHE D1325 TRP 0.014 0.001 TRP D 409 HIS 0.008 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 (33497) covalent geometry : angle 0.66793 / 0.35 (45782) hydrogen bonds : bond 0.04826 / 3.23 ( 1517) hydrogen bonds : angle 4.80282 / 3.35 ( 4226) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7614 Ramachandran restraints generated. 3807 Oldfield, 0 Emsley, 3807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 329 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 487 LEU cc_start: 0.6356 (OUTLIER) cc_final: 0.5838 (tp) REVERT: C 551 HIS cc_start: 0.7893 (t-90) cc_final: 0.7465 (t-90) REVERT: C 1231 TYR cc_start: 0.8953 (t80) cc_final: 0.8429 (t80) REVERT: C 1308 ILE cc_start: 0.9141 (mm) cc_final: 0.8894 (mm) REVERT: D 180 MET cc_start: 0.7722 (ttp) cc_final: 0.7390 (ptt) REVERT: D 727 ASP cc_start: 0.8287 (t0) cc_final: 0.8004 (t0) REVERT: D 770 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8632 (mt) REVERT: D 1095 MET cc_start: 0.0058 (tpp) cc_final: -0.0694 (tpp) REVERT: D 1243 LEU cc_start: 0.8624 (tp) cc_final: 0.8098 (mp) REVERT: F 100 MET cc_start: 0.3392 (ppp) cc_final: 0.1713 (tpt) REVERT: F 102 MET cc_start: 0.4548 (mmm) cc_final: 0.3318 (mmm) REVERT: F 105 MET cc_start: 0.5042 (ppp) cc_final: 0.4334 (ppp) REVERT: F 113 ARG cc_start: 0.4722 (tpt90) cc_final: 0.4461 (tpm170) REVERT: F 288 MET cc_start: -0.0471 (mmm) cc_final: -0.1295 (ppp) REVERT: F 433 TRP cc_start: 0.4528 (m100) cc_final: 0.3978 (m100) REVERT: F 456 MET cc_start: 0.8463 (tpp) cc_final: 0.8245 (tpt) REVERT: F 540 LEU cc_start: 0.7415 (tp) cc_final: 0.7030 (tp) REVERT: A 185 TYR cc_start: 0.8172 (p90) cc_final: 0.7803 (p90) REVERT: G 36 TRP cc_start: 0.6148 (OUTLIER) cc_final: 0.5639 (p-90) REVERT: G 50 ASN cc_start: 0.5319 (p0) cc_final: 0.4908 (m-40) REVERT: G 67 ARG cc_start: 0.7284 (tpp-160) cc_final: 0.6988 (tpp-160) REVERT: G 73 TRP cc_start: 0.7127 (t60) cc_final: 0.6391 (t60) REVERT: G 99 ARG cc_start: 0.3548 (ttt180) cc_final: 0.2967 (tpp80) outliers start: 78 outliers final: 60 residues processed: 387 average time/residue: 0.1882 time to fit residues: 119.9232 Evaluate side-chains 377 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 314 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 666 SER Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 845 LEU Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 1026 GLU Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 190 LYS Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain E residue 72 GLN Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 603 ARG Chi-restraints excluded: chain F residue 611 LEU Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain G residue 36 TRP Chi-restraints excluded: chain G residue 59 HIS Chi-restraints excluded: chain G residue 81 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 33 optimal weight: 20.0000 chunk 108 optimal weight: 0.6980 chunk 37 optimal weight: 8.9990 chunk 288 optimal weight: 20.0000 chunk 263 optimal weight: 0.7980 chunk 324 optimal weight: 10.0000 chunk 316 optimal weight: 5.9990 chunk 218 optimal weight: 2.9990 chunk 384 optimal weight: 30.0000 chunk 245 optimal weight: 3.9990 chunk 372 optimal weight: 0.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 834 GLN ** C1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 HIS D 712 GLN B 227 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.184491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.145593 restraints weight = 51398.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.148039 restraints weight = 121032.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.149079 restraints weight = 62563.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.149520 restraints weight = 42612.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.150431 restraints weight = 37269.142| |-----------------------------------------------------------------------------| r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 33497 Z= 0.175 Angle : 0.657 13.623 45782 Z= 0.344 Chirality : 0.044 0.275 5210 Planarity : 0.005 0.072 5542 Dihedral : 17.932 172.930 5628 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.86 % Favored : 94.98 % Rotamer: Outliers : 2.50 % Allowed : 17.77 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.27 % Twisted Proline : 0.68 % 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: -0.38 (0.13), residues: 3807 helix: 1.03 (0.13), residues: 1582 sheet: -0.55 (0.25), residues: 394 loop : -1.36 (0.14), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG G 111 TYR 0.033 0.002 TYR B 177 PHE 0.030 0.002 PHE D1325 TRP 0.011 0.001 TRP G 36 HIS 0.007 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (33497) covalent geometry : angle 0.65663 / 0.34 (45782) hydrogen bonds : bond 0.04761 / 3.20 ( 1517) hydrogen bonds : angle 4.77977 / 3.33 ( 4226) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5306.06 seconds wall clock time: 92 minutes 46.50 seconds (5566.50 seconds total)