Starting phenix.real_space_refine on Tue Aug 26 03:05:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k59_36898/08_2025/8k59_36898.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k59_36898/08_2025/8k59_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_2025/8k59_36898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k59_36898/08_2025/8k59_36898.map" model { file = "/net/cci-nas-00/data/ceres_data/8k59_36898/08_2025/8k59_36898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k59_36898/08_2025/8k59_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 6.17, per 1000 atoms: 0.19 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: 2.32 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 238.4 nanoseconds 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: 4.95 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: 9.19 Time building geometry restraints manager: 3.03 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=" C GLU D 925 " pdb=" N PRO D 926 " ideal model delta sigma weight residual 1.335 1.354 -0.019 9.40e-03 1.13e+04 4.04e+00 bond pdb=" CB PRO D1191 " pdb=" CG PRO D1191 " ideal model delta sigma weight residual 1.492 1.592 -0.100 5.00e-02 4.00e+02 3.97e+00 bond pdb=" N THR D1178 " pdb=" CA THR D1178 " ideal model delta sigma weight residual 1.463 1.444 0.019 1.22e-02 6.72e+03 2.40e+00 bond pdb=" N GLU B 193 " pdb=" CA GLU B 193 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.29e-02 6.01e+03 2.38e+00 bond pdb=" CB PRO D1185 " pdb=" CG PRO D1185 " ideal model delta sigma weight residual 1.492 1.561 -0.069 5.00e-02 4.00e+02 1.91e+00 ... (remaining 33492 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 45485 3.21 - 6.41: 273 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: 4128 0.047 - 0.095: 858 0.095 - 0.142: 208 0.142 - 0.189: 13 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: 2.540 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: 0.040 Extract box with map and model: 0.560 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 32.730 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6581 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= 0.187 Angle : 0.712 16.034 45782 Z= 0.421 Chirality : 0.041 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 aren 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 covalent geometry : bond 0.00384 (33497) covalent geometry : angle 0.71207 (45782) hydrogen bonds : bond 0.15689 ( 1517) hydrogen bonds : angle 6.68737 ( 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 : 1.148 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: 0.7088 (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: 0.6346 (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: 0.7681 (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: 0.8029 (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: 0.7747 (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: 0.7295 (t) REVERT: C 1259 LEU cc_start: 0.6059 (tp) cc_final: 0.5744 (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: 0.8752 (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: 0.7679 (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: 0.7198 (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: 0.7753 (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: 0.7984 (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: 0.6352 (pm20) REVERT: D 1243 LEU cc_start: 0.8023 (tp) cc_final: 0.7700 (tp) REVERT: D 1244 GLN cc_start: 0.7955 (mm110) cc_final: 0.7677 (mp10) REVERT: D 1281 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8279 (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: 0.7533 (mm-30) REVERT: E 11 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7479 (mm-30) REVERT: E 61 ASN cc_start: 0.6260 (p0) cc_final: 0.5388 (p0) REVERT: F 100 MET cc_start: 0.2939 (ppp) cc_final: 0.2183 (tpp) REVERT: F 288 MET cc_start: -0.0249 (mmm) cc_final: -0.0826 (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 392 LYS cc_start: 0.7409 (mtmt) cc_final: 0.6706 (tppt) 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: 0.5355 (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: 0.7649 (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: 0.3896 (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: 0.2393 time to fit residues: 294.4277 Evaluate side-chains 467 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 467 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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: 20.0000 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... Flipped N/Q/H residues before XYZ refinement: C 46 GLN C 65 ASN C 133 ASN C 490 GLN C 519 ASN C 677 ASN C 799 ASN C1288 GLN C1299 ASN ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 HIS ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1197 ASN D1279 GLN F 383 ASN F 409 ASN B 37 HIS B 41 ASN ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.184961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.137145 restraints weight = 51926.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.132814 restraints weight = 55614.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.135176 restraints weight = 55835.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.135052 restraints weight = 37311.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.138470 restraints weight = 32231.651| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.119 33497 Z= 0.315 Angle : 0.753 10.904 45782 Z= 0.396 Chirality : 0.047 0.242 5210 Planarity : 0.006 0.084 5542 Dihedral : 18.267 172.750 5628 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.36 % Favored : 94.35 % Rotamer: Outliers : 2.35 % Allowed : 10.29 % Favored : 87.36 % 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 aren not related in a simple way. whole: -0.49 (0.13), residues: 3807 helix: 0.99 (0.13), residues: 1552 sheet: -0.59 (0.26), residues: 368 loop : -1.41 (0.13), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 297 TYR 0.040 0.002 TYR D 46 PHE 0.023 0.002 PHE D1325 TRP 0.010 0.002 TRP D 409 HIS 0.009 0.002 HIS D1366 Details of bonding type rmsd covalent geometry : bond 0.00748 (33497) covalent geometry : angle 0.75337 (45782) hydrogen bonds : bond 0.05524 ( 1517) hydrogen bonds : angle 5.28847 ( 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 545 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 468 time to evaluate : 1.170 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 371 ARG cc_start: 0.7619 (mpt-90) cc_final: 0.7210 (mmm-85) REVERT: C 414 ILE cc_start: 0.8329 (pt) cc_final: 0.8084 (mm) REVERT: C 423 ASP cc_start: 0.7961 (m-30) cc_final: 0.7687 (m-30) REVERT: C 478 ARG cc_start: 0.7087 (tpt90) cc_final: 0.6716 (tpt90) REVERT: C 559 CYS cc_start: 0.8687 (t) cc_final: 0.8435 (t) REVERT: C 737 ASN cc_start: 0.7523 (m-40) cc_final: 0.7221 (m-40) REVERT: C 1146 GLN cc_start: 0.8353 (tp40) cc_final: 0.7860 (tp-100) REVERT: C 1229 TYR cc_start: 0.8598 (m-80) cc_final: 0.8379 (m-80) REVERT: C 1296 ASP cc_start: 0.7085 (m-30) cc_final: 0.6830 (m-30) REVERT: D 164 GLN cc_start: 0.8058 (tm-30) cc_final: 0.7832 (tm-30) REVERT: D 166 LEU cc_start: 0.9075 (tp) cc_final: 0.8444 (tp) REVERT: D 196 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7558 (pp30) REVERT: D 680 ASN cc_start: 0.8336 (t0) cc_final: 0.8047 (t0) REVERT: D 681 LYS cc_start: 0.8421 (tppt) cc_final: 0.8146 (mmtp) REVERT: D 727 ASP cc_start: 0.8435 (t0) cc_final: 0.8151 (t0) REVERT: D 790 THR cc_start: 0.8990 (m) cc_final: 0.8680 (p) REVERT: D 1243 LEU cc_start: 0.8743 (tp) cc_final: 0.8015 (mp) REVERT: E 11 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7576 (mm-30) REVERT: E 52 ARG cc_start: 0.8207 (mtp85) cc_final: 0.7895 (mtp180) REVERT: F 100 MET cc_start: 0.2819 (ppp) cc_final: 0.1576 (mtp) REVERT: F 288 MET cc_start: -0.0808 (mmm) cc_final: -0.1318 (mmm) REVERT: F 392 LYS cc_start: 0.7634 (mtmt) cc_final: 0.7431 (tppt) REVERT: F 419 PHE cc_start: 0.5314 (t80) cc_final: 0.5068 (t80) REVERT: F 433 TRP cc_start: 0.5107 (m100) cc_final: 0.4030 (m100) REVERT: F 541 ARG cc_start: 0.7366 (mtt-85) cc_final: 0.6970 (tmt170) REVERT: F 611 LEU cc_start: 0.7735 (mt) cc_final: 0.7182 (pp) REVERT: A 185 TYR cc_start: 0.8555 (p90) cc_final: 0.8202 (p90) REVERT: B 68 TYR cc_start: 0.7565 (p90) cc_final: 0.7099 (p90) REVERT: B 129 VAL cc_start: 0.9120 (t) cc_final: 0.8754 (p) REVERT: B 194 GLN cc_start: 0.7003 (pp30) cc_final: 0.6729 (pp30) REVERT: G 73 TRP cc_start: 0.7751 (t60) cc_final: 0.7128 (t60) outliers start: 77 outliers final: 47 residues processed: 523 average time/residue: 0.2182 time to fit residues: 178.8968 Evaluate side-chains 382 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 334 time to evaluate : 1.170 ------------------------------------------------------------------------------- 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 442 VAL Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 600 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 736 VAL Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 873 ILE Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 1024 GLU 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 D residue 44 ILE Chi-restraints excluded: chain D residue 196 GLN Chi-restraints excluded: chain D residue 201 LEU 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 641 ILE Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 925 GLU Chi-restraints excluded: chain D residue 1230 THR Chi-restraints excluded: chain D residue 1290 ARG 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 F residue 466 ILE Chi-restraints excluded: chain F residue 506 SER Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 59 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 46 optimal weight: 1.9990 chunk 272 optimal weight: 0.4980 chunk 298 optimal weight: 6.9990 chunk 377 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 329 optimal weight: 2.9990 chunk 367 optimal weight: 3.9990 chunk 188 optimal weight: 0.5980 chunk 149 optimal weight: 9.9990 chunk 291 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 447 HIS C 490 GLN ** C 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 834 GLN C1244 HIS ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN D 651 HIS D 669 GLN ** D 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 875 ASN F 464 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.186820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.148355 restraints weight = 51244.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.147876 restraints weight = 119755.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.149928 restraints weight = 87517.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.150090 restraints weight = 56710.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.151051 restraints weight = 49118.990| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33497 Z= 0.138 Angle : 0.597 9.794 45782 Z= 0.317 Chirality : 0.042 0.179 5210 Planarity : 0.004 0.053 5542 Dihedral : 17.926 169.475 5628 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.47 % Favored : 95.30 % Rotamer: Outliers : 2.53 % Allowed : 12.58 % Favored : 84.89 % 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 aren not related in a simple way. whole: -0.28 (0.13), residues: 3807 helix: 1.15 (0.13), residues: 1576 sheet: -0.43 (0.26), residues: 341 loop : -1.33 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 69 TYR 0.029 0.001 TYR D 46 PHE 0.016 0.001 PHE F 306 TRP 0.009 0.001 TRP G 36 HIS 0.006 0.001 HIS C1244 Details of bonding type rmsd covalent geometry : bond 0.00313 (33497) covalent geometry : angle 0.59718 (45782) hydrogen bonds : bond 0.04897 ( 1517) hydrogen bonds : angle 4.88282 ( 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: 83 poor density : 431 time to evaluate : 1.110 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 1259 LEU cc_start: 0.6326 (tp) cc_final: 0.6009 (tp) REVERT: D 81 ARG cc_start: 0.7366 (ttp80) cc_final: 0.7030 (tmm-80) REVERT: D 805 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.8004 (tm-30) REVERT: D 821 MET cc_start: 0.7228 (tpp) cc_final: 0.6925 (tpt) REVERT: D 1095 MET cc_start: -0.0211 (tpp) cc_final: -0.0948 (tpp) REVERT: D 1243 LEU cc_start: 0.8536 (tp) cc_final: 0.7959 (mp) REVERT: D 1326 GLN cc_start: 0.7031 (mp10) cc_final: 0.4506 (tp40) REVERT: E 30 MET cc_start: 0.7542 (tpp) cc_final: 0.7026 (tpp) REVERT: F 100 MET cc_start: 0.2589 (ppp) cc_final: 0.2030 (tpp) REVERT: F 113 ARG cc_start: 0.4796 (tpt90) cc_final: 0.4226 (tpm170) REVERT: F 288 MET cc_start: -0.0506 (mmm) cc_final: -0.0957 (ppp) REVERT: F 297 MET cc_start: 0.0965 (ppp) cc_final: -0.1752 (tpt) REVERT: F 433 TRP cc_start: 0.4356 (m100) cc_final: 0.3901 (m100) REVERT: F 540 LEU cc_start: 0.7391 (tp) cc_final: 0.6929 (tp) REVERT: A 185 TYR cc_start: 0.8142 (p90) cc_final: 0.7809 (p90) REVERT: B 68 TYR cc_start: 0.6199 (p90) cc_final: 0.5926 (p90) REVERT: G 36 TRP cc_start: 0.6110 (OUTLIER) cc_final: 0.5549 (p-90) REVERT: G 73 TRP cc_start: 0.6956 (t60) cc_final: 0.6326 (t60) outliers start: 83 outliers final: 51 residues processed: 484 average time/residue: 0.2082 time to fit residues: 162.1818 Evaluate side-chains 402 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 349 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 347 ILE 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 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 862 LEU 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 1056 VAL 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 D residue 29 MET Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 92 VAL 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 416 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 528 THR Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 925 GLU 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 59 ILE Chi-restraints excluded: chain F residue 466 ILE 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 233 optimal weight: 0.0670 chunk 209 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 372 optimal weight: 20.0000 chunk 272 optimal weight: 7.9990 chunk 348 optimal weight: 5.9990 chunk 281 optimal weight: 50.0000 chunk 315 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 190 optimal weight: 0.7980 chunk 331 optimal weight: 8.9990 overall best weight: 2.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 GLN C 551 HIS C 649 GLN C 673 HIS C 834 GLN ** D 158 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 680 ASN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 875 ASN G 50 ASN G 128 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.184102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.144608 restraints weight = 50958.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.146259 restraints weight = 115158.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.147608 restraints weight = 73696.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.147059 restraints weight = 56856.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.148266 restraints weight = 45426.375| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 33497 Z= 0.193 Angle : 0.621 8.394 45782 Z= 0.329 Chirality : 0.043 0.179 5210 Planarity : 0.004 0.065 5542 Dihedral : 17.882 170.691 5628 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.10 % Favored : 94.69 % Rotamer: Outliers : 3.24 % Allowed : 13.74 % Favored : 83.02 % 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 aren not related in a simple way. whole: -0.33 (0.13), residues: 3807 helix: 1.13 (0.13), residues: 1580 sheet: -0.47 (0.25), residues: 385 loop : -1.39 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 69 TYR 0.035 0.002 TYR G 8 PHE 0.026 0.002 PHE D1325 TRP 0.010 0.001 TRP G 36 HIS 0.005 0.001 HIS D 777 Details of bonding type rmsd covalent geometry : bond 0.00454 (33497) covalent geometry : angle 0.62054 (45782) hydrogen bonds : bond 0.04769 ( 1517) hydrogen bonds : angle 4.80793 ( 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 489 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 383 time to evaluate : 1.204 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 179 TYR cc_start: 0.7107 (t80) cc_final: 0.6727 (t80) REVERT: C 369 MET cc_start: 0.8767 (ppp) cc_final: 0.8508 (ppp) REVERT: C 487 LEU cc_start: 0.6295 (OUTLIER) cc_final: 0.5814 (tp) REVERT: C 737 ASN cc_start: 0.6896 (m-40) cc_final: 0.6680 (m-40) REVERT: C 1259 LEU cc_start: 0.6443 (tp) cc_final: 0.6144 (tp) REVERT: C 1296 ASP cc_start: 0.7201 (m-30) cc_final: 0.6912 (m-30) REVERT: C 1329 GLU cc_start: 0.6806 (mt-10) cc_final: 0.6401 (mt-10) REVERT: D 81 ARG cc_start: 0.7337 (ttp80) cc_final: 0.7021 (tmm-80) REVERT: D 330 MET cc_start: 0.7501 (ptm) cc_final: 0.7215 (ptm) REVERT: D 712 GLN cc_start: 0.7932 (tm-30) cc_final: 0.7721 (tm-30) REVERT: D 727 ASP cc_start: 0.8081 (t0) cc_final: 0.7852 (t0) REVERT: D 1095 MET cc_start: 0.0016 (tpp) cc_final: -0.0716 (tpp) REVERT: D 1243 LEU cc_start: 0.8571 (tp) cc_final: 0.8031 (mp) REVERT: F 100 MET cc_start: 0.3060 (ppp) cc_final: 0.1756 (mmm) REVERT: F 105 MET cc_start: 0.5223 (ppp) cc_final: 0.4285 (ppp) REVERT: F 113 ARG cc_start: 0.4743 (tpt90) cc_final: 0.4357 (tpm170) REVERT: F 288 MET cc_start: -0.0194 (mmm) cc_final: -0.1307 (ppp) REVERT: F 433 TRP cc_start: 0.4453 (m100) cc_final: 0.3957 (m100) REVERT: F 603 ARG cc_start: 0.4340 (mpp80) cc_final: 0.3106 (mmt90) REVERT: B 68 TYR cc_start: 0.6199 (p90) cc_final: 0.5907 (p90) REVERT: G 36 TRP cc_start: 0.6083 (OUTLIER) cc_final: 0.5565 (p-90) REVERT: G 73 TRP cc_start: 0.6976 (t60) cc_final: 0.6164 (t60) outliers start: 106 outliers final: 69 residues processed: 458 average time/residue: 0.2062 time to fit residues: 153.6112 Evaluate side-chains 412 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 341 time to evaluate : 1.229 ------------------------------------------------------------------------------- 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 516 ASP Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 615 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 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 953 LEU Chi-restraints excluded: chain C residue 1024 GLU 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 160 LEU Chi-restraints excluded: chain D residue 198 CYS 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 416 ILE 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 590 SER Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 925 GLU Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1290 ARG 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 F residue 365 MET Chi-restraints excluded: chain F residue 386 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 69 SER 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 129 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain G residue 6 VAL 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 119 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 1 optimal weight: 6.9990 chunk 157 optimal weight: 0.9980 chunk 185 optimal weight: 5.9990 chunk 243 optimal weight: 30.0000 chunk 264 optimal weight: 0.9990 chunk 360 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 chunk 114 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 251 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 649 GLN C 834 GLN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 HIS D 805 GLN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.185297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.148717 restraints weight = 51388.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.151507 restraints weight = 114810.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.151100 restraints weight = 51885.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.151431 restraints weight = 43459.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.151803 restraints weight = 36396.986| |-----------------------------------------------------------------------------| r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33497 Z= 0.151 Angle : 0.590 10.805 45782 Z= 0.312 Chirality : 0.042 0.199 5210 Planarity : 0.004 0.061 5542 Dihedral : 17.786 170.054 5628 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.62 % Favored : 95.19 % Rotamer: Outliers : 2.81 % Allowed : 15.48 % Favored : 81.71 % 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 aren not related in a simple way. whole: -0.20 (0.13), residues: 3807 helix: 1.25 (0.13), residues: 1558 sheet: -0.45 (0.26), residues: 375 loop : -1.29 (0.14), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 69 TYR 0.025 0.001 TYR B 177 PHE 0.017 0.001 PHE D1325 TRP 0.009 0.001 TRP D1193 HIS 0.004 0.001 HIS G 59 Details of bonding type rmsd covalent geometry : bond 0.00347 (33497) covalent geometry : angle 0.58982 (45782) hydrogen bonds : bond 0.04620 ( 1517) hydrogen bonds : angle 4.69615 ( 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 464 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 372 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: C 179 TYR cc_start: 0.7170 (t80) cc_final: 0.6768 (t80) REVERT: C 1259 LEU cc_start: 0.6266 (tp) cc_final: 0.5971 (tp) REVERT: C 1329 GLU cc_start: 0.6762 (mt-10) cc_final: 0.6036 (mt-10) REVERT: D 81 ARG cc_start: 0.7257 (ttp80) cc_final: 0.7000 (tmm-80) REVERT: D 133 ARG cc_start: 0.6628 (ttm110) cc_final: 0.6203 (ptp90) REVERT: D 330 MET cc_start: 0.7514 (ptm) cc_final: 0.7046 (ptm) REVERT: D 1095 MET cc_start: -0.0075 (tpp) cc_final: -0.0749 (tpp) REVERT: D 1243 LEU cc_start: 0.8564 (tp) cc_final: 0.8062 (mp) REVERT: F 100 MET cc_start: 0.3126 (ppp) cc_final: 0.2079 (tpt) REVERT: F 105 MET cc_start: 0.5044 (ppp) cc_final: 0.4280 (ppp) REVERT: F 113 ARG cc_start: 0.4899 (tpt90) cc_final: 0.4464 (tpm170) REVERT: F 288 MET cc_start: -0.0269 (mmm) cc_final: -0.1024 (ppp) REVERT: F 297 MET cc_start: 0.0934 (ppp) cc_final: -0.1851 (tpt) REVERT: F 414 LYS cc_start: 0.7333 (mmmm) cc_final: 0.7039 (mtpt) REVERT: F 433 TRP cc_start: 0.4216 (m100) cc_final: 0.3884 (m100) REVERT: F 603 ARG cc_start: 0.4064 (mpp80) cc_final: 0.3017 (mmt90) REVERT: A 185 TYR cc_start: 0.7950 (p90) cc_final: 0.7533 (p90) REVERT: B 68 TYR cc_start: 0.5817 (p90) cc_final: 0.5583 (p90) REVERT: G 36 TRP cc_start: 0.6026 (OUTLIER) cc_final: 0.5456 (p-90) outliers start: 92 outliers final: 64 residues processed: 432 average time/residue: 0.2093 time to fit residues: 145.5618 Evaluate side-chains 399 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 334 time to evaluate : 1.157 ------------------------------------------------------------------------------- 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 516 ASP Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 615 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 748 ILE 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 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 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 416 ILE 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 697 MET 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 1281 GLU Chi-restraints excluded: chain D residue 1307 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 365 MET 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 69 SER Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 129 VAL 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 119 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 194 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 291 optimal weight: 4.9990 chunk 274 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 360 optimal weight: 9.9990 chunk 118 optimal weight: 0.9990 chunk 299 optimal weight: 20.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 165 HIS ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 737 ASN C 799 ASN ** D 158 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 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 HIS A 41 ASN G 50 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.184315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.148187 restraints weight = 51245.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.150826 restraints weight = 116475.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.149849 restraints weight = 50418.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.150205 restraints weight = 38640.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.150557 restraints weight = 34057.648| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 33497 Z= 0.167 Angle : 0.609 14.083 45782 Z= 0.319 Chirality : 0.042 0.213 5210 Planarity : 0.004 0.060 5542 Dihedral : 17.705 170.315 5628 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.10 % Favored : 94.72 % Rotamer: Outliers : 3.08 % Allowed : 15.88 % Favored : 81.04 % 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 aren not related in a simple way. whole: -0.20 (0.13), residues: 3807 helix: 1.26 (0.13), residues: 1559 sheet: -0.35 (0.25), residues: 381 loop : -1.32 (0.14), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 69 TYR 0.027 0.001 TYR B 177 PHE 0.015 0.001 PHE D1325 TRP 0.009 0.001 TRP D1193 HIS 0.007 0.001 HIS G 59 Details of bonding type rmsd covalent geometry : bond 0.00390 (33497) covalent geometry : angle 0.60908 (45782) hydrogen bonds : bond 0.04560 ( 1517) hydrogen bonds : angle 4.66611 ( 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 464 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 363 time to evaluate : 1.084 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 179 TYR cc_start: 0.7275 (t80) cc_final: 0.6889 (t80) REVERT: C 487 LEU cc_start: 0.6306 (OUTLIER) cc_final: 0.5825 (tp) REVERT: C 551 HIS cc_start: 0.7797 (t-90) cc_final: 0.7401 (t-90) REVERT: C 1216 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7446 (mtp85) REVERT: C 1259 LEU cc_start: 0.6417 (tp) cc_final: 0.6087 (tp) REVERT: C 1329 GLU cc_start: 0.6783 (mt-10) cc_final: 0.6224 (mt-10) REVERT: D 1243 LEU cc_start: 0.8598 (tp) cc_final: 0.8111 (mp) REVERT: F 100 MET cc_start: 0.3337 (OUTLIER) cc_final: 0.1745 (mmm) REVERT: F 105 MET cc_start: 0.5052 (ppp) cc_final: 0.4325 (ppp) REVERT: F 113 ARG cc_start: 0.4825 (tpt90) cc_final: 0.4363 (tpm170) REVERT: F 288 MET cc_start: -0.0175 (mmm) cc_final: -0.1589 (ptm) REVERT: F 297 MET cc_start: 0.0828 (ppp) cc_final: -0.2015 (ttp) REVERT: F 414 LYS cc_start: 0.7405 (mmmm) cc_final: 0.6622 (ttmt) REVERT: F 433 TRP cc_start: 0.4300 (m100) cc_final: 0.3936 (m100) REVERT: A 185 TYR cc_start: 0.8172 (p90) cc_final: 0.7818 (p90) REVERT: B 68 TYR cc_start: 0.5924 (p90) cc_final: 0.5652 (p90) REVERT: G 36 TRP cc_start: 0.6134 (OUTLIER) cc_final: 0.5577 (p-90) REVERT: G 73 TRP cc_start: 0.6928 (t60) cc_final: 0.6394 (t60) outliers start: 101 outliers final: 79 residues processed: 432 average time/residue: 0.2098 time to fit residues: 146.8684 Evaluate side-chains 417 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 334 time to evaluate : 1.168 ------------------------------------------------------------------------------- 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 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 516 ASP Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 635 THR 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 748 ILE 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 1056 VAL Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1216 ARG 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 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 416 ILE 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 697 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 925 GLU Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1281 GLU Chi-restraints excluded: chain D residue 1307 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 100 MET Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 488 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 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 107 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 36 TRP Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 119 VAL 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: 20.0000 chunk 212 optimal weight: 0.5980 chunk 91 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 109 optimal weight: 0.6980 chunk 357 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 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 430 HIS ** D 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 HIS G 59 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.183888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.147131 restraints weight = 51394.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.149856 restraints weight = 119413.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.150068 restraints weight = 52722.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.150214 restraints weight = 41850.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.150880 restraints weight = 35522.565| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.4404 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= 0.171 Angle : 0.615 12.818 45782 Z= 0.322 Chirality : 0.042 0.220 5210 Planarity : 0.004 0.066 5542 Dihedral : 17.667 170.077 5628 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.04 % Favored : 94.77 % Rotamer: Outliers : 3.18 % Allowed : 16.06 % Favored : 80.76 % 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 aren not related in a simple way. whole: -0.26 (0.13), residues: 3807 helix: 1.19 (0.13), residues: 1573 sheet: -0.41 (0.25), residues: 389 loop : -1.36 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 69 TYR 0.026 0.001 TYR B 177 PHE 0.015 0.001 PHE D1325 TRP 0.014 0.001 TRP F 434 HIS 0.005 0.001 HIS G 59 Details of bonding type rmsd covalent geometry : bond 0.00399 (33497) covalent geometry : angle 0.61457 (45782) hydrogen bonds : bond 0.04547 ( 1517) hydrogen bonds : angle 4.68169 ( 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 456 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 352 time to evaluate : 1.264 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: C 179 TYR cc_start: 0.7329 (t80) cc_final: 0.6915 (t80) REVERT: C 487 LEU cc_start: 0.6436 (OUTLIER) cc_final: 0.5971 (tp) REVERT: C 551 HIS cc_start: 0.7814 (t-90) cc_final: 0.7411 (t-90) REVERT: C 1216 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7483 (mtp85) REVERT: C 1259 LEU cc_start: 0.6445 (tp) cc_final: 0.6126 (tp) REVERT: C 1296 ASP cc_start: 0.7306 (m-30) cc_final: 0.7049 (m-30) REVERT: D 1243 LEU cc_start: 0.8576 (tp) cc_final: 0.8076 (mp) REVERT: E 42 GLU cc_start: 0.5507 (mp0) cc_final: 0.5232 (mp0) REVERT: F 100 MET cc_start: 0.3546 (OUTLIER) cc_final: 0.2590 (ptp) REVERT: F 105 MET cc_start: 0.5091 (ppp) cc_final: 0.4372 (ppp) REVERT: F 113 ARG cc_start: 0.4797 (tpt90) cc_final: 0.4305 (tpm170) REVERT: F 288 MET cc_start: -0.0061 (mmm) cc_final: -0.1682 (ptm) REVERT: F 297 MET cc_start: 0.0823 (ppp) cc_final: -0.2018 (ttp) REVERT: F 433 TRP cc_start: 0.4304 (m100) cc_final: 0.3957 (m100) REVERT: F 603 ARG cc_start: 0.3815 (mpp80) cc_final: 0.3053 (mmt90) REVERT: B 68 TYR cc_start: 0.5861 (p90) cc_final: 0.5622 (p90) REVERT: G 36 TRP cc_start: 0.6108 (OUTLIER) cc_final: 0.5530 (p-90) REVERT: G 73 TRP cc_start: 0.6881 (t60) cc_final: 0.6432 (t60) REVERT: G 119 VAL cc_start: 0.7880 (t) cc_final: 0.7648 (t) outliers start: 104 outliers final: 81 residues processed: 423 average time/residue: 0.1965 time to fit residues: 136.3488 Evaluate side-chains 417 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 332 time to evaluate : 1.134 ------------------------------------------------------------------------------- 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 287 VAL Chi-restraints excluded: chain C residue 448 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 576 SER Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 635 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 748 ILE 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 1024 GLU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1216 ARG Chi-restraints excluded: chain C residue 1248 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 160 LEU 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 416 ILE Chi-restraints excluded: chain D residue 434 ILE 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 697 MET Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 803 VAL 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 1281 GLU Chi-restraints excluded: chain D residue 1307 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 100 MET Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 488 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 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 107 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 188 GLU 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 81 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 310 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 206 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 205 optimal weight: 8.9990 chunk 60 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 96 optimal weight: 20.0000 chunk 276 optimal weight: 20.0000 chunk 287 optimal weight: 20.0000 chunk 233 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 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 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 HIS F 406 GLN A 41 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.178961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.140970 restraints weight = 51342.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.143748 restraints weight = 123667.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.143749 restraints weight = 52998.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.144004 restraints weight = 41548.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.144553 restraints weight = 35812.275| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 33497 Z= 0.257 Angle : 0.691 13.418 45782 Z= 0.361 Chirality : 0.044 0.224 5210 Planarity : 0.005 0.062 5542 Dihedral : 17.729 169.580 5628 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.81 % Favored : 94.01 % Rotamer: Outliers : 3.11 % Allowed : 16.61 % Favored : 80.27 % 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 aren not related in a simple way. whole: -0.50 (0.13), residues: 3807 helix: 0.99 (0.13), residues: 1566 sheet: -0.69 (0.24), residues: 425 loop : -1.44 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 69 TYR 0.031 0.002 TYR B 177 PHE 0.019 0.002 PHE D1325 TRP 0.013 0.001 TRP F 433 HIS 0.008 0.001 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00608 (33497) covalent geometry : angle 0.69080 (45782) hydrogen bonds : bond 0.04859 ( 1517) hydrogen bonds : angle 4.90512 ( 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 454 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 352 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 179 TYR cc_start: 0.7605 (t80) cc_final: 0.7168 (t80) REVERT: C 487 LEU cc_start: 0.6450 (OUTLIER) cc_final: 0.5993 (tp) REVERT: C 1216 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.8117 (mtp85) REVERT: C 1296 ASP cc_start: 0.7497 (m-30) cc_final: 0.7263 (m-30) REVERT: D 133 ARG cc_start: 0.6830 (ttm110) cc_final: 0.6440 (ptp90) REVERT: D 1187 GLU cc_start: 0.7181 (pm20) cc_final: 0.6948 (pm20) REVERT: D 1243 LEU cc_start: 0.8640 (tp) cc_final: 0.8103 (mp) REVERT: F 100 MET cc_start: 0.3767 (OUTLIER) cc_final: 0.2776 (ptp) REVERT: F 105 MET cc_start: 0.5351 (ppp) cc_final: 0.4383 (ppp) REVERT: F 113 ARG cc_start: 0.4777 (tpt90) cc_final: 0.4250 (tpm170) REVERT: F 288 MET cc_start: -0.0352 (mmm) cc_final: -0.2163 (ptm) REVERT: F 433 TRP cc_start: 0.4713 (m100) cc_final: 0.4066 (m100) REVERT: F 603 ARG cc_start: 0.3943 (mpp80) cc_final: 0.3040 (mmt90) REVERT: A 185 TYR cc_start: 0.8300 (p90) cc_final: 0.7940 (p90) REVERT: B 20 SER cc_start: 0.8122 (p) cc_final: 0.7829 (p) REVERT: B 68 TYR cc_start: 0.6307 (p90) cc_final: 0.6062 (p90) REVERT: G 36 TRP cc_start: 0.6374 (OUTLIER) cc_final: 0.5667 (p-90) REVERT: G 73 TRP cc_start: 0.7104 (t60) cc_final: 0.6653 (t60) REVERT: G 112 LEU cc_start: 0.8739 (tp) cc_final: 0.8484 (tp) outliers start: 102 outliers final: 77 residues processed: 427 average time/residue: 0.1957 time to fit residues: 137.8513 Evaluate side-chains 411 residues out of total 3275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 330 time to evaluate : 1.174 ------------------------------------------------------------------------------- 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 158 ASP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 448 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 576 SER Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 615 VAL 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 748 ILE Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 764 CYS 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 1024 GLU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1216 ARG 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 84 ILE Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 97 VAL 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 416 ILE 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 697 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 925 GLU Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1281 GLU Chi-restraints excluded: chain D residue 1290 ARG Chi-restraints excluded: chain D residue 1307 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 100 MET Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 526 THR 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 107 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 36 TRP Chi-restraints excluded: chain G residue 81 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.3301 > 50: distance: 35 - 159: 31.010 distance: 98 - 118: 35.011 distance: 103 - 126: 31.565 distance: 114 - 118: 35.294 distance: 118 - 119: 11.273 distance: 119 - 120: 24.775 distance: 119 - 122: 42.673 distance: 120 - 121: 22.542 distance: 120 - 126: 44.995 distance: 122 - 123: 23.411 distance: 122 - 124: 30.435 distance: 123 - 125: 40.691 distance: 126 - 127: 26.839 distance: 127 - 128: 31.540 distance: 127 - 130: 35.041 distance: 128 - 129: 23.255 distance: 128 - 131: 31.000 distance: 131 - 132: 14.759 distance: 132 - 133: 59.254 distance: 133 - 134: 15.826 distance: 133 - 140: 47.273 distance: 136 - 137: 12.112 distance: 137 - 138: 11.051 distance: 138 - 139: 60.788 distance: 141 - 142: 8.016 distance: 141 - 144: 14.069 distance: 142 - 143: 35.013 distance: 142 - 149: 31.133 distance: 144 - 145: 8.616 distance: 145 - 146: 40.920 distance: 146 - 147: 50.576 distance: 146 - 148: 40.168 distance: 149 - 150: 40.447 distance: 149 - 155: 40.817 distance: 150 - 151: 20.909 distance: 150 - 153: 40.063 distance: 151 - 152: 30.238 distance: 151 - 156: 23.983 distance: 153 - 154: 22.306 distance: 154 - 155: 21.888 distance: 156 - 157: 36.739 distance: 157 - 158: 24.429 distance: 157 - 160: 20.673 distance: 158 - 159: 5.297 distance: 158 - 164: 40.089 distance: 160 - 161: 24.517 distance: 160 - 162: 16.142 distance: 161 - 163: 42.522 distance: 164 - 165: 38.349 distance: 165 - 166: 40.895 distance: 165 - 168: 52.477 distance: 166 - 167: 25.456 distance: 166 - 170: 40.881 distance: 168 - 169: 4.380 distance: 170 - 171: 23.837 distance: 171 - 172: 8.295 distance: 171 - 174: 29.889 distance: 172 - 173: 31.880 distance: 172 - 178: 34.228 distance: 174 - 175: 7.073 distance: 175 - 176: 33.595 distance: 176 - 177: 9.530 distance: 178 - 179: 19.627 distance: 179 - 180: 33.025 distance: 179 - 182: 16.616 distance: 180 - 181: 18.383 distance: 180 - 187: 25.363 distance: 182 - 183: 10.633 distance: 183 - 184: 28.806 distance: 184 - 185: 15.192 distance: 184 - 186: 26.041 distance: 187 - 188: 45.862 distance: 188 - 189: 15.514 distance: 188 - 191: 15.428 distance: 189 - 194: 34.249