Starting phenix.real_space_refine on Mon May 26 01:40:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k58_36897/05_2025/8k58_36897.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k58_36897/05_2025/8k58_36897.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k58_36897/05_2025/8k58_36897.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k58_36897/05_2025/8k58_36897.map" model { file = "/net/cci-nas-00/data/ceres_data/8k58_36897/05_2025/8k58_36897.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k58_36897/05_2025/8k58_36897.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.028 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 57 5.49 5 S 112 5.16 5 C 17026 2.51 5 N 4875 2.21 5 O 5435 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 27505 Number of models: 1 Model: "" Number of chains: 9 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: "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: "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: "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: "I" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 448 Inner-chain residues flagged as termini: ['pdbres=" DA I 14 "'] Classifications: {'DNA': 22} Modifications used: {'5*END': 2} Link IDs: {'rna3p': 21} Chain: "H" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 583 Classifications: {'DNA': 29} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 28} Chain: "J" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 218 Classifications: {'RNA': 10} Modifications used: {'5*END': 1, 'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna3p': 9} Time building chain proxies: 17.23, per 1000 atoms: 0.63 Number of scatterers: 27505 At special positions: 0 Unit cell: (128.74, 161.54, 164, 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 112 16.00 P 57 15.00 O 5435 8.00 N 4875 7.00 C 17026 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: 6.44 Conformation dependent library (CDL) restraints added in 3.1 seconds 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6204 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 50 sheets defined 40.1% alpha, 18.3% beta 18 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 10.48 Creating SS restraints... Processing helix chain 'C' and resid 4 through 10 removed outlier: 3.786A pdb=" N ARG C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.513A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) 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: 4.354A 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 242 through 246 removed outlier: 3.836A pdb=" N LEU C 246 " --> pdb=" O PRO C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 288 through 295 removed outlier: 3.708A pdb=" N LYS C 295 " --> pdb=" O TYR C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 391 removed outlier: 3.895A pdb=" N SER C 391 " --> pdb=" O ASN C 387 " (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: 3.559A pdb=" N SER C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 492 removed outlier: 3.695A pdb=" N MET C 492 " --> pdb=" O PRO C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 509 removed outlier: 4.729A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER C 509 " --> pdb=" O PHE C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 544 through 549 removed outlier: 3.534A pdb=" N ASP C 549 " --> pdb=" O PHE C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 614 removed outlier: 3.528A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 608 through 614' 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 688 removed outlier: 3.697A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN C 688 " --> pdb=" O ASN C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 712 removed outlier: 4.446A pdb=" N ALA C 707 " --> pdb=" O GLY C 703 " (cutoff:3.500A) Processing helix 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: 3.883A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) removed outlier: 4.238A 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 removed outlier: 3.513A pdb=" N ALA C 981 " --> pdb=" O ALA C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 992 removed outlier: 3.843A pdb=" N LEU C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1000 removed outlier: 3.869A pdb=" N TRP C 997 " --> pdb=" O ARG C 994 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU C 998 " --> pdb=" O ASP C 995 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU C1000 " --> pdb=" O TRP C 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1038 Processing helix chain 'C' and resid 1102 through 1107 Processing helix chain 'C' and resid 1109 through 1134 Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 3.766A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1166 through 1176 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: 3.617A 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: 3.516A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C1333 " --> pdb=" O GLU C1329 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 96 through 101 removed outlier: 3.580A pdb=" N GLU D 100 " --> pdb=" O LYS D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 180 through 192 removed outlier: 3.809A pdb=" N ALA D 184 " --> pdb=" O MET D 180 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 208 removed outlier: 3.645A pdb=" N GLU D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 Processing helix chain 'D' and resid 233 through 238 Processing helix chain 'D' and resid 263 through 285 Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 332 removed outlier: 3.508A pdb=" N MET D 330 " --> pdb=" O SER D 326 " (cutoff:3.500A) 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 406 through 418 removed outlier: 3.763A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE D 411 " --> pdb=" O VAL D 407 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLU D 418 " --> pdb=" O GLU D 414 " (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 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 485 through 490 removed outlier: 4.159A 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: 3.967A pdb=" N ALA D 533 " --> pdb=" O GLY D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 583 removed outlier: 3.544A pdb=" N ILE D 582 " --> pdb=" O ILE D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.699A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) 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: 3.904A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 removed outlier: 3.567A pdb=" N MET D 724 " --> pdb=" O ASN D 720 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 739 removed outlier: 3.583A pdb=" N GLN D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 805 removed outlier: 3.573A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 4.202A 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 removed outlier: 3.520A pdb=" N GLY D 900 " --> pdb=" O ALA D 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 896 through 900' Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.545A 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 1069 through 1074 removed outlier: 4.091A pdb=" N ASP D1073 " --> pdb=" O ALA D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1147 Processing helix chain 'D' and resid 1216 through 1223 Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.745A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.313A 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: 4.083A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.815A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 3.739A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1373 removed outlier: 4.057A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 4.279A 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 Processing helix chain 'E' and resid 60 through 77 removed outlier: 3.573A pdb=" N ALA E 77 " --> pdb=" O GLN E 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.844A 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: 4.472A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 15 removed outlier: 3.585A pdb=" N ILE G 15 " --> pdb=" O VAL G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 39 removed outlier: 3.564A pdb=" N SER G 39 " --> pdb=" O ALA G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 52 removed outlier: 3.846A pdb=" N MET G 45 " --> pdb=" O SER G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 87 Processing helix chain 'G' and resid 107 through 128 Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.512A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER B 50 " --> pdb=" O ILE B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.774A pdb=" N ILE B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) removed outlier: 4.109A 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 162 Processing helix chain 'B' and resid 212 through 230 removed outlier: 4.670A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.477A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.907A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 11.348A pdb=" N ALA C 94 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 9.017A pdb=" N MET C 124 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU C 96 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL C 122 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL C 98 " --> pdb=" O GLN C 120 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N GLN C 120 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU C 100 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LYS C 118 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU C 102 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASP C 116 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE C 104 " --> pdb=" O VAL C 114 " (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: 6.406A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 154 through 160 Processing sheet with id=AA6, first strand: chain 'C' and resid 284 through 286 removed outlier: 3.746A pdb=" N GLU C 240 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 5.346A 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: 6.775A 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: 5.904A 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 removed outlier: 3.617A pdb=" N HIS C 628 " --> pdb=" O ASP C 624 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.926A 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: 6.692A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.632A 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: 4.267A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.634A 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: 5.912A pdb=" N ASP C 842 " --> pdb=" O VAL C1046 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N VAL C1046 " --> pdb=" O ASP C 842 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 9.066A 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: 6.867A 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: 6.084A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 1335 through 1341 removed outlier: 3.723A pdb=" N GLU C1338 " --> pdb=" O LYS D 21 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA D 19 " --> pdb=" O GLU C1340 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 44 through 45 Processing sheet with id=AC6, first strand: chain 'D' and resid 103 through 111 removed outlier: 6.639A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 144 through 145 Processing sheet with id=AC8, first strand: chain 'D' and resid 316 through 317 removed outlier: 4.065A pdb=" N THR D 317 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN D 320 " --> pdb=" O THR D 317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'D' and resid 526 through 528 removed outlier: 7.042A pdb=" N LEU D 527 " --> pdb=" O ARG D 551 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N THR D 553 " --> pdb=" O LEU D 527 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 707 through 708 removed outlier: 3.817A pdb=" N ILE D 707 " --> pdb=" O GLU D 714 " (cutoff:3.500A) Processing sheet with id=AD2, 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: 4.005A pdb=" N GLU D 811 " --> pdb=" O VAL D 894 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AD4, first strand: chain 'D' and resid 825 through 827 removed outlier: 6.690A pdb=" N VAL D 825 " --> pdb=" O LYS D 832 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP D 830 " --> pdb=" O GLU D 827 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 949 through 952 removed outlier: 7.394A pdb=" N ILE D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 991 through 997 removed outlier: 4.002A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N THR D 980 " --> pdb=" O VAL D 997 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY D 956 " --> pdb=" O VAL D1011 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL D1011 " --> pdb=" O GLY D 956 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 964 through 968 removed outlier: 4.392A pdb=" N LYS D 964 " --> pdb=" O THR D 976 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL D 966 " --> pdb=" O VAL D 974 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL D 974 " --> pdb=" O VAL D 966 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 1024 through 1028 removed outlier: 6.261A pdb=" N MET D1025 " --> pdb=" O ARG D1123 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ARG D1123 " --> pdb=" O MET D1025 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL D1027 " --> pdb=" O LEU D1121 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU D1121 " --> pdb=" O GLN D1108 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU D1109 " --> pdb=" O SER D1057 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N SER D1057 " --> pdb=" O LEU D1109 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL D1060 " --> pdb=" O THR D1047 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR D1047 " --> pdb=" O VAL D1060 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 1034 through 1038 Processing sheet with id=AE1, first strand: chain 'D' and resid 1156 through 1157 removed outlier: 4.189A pdb=" N ASP D1208 " --> pdb=" O ALA D1157 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1162 through 1165 Processing sheet with id=AE3, first strand: chain 'D' and resid 1277 through 1279 removed outlier: 6.403A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 13 through 18 removed outlier: 4.380A pdb=" N THR A 27 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ILE A 16 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LYS A 25 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLN A 18 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N HIS A 23 " --> pdb=" O GLN A 18 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N HIS A 23 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N THR A 207 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LYS A 25 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N MET A 205 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N THR A 27 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ILE A 203 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLU A 29 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU A 201 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N LEU A 198 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A 190 " --> pdb=" O LEU A 198 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 97 through 105 removed outlier: 3.776A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N GLY A 151 " --> pdb=" O PRO A 52 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 97 through 105 removed outlier: 3.939A pdb=" N GLY A 151 " --> pdb=" O TYR A 177 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AE8, first strand: chain 'A' and resid 108 through 111 Processing sheet with id=AE9, first strand: chain 'G' and resid 92 through 94 Processing sheet with id=AF1, first strand: chain 'B' and resid 15 through 19 removed outlier: 6.737A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU B 198 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 98 through 105 removed outlier: 6.592A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AF4, first strand: chain 'B' and resid 108 through 111 Processing sheet with id=AF5, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.582A pdb=" N VAL B 153 " --> pdb=" O ALA B 175 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA B 175 " --> pdb=" O VAL B 153 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 1163 hydrogen bonds defined for protein. 3294 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 13.29 Time building geometry restraints manager: 7.49 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: 7938 1.33 - 1.45: 4098 1.45 - 1.57: 15696 1.57 - 1.69: 116 1.69 - 1.81: 194 Bond restraints: 28042 Sorted by residual: bond pdb=" CB PRO D 251 " pdb=" CG PRO D 251 " ideal model delta sigma weight residual 1.492 1.603 -0.111 5.00e-02 4.00e+02 4.92e+00 bond pdb=" CB PRO D 498 " pdb=" CG PRO D 498 " ideal model delta sigma weight residual 1.492 1.577 -0.085 5.00e-02 4.00e+02 2.87e+00 bond pdb=" CD GLU C1143 " pdb=" OE1 GLU C1143 " ideal model delta sigma weight residual 1.249 1.219 0.030 1.90e-02 2.77e+03 2.41e+00 bond pdb=" CA GLY D 828 " pdb=" C GLY D 828 " ideal model delta sigma weight residual 1.530 1.515 0.016 1.04e-02 9.25e+03 2.35e+00 bond pdb=" CB ARG B 44 " pdb=" CG ARG B 44 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.29e+00 ... (remaining 28037 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.19: 37896 3.19 - 6.38: 228 6.38 - 9.58: 15 9.58 - 12.77: 0 12.77 - 15.96: 1 Bond angle restraints: 38140 Sorted by residual: angle pdb=" N ILE C 414 " pdb=" CA ILE C 414 " pdb=" C ILE C 414 " ideal model delta sigma weight residual 113.10 107.46 5.64 9.70e-01 1.06e+00 3.39e+01 angle pdb=" N SER C1162 " pdb=" CA SER C1162 " pdb=" C SER C1162 " ideal model delta sigma weight residual 114.31 106.99 7.32 1.29e+00 6.01e-01 3.22e+01 angle pdb=" CA PRO D 251 " pdb=" N PRO D 251 " pdb=" CD PRO D 251 " ideal model delta sigma weight residual 112.00 104.56 7.44 1.40e+00 5.10e-01 2.82e+01 angle pdb=" CA PRO D 498 " pdb=" N PRO D 498 " pdb=" CD PRO D 498 " ideal model delta sigma weight residual 112.00 105.25 6.75 1.40e+00 5.10e-01 2.32e+01 angle pdb=" C ASP C 234 " pdb=" CA ASP C 234 " pdb=" CB ASP C 234 " ideal model delta sigma weight residual 115.79 110.34 5.45 1.19e+00 7.06e-01 2.10e+01 ... (remaining 38135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.19: 16322 30.19 - 60.38: 630 60.38 - 90.57: 178 90.57 - 120.76: 0 120.76 - 150.95: 2 Dihedral angle restraints: 17132 sinusoidal: 7491 harmonic: 9641 Sorted by residual: dihedral pdb=" CA MET D 330 " pdb=" C MET D 330 " pdb=" N ILE D 331 " pdb=" CA ILE D 331 " ideal model delta harmonic sigma weight residual 180.00 151.87 28.13 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA GLN E 29 " pdb=" C GLN E 29 " pdb=" N MET E 30 " pdb=" CA MET E 30 " ideal model delta harmonic sigma weight residual 180.00 154.19 25.81 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA ARG C 827 " pdb=" C ARG C 827 " pdb=" N PHE C 828 " pdb=" CA PHE C 828 " ideal model delta harmonic sigma weight residual -180.00 -157.83 -22.17 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 17129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 3409 0.049 - 0.097: 723 0.097 - 0.146: 199 0.146 - 0.195: 16 0.195 - 0.243: 2 Chirality restraints: 4349 Sorted by residual: chirality pdb=" CA GLN E 29 " pdb=" N GLN E 29 " pdb=" C GLN E 29 " pdb=" CB GLN E 29 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB VAL C 690 " pdb=" CA VAL C 690 " pdb=" CG1 VAL C 690 " pdb=" CG2 VAL C 690 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA PRO D 498 " pdb=" N PRO D 498 " pdb=" C PRO D 498 " pdb=" CB PRO D 498 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.06e-01 ... (remaining 4346 not shown) Planarity restraints: 4796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 497 " -0.082 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO D 498 " 0.207 5.00e-02 4.00e+02 pdb=" CA PRO D 498 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO D 498 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 250 " -0.077 5.00e-02 4.00e+02 1.12e-01 2.01e+01 pdb=" N PRO D 251 " 0.194 5.00e-02 4.00e+02 pdb=" CA PRO D 251 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO D 251 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 39 " -0.055 5.00e-02 4.00e+02 8.19e-02 1.07e+01 pdb=" N PRO E 40 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO E 40 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO E 40 " -0.045 5.00e-02 4.00e+02 ... (remaining 4793 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 815 2.70 - 3.25: 28559 3.25 - 3.80: 46321 3.80 - 4.35: 60188 4.35 - 4.90: 97542 Nonbonded interactions: 233425 Sorted by model distance: nonbonded pdb=" OG SER D 969 " pdb=" O SER D1117 " model vdw 2.144 3.040 nonbonded pdb=" OG SER D 568 " pdb=" NZ LYS D 570 " model vdw 2.198 3.120 nonbonded pdb=" O VAL C 700 " pdb=" NH1 ARG C1069 " model vdw 2.207 3.120 nonbonded pdb=" OD1 ASP D 134 " pdb=" NH2 ARG D 137 " model vdw 2.213 3.120 nonbonded pdb=" OD1 ASP C1240 " pdb=" NZ LYS D 445 " model vdw 2.215 3.120 ... (remaining 233420 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.150 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 69.910 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.120 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5693 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 : 0.003 0.111 28042 Z= 0.166 Angle : 0.713 15.961 38140 Z= 0.413 Chirality : 0.044 0.243 4349 Planarity : 0.005 0.120 4796 Dihedral : 17.145 150.954 10928 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.79 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.14), residues: 3341 helix: 0.74 (0.15), residues: 1202 sheet: -0.31 (0.25), residues: 381 loop : -1.39 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP D 115 HIS 0.018 0.001 HIS B 37 PHE 0.024 0.002 PHE C1270 TYR 0.017 0.001 TYR C 555 ARG 0.014 0.001 ARG D 610 Details of bonding type rmsd hydrogen bonds : bond 0.16164 ( 1198) hydrogen bonds : angle 6.90204 ( 3388) covalent geometry : bond 0.00345 (28042) covalent geometry : angle 0.71315 (38140) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 606 time to evaluate : 2.732 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 8 LYS cc_start: 0.6065 (mmtp) cc_final: 0.5722 (mmtm) REVERT: C 124 MET cc_start: 0.5699 (pmm) cc_final: 0.5226 (pmm) REVERT: C 130 MET cc_start: 0.6591 (ttm) cc_final: 0.6334 (ttm) REVERT: C 193 ASN cc_start: 0.7276 (m-40) cc_final: 0.6953 (m-40) REVERT: C 205 PRO cc_start: 0.7942 (Cg_exo) cc_final: 0.7606 (Cg_endo) REVERT: C 396 ASP cc_start: 0.7043 (t70) cc_final: 0.6609 (t0) REVERT: C 411 ARG cc_start: 0.5640 (mtt180) cc_final: 0.5397 (mtt180) REVERT: C 422 LYS cc_start: 0.6870 (mttm) cc_final: 0.6289 (pttp) REVERT: C 445 ILE cc_start: 0.7537 (mm) cc_final: 0.7304 (mt) REVERT: C 512 SER cc_start: 0.8595 (t) cc_final: 0.7964 (t) REVERT: C 562 GLU cc_start: 0.6817 (tp30) cc_final: 0.6410 (tt0) REVERT: C 631 GLU cc_start: 0.7688 (mt-10) cc_final: 0.6785 (mp0) REVERT: C 653 MET cc_start: 0.7027 (tmm) cc_final: 0.6668 (tmm) REVERT: C 805 MET cc_start: 0.7523 (ptt) cc_final: 0.7320 (ptt) REVERT: C 842 ASP cc_start: 0.7678 (t0) cc_final: 0.7383 (t0) REVERT: C 876 GLU cc_start: 0.6753 (mt-10) cc_final: 0.6475 (mm-30) REVERT: C 917 SER cc_start: 0.7678 (p) cc_final: 0.6951 (m) REVERT: C 1079 ILE cc_start: 0.6138 (pt) cc_final: 0.5751 (mt) REVERT: C 1119 MET cc_start: 0.6339 (tpt) cc_final: 0.4609 (ttt) REVERT: C 1151 LEU cc_start: 0.5702 (tp) cc_final: 0.5220 (mp) REVERT: C 1170 MET cc_start: 0.6448 (tpp) cc_final: 0.6169 (mmt) REVERT: C 1188 ASP cc_start: 0.6425 (t70) cc_final: 0.6089 (t0) REVERT: C 1209 GLN cc_start: 0.7819 (mt0) cc_final: 0.7407 (mt0) REVERT: C 1231 TYR cc_start: 0.7364 (t80) cc_final: 0.6966 (t80) REVERT: C 1297 ASP cc_start: 0.5112 (t0) cc_final: 0.4868 (t0) REVERT: D 26 SER cc_start: 0.7052 (t) cc_final: 0.6504 (p) REVERT: D 53 ARG cc_start: 0.5671 (mtm180) cc_final: 0.4843 (mpt90) REVERT: D 180 MET cc_start: 0.3074 (mmp) cc_final: 0.2513 (mmt) REVERT: D 278 ARG cc_start: 0.6900 (ttp-170) cc_final: 0.6688 (ttp-170) REVERT: D 283 LEU cc_start: 0.6408 (mm) cc_final: 0.6177 (mt) REVERT: D 298 MET cc_start: 0.4903 (ptm) cc_final: 0.3839 (tpp) REVERT: D 332 LYS cc_start: 0.6680 (ttpt) cc_final: 0.6081 (mtpp) REVERT: D 395 LYS cc_start: 0.7276 (ttpp) cc_final: 0.7035 (tptt) REVERT: D 457 TYR cc_start: 0.6920 (m-80) cc_final: 0.6241 (m-80) REVERT: D 488 ASN cc_start: 0.7496 (m-40) cc_final: 0.7261 (m110) REVERT: D 490 ILE cc_start: 0.8582 (pt) cc_final: 0.8264 (mt) REVERT: D 505 ASP cc_start: 0.7053 (t70) cc_final: 0.6328 (t0) REVERT: D 685 ILE cc_start: 0.7526 (mt) cc_final: 0.7218 (mt) REVERT: D 713 GLU cc_start: 0.6488 (pm20) cc_final: 0.6056 (mt-10) REVERT: D 725 MET cc_start: 0.5405 (tpt) cc_final: 0.5204 (tpp) REVERT: D 743 MET cc_start: 0.6530 (ptm) cc_final: 0.5822 (ptm) REVERT: D 785 ASP cc_start: 0.6956 (t0) cc_final: 0.6713 (t0) REVERT: D 870 ASP cc_start: 0.7116 (m-30) cc_final: 0.6903 (t70) REVERT: D 881 LYS cc_start: 0.7124 (tttt) cc_final: 0.6474 (tttm) REVERT: D 892 PHE cc_start: 0.7574 (m-10) cc_final: 0.6674 (m-80) REVERT: D 1146 GLU cc_start: 0.6690 (mm-30) cc_final: 0.6331 (mm-30) REVERT: D 1151 LYS cc_start: 0.7400 (mppt) cc_final: 0.7071 (mmmt) REVERT: D 1152 GLU cc_start: 0.6551 (mt-10) cc_final: 0.6171 (mt-10) REVERT: D 1156 LEU cc_start: 0.4826 (mt) cc_final: 0.3997 (pp) REVERT: D 1263 LYS cc_start: 0.6920 (mmtt) cc_final: 0.6303 (mtpt) REVERT: D 1279 GLN cc_start: 0.7124 (mm110) cc_final: 0.6660 (mm-40) REVERT: D 1281 GLU cc_start: 0.6605 (mm-30) cc_final: 0.6382 (pt0) REVERT: D 1314 LEU cc_start: 0.6126 (mt) cc_final: 0.5925 (mt) REVERT: D 1369 ARG cc_start: 0.7477 (ttt180) cc_final: 0.6703 (ttp80) REVERT: E 12 LYS cc_start: 0.6023 (mmtm) cc_final: 0.5807 (mmtp) REVERT: E 63 ILE cc_start: 0.7316 (mm) cc_final: 0.6765 (mt) REVERT: E 67 ARG cc_start: 0.7322 (ttm110) cc_final: 0.7087 (mtt-85) REVERT: A 105 SER cc_start: 0.7840 (p) cc_final: 0.7417 (m) REVERT: A 204 GLU cc_start: 0.5017 (pt0) cc_final: 0.4727 (mt-10) REVERT: G 1 MET cc_start: 0.3074 (mmp) cc_final: 0.2031 (tmm) REVERT: B 18 GLN cc_start: 0.6564 (pt0) cc_final: 0.6289 (pt0) REVERT: B 29 GLU cc_start: 0.5142 (pm20) cc_final: 0.4151 (pm20) REVERT: B 33 ARG cc_start: 0.6859 (ttt-90) cc_final: 0.6400 (tmm-80) REVERT: B 99 ILE cc_start: 0.6686 (mm) cc_final: 0.6425 (mt) REVERT: B 101 THR cc_start: 0.5557 (t) cc_final: 0.5284 (t) outliers start: 0 outliers final: 0 residues processed: 606 average time/residue: 0.4594 time to fit residues: 413.2415 Evaluate side-chains 375 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 2.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 285 optimal weight: 8.9990 chunk 256 optimal weight: 0.9980 chunk 142 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 172 optimal weight: 7.9990 chunk 136 optimal weight: 1.9990 chunk 264 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 chunk 197 optimal weight: 0.0050 chunk 306 optimal weight: 20.0000 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 ASN ** C 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 752 ASN C 811 ASN C 955 GLN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 GLN D 206 ASN D 232 ASN D 294 ASN D 320 ASN ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 488 ASN D 489 ASN D 690 ASN D 739 GLN ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN B 41 ASN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4940 r_free = 0.4940 target = 0.241580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.199024 restraints weight = 34385.009| |-----------------------------------------------------------------------------| r_work (start): 0.4564 rms_B_bonded: 2.53 r_work: 0.4236 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.4236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 28042 Z= 0.210 Angle : 0.691 9.786 38140 Z= 0.365 Chirality : 0.046 0.222 4349 Planarity : 0.005 0.069 4796 Dihedral : 13.902 150.765 4363 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.18 % Favored : 94.73 % Rotamer: Outliers : 1.61 % Allowed : 9.49 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.14), residues: 3341 helix: 0.68 (0.15), residues: 1222 sheet: -0.59 (0.25), residues: 398 loop : -1.38 (0.14), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 115 HIS 0.016 0.002 HIS C 554 PHE 0.020 0.002 PHE C 157 TYR 0.026 0.002 TYR D 772 ARG 0.010 0.001 ARG G 21 Details of bonding type rmsd hydrogen bonds : bond 0.04641 ( 1198) hydrogen bonds : angle 5.46857 ( 3388) covalent geometry : bond 0.00491 (28042) covalent geometry : angle 0.69148 (38140) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 399 time to evaluate : 2.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 422 LYS cc_start: 0.7451 (mttm) cc_final: 0.6972 (pttp) REVERT: C 631 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7373 (mp0) REVERT: C 768 MET cc_start: 0.7316 (tpt) cc_final: 0.7090 (tpt) REVERT: C 800 MET cc_start: 0.7745 (mtt) cc_final: 0.7163 (mtt) REVERT: C 851 THR cc_start: 0.8071 (t) cc_final: 0.7835 (p) REVERT: C 917 SER cc_start: 0.7926 (p) cc_final: 0.7522 (m) REVERT: C 967 LEU cc_start: 0.7461 (mt) cc_final: 0.7225 (mt) REVERT: C 1143 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6187 (mp0) REVERT: C 1151 LEU cc_start: 0.6229 (tp) cc_final: 0.5999 (mt) REVERT: C 1170 MET cc_start: 0.7510 (tpp) cc_final: 0.7265 (mmp) REVERT: D 26 SER cc_start: 0.7807 (t) cc_final: 0.7521 (p) REVERT: D 53 ARG cc_start: 0.6186 (mtm180) cc_final: 0.5578 (mpt180) REVERT: D 180 MET cc_start: 0.2363 (mmp) cc_final: 0.0563 (pmm) REVERT: D 196 GLN cc_start: 0.6614 (OUTLIER) cc_final: 0.6126 (tp-100) REVERT: D 298 MET cc_start: 0.5137 (ptm) cc_final: 0.4112 (mmt) REVERT: D 332 LYS cc_start: 0.7798 (ttpt) cc_final: 0.7363 (mtpp) REVERT: D 685 ILE cc_start: 0.8065 (mt) cc_final: 0.7825 (mt) REVERT: D 892 PHE cc_start: 0.7387 (m-10) cc_final: 0.6863 (m-80) REVERT: D 1146 GLU cc_start: 0.7292 (mm-30) cc_final: 0.7091 (mm-30) REVERT: D 1156 LEU cc_start: 0.5695 (mt) cc_final: 0.4612 (pp) REVERT: E 74 GLU cc_start: 0.5619 (OUTLIER) cc_final: 0.4595 (tt0) REVERT: A 204 GLU cc_start: 0.6337 (pt0) cc_final: 0.5985 (mt-10) REVERT: G 1 MET cc_start: 0.2034 (mmp) cc_final: 0.1795 (tmm) REVERT: B 29 GLU cc_start: 0.5665 (pm20) cc_final: 0.4826 (pm20) REVERT: B 51 MET cc_start: 0.6609 (tpt) cc_final: 0.5719 (tpt) REVERT: B 152 TYR cc_start: 0.7853 (t80) cc_final: 0.7646 (t80) outliers start: 46 outliers final: 28 residues processed: 431 average time/residue: 0.4308 time to fit residues: 288.9563 Evaluate side-chains 364 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 333 time to evaluate : 2.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 1143 GLU Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 196 GLN Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 655 SER Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 990 ARG Chi-restraints excluded: chain D residue 1190 ILE Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1332 LEU Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 186 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 313 optimal weight: 2.9990 chunk 291 optimal weight: 7.9990 chunk 234 optimal weight: 7.9990 chunk 68 optimal weight: 0.5980 chunk 304 optimal weight: 7.9990 chunk 176 optimal weight: 0.7980 chunk 185 optimal weight: 7.9990 chunk 273 optimal weight: 4.9990 chunk 265 optimal weight: 0.6980 chunk 213 optimal weight: 0.6980 chunk 136 optimal weight: 3.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 238 GLN C 526 HIS ** C 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1209 GLN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 ASN ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 GLN ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1279 GLN ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 HIS ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4946 r_free = 0.4946 target = 0.242319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.198519 restraints weight = 34395.816| |-----------------------------------------------------------------------------| r_work (start): 0.4557 rms_B_bonded: 2.40 r_work: 0.4272 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 28042 Z= 0.156 Angle : 0.622 8.960 38140 Z= 0.327 Chirality : 0.044 0.217 4349 Planarity : 0.005 0.053 4796 Dihedral : 13.751 147.517 4363 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.52 % Favored : 95.39 % Rotamer: Outliers : 2.21 % Allowed : 12.75 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.14), residues: 3341 helix: 0.72 (0.15), residues: 1223 sheet: -0.55 (0.26), residues: 380 loop : -1.38 (0.14), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 115 HIS 0.014 0.001 HIS C 554 PHE 0.014 0.002 PHE C 157 TYR 0.041 0.002 TYR G 62 ARG 0.007 0.001 ARG G 21 Details of bonding type rmsd hydrogen bonds : bond 0.04144 ( 1198) hydrogen bonds : angle 5.19233 ( 3388) covalent geometry : bond 0.00360 (28042) covalent geometry : angle 0.62245 (38140) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 361 time to evaluate : 2.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 194 LEU cc_start: 0.6737 (tp) cc_final: 0.6425 (mt) REVERT: C 239 MET cc_start: 0.5525 (mmm) cc_final: 0.5065 (mmt) REVERT: C 368 ARG cc_start: 0.7588 (tpt90) cc_final: 0.7331 (tpt90) REVERT: C 422 LYS cc_start: 0.7392 (mttm) cc_final: 0.6940 (pttp) REVERT: C 631 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7407 (mp0) REVERT: C 851 THR cc_start: 0.8012 (t) cc_final: 0.7764 (p) REVERT: C 917 SER cc_start: 0.7907 (p) cc_final: 0.7490 (m) REVERT: C 967 LEU cc_start: 0.7456 (mt) cc_final: 0.7229 (mt) REVERT: C 1079 ILE cc_start: 0.7089 (pt) cc_final: 0.6709 (mt) REVERT: C 1143 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6175 (mp0) REVERT: C 1170 MET cc_start: 0.7440 (tpp) cc_final: 0.7170 (mmp) REVERT: D 193 ASP cc_start: 0.4676 (t70) cc_final: 0.4401 (t70) REVERT: D 298 MET cc_start: 0.5429 (ptm) cc_final: 0.4606 (mmt) REVERT: D 332 LYS cc_start: 0.7707 (ttpt) cc_final: 0.7313 (mtpp) REVERT: D 594 GLN cc_start: 0.6016 (tp-100) cc_final: 0.5579 (pt0) REVERT: D 685 ILE cc_start: 0.8088 (mt) cc_final: 0.7786 (mt) REVERT: D 838 ARG cc_start: 0.7026 (mtm110) cc_final: 0.6727 (mtp85) REVERT: D 913 GLU cc_start: 0.7018 (tt0) cc_final: 0.6796 (tt0) REVERT: D 1156 LEU cc_start: 0.5498 (mt) cc_final: 0.4515 (pp) REVERT: D 1189 MET cc_start: 0.6366 (tmm) cc_final: 0.5767 (mmp) REVERT: D 1367 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7769 (mm110) REVERT: E 74 GLU cc_start: 0.5585 (OUTLIER) cc_final: 0.4489 (tt0) REVERT: A 75 GLN cc_start: 0.5723 (tt0) cc_final: 0.5445 (tt0) REVERT: A 204 GLU cc_start: 0.6192 (pt0) cc_final: 0.5846 (mt-10) REVERT: G 1 MET cc_start: 0.2008 (mmp) cc_final: 0.1803 (tmm) REVERT: G 75 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7438 (tp30) REVERT: G 77 MET cc_start: 0.6096 (mpp) cc_final: 0.5690 (mpp) REVERT: B 29 GLU cc_start: 0.5611 (pm20) cc_final: 0.4831 (pm20) REVERT: B 51 MET cc_start: 0.6694 (tpt) cc_final: 0.5745 (tpt) REVERT: B 127 GLN cc_start: 0.6578 (mt0) cc_final: 0.6273 (mm110) outliers start: 63 outliers final: 38 residues processed: 407 average time/residue: 0.4024 time to fit residues: 258.1443 Evaluate side-chains 365 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 324 time to evaluate : 2.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 554 HIS Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 1143 GLU Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 655 SER Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 870 ASP Chi-restraints excluded: chain D residue 990 ARG Chi-restraints excluded: chain D residue 1190 ILE Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1332 LEU Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1367 GLN Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 186 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 296 optimal weight: 10.0000 chunk 283 optimal weight: 0.5980 chunk 280 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 chunk 301 optimal weight: 3.9990 chunk 10 optimal weight: 30.0000 chunk 169 optimal weight: 0.9980 chunk 156 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 15 optimal weight: 0.3980 chunk 282 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 673 HIS C1080 ASN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 GLN D 232 ASN ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN D 865 HIS ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 29 GLN ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4960 r_free = 0.4960 target = 0.243860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.201245 restraints weight = 34513.451| |-----------------------------------------------------------------------------| r_work (start): 0.4587 rms_B_bonded: 2.41 r_work: 0.4286 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28042 Z= 0.132 Angle : 0.589 8.778 38140 Z= 0.310 Chirality : 0.043 0.278 4349 Planarity : 0.004 0.056 4796 Dihedral : 13.644 146.845 4363 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.79 % Favored : 95.12 % Rotamer: Outliers : 2.63 % Allowed : 14.50 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.14), residues: 3341 helix: 0.82 (0.15), residues: 1230 sheet: -0.52 (0.26), residues: 381 loop : -1.34 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 36 HIS 0.011 0.001 HIS C 554 PHE 0.012 0.001 PHE C 35 TYR 0.017 0.001 TYR C 555 ARG 0.006 0.000 ARG G 21 Details of bonding type rmsd hydrogen bonds : bond 0.03774 ( 1198) hydrogen bonds : angle 4.96967 ( 3388) covalent geometry : bond 0.00297 (28042) covalent geometry : angle 0.58943 (38140) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 354 time to evaluate : 2.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 176 ILE cc_start: 0.7652 (mm) cc_final: 0.7405 (mm) REVERT: C 347 ILE cc_start: 0.7204 (mm) cc_final: 0.6923 (mm) REVERT: C 422 LYS cc_start: 0.7364 (mttm) cc_final: 0.6936 (pttp) REVERT: C 631 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7429 (mp0) REVERT: C 768 MET cc_start: 0.7139 (tpt) cc_final: 0.6903 (tpt) REVERT: C 851 THR cc_start: 0.7885 (t) cc_final: 0.7639 (p) REVERT: C 917 SER cc_start: 0.7935 (p) cc_final: 0.7585 (m) REVERT: C 955 GLN cc_start: 0.7215 (tm130) cc_final: 0.6990 (tt0) REVERT: C 967 LEU cc_start: 0.7403 (mt) cc_final: 0.7155 (mt) REVERT: C 1079 ILE cc_start: 0.6844 (pt) cc_final: 0.6551 (mt) REVERT: C 1143 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6200 (mp0) REVERT: D 92 VAL cc_start: 0.5614 (OUTLIER) cc_final: 0.5410 (t) REVERT: D 193 ASP cc_start: 0.4599 (t70) cc_final: 0.4351 (t0) REVERT: D 298 MET cc_start: 0.5320 (ptm) cc_final: 0.4425 (mmt) REVERT: D 332 LYS cc_start: 0.7701 (ttpt) cc_final: 0.7304 (mtpp) REVERT: D 537 TYR cc_start: 0.6676 (t80) cc_final: 0.6302 (t80) REVERT: D 685 ILE cc_start: 0.8105 (mt) cc_final: 0.7862 (mt) REVERT: D 1040 MET cc_start: 0.2453 (tpt) cc_final: 0.2036 (ttp) REVERT: D 1095 MET cc_start: 0.1552 (tpt) cc_final: -0.0631 (ptt) REVERT: D 1156 LEU cc_start: 0.5564 (mt) cc_final: 0.4535 (pp) REVERT: D 1282 TYR cc_start: 0.6372 (m-80) cc_final: 0.6143 (m-80) REVERT: D 1367 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7690 (mm-40) REVERT: E 73 GLN cc_start: 0.5570 (OUTLIER) cc_final: 0.4948 (mm-40) REVERT: E 74 GLU cc_start: 0.5584 (OUTLIER) cc_final: 0.4586 (tt0) REVERT: A 204 GLU cc_start: 0.6231 (pt0) cc_final: 0.5966 (mt-10) REVERT: G 1 MET cc_start: 0.1996 (mmp) cc_final: 0.1747 (tmm) REVERT: G 46 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.6871 (pt0) REVERT: G 75 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7370 (tp30) REVERT: B 29 GLU cc_start: 0.5483 (pm20) cc_final: 0.4830 (pm20) REVERT: B 35 PHE cc_start: 0.6207 (OUTLIER) cc_final: 0.5977 (t80) REVERT: B 51 MET cc_start: 0.6680 (tpt) cc_final: 0.5745 (tpt) REVERT: B 127 GLN cc_start: 0.6601 (mt0) cc_final: 0.6292 (mm110) outliers start: 75 outliers final: 44 residues processed: 411 average time/residue: 0.3984 time to fit residues: 257.8266 Evaluate side-chains 368 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 317 time to evaluate : 2.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 554 HIS Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1143 GLU Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 655 SER Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 744 ARG Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 870 ASP Chi-restraints excluded: chain D residue 990 ARG Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1190 ILE Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1367 GLN Chi-restraints excluded: chain E residue 73 GLN Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 217 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 297 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 280 optimal weight: 0.6980 chunk 284 optimal weight: 7.9990 chunk 143 optimal weight: 10.0000 chunk 28 optimal weight: 30.0000 chunk 248 optimal weight: 40.0000 chunk 197 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 447 HIS ** C 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 554 HIS C 573 ASN C1256 GLN D 94 GLN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 ASN D 232 ASN ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 667 GLN D 739 GLN ** D 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 921 GLN ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN A 194 GLN ** G 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.227586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.182224 restraints weight = 34498.137| |-----------------------------------------------------------------------------| r_work (start): 0.4388 rms_B_bonded: 2.72 r_work: 0.4026 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.087 28042 Z= 0.366 Angle : 0.841 11.396 38140 Z= 0.438 Chirality : 0.052 0.418 4349 Planarity : 0.006 0.069 4796 Dihedral : 14.019 145.782 4363 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 20.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.08 % Favored : 93.83 % Rotamer: Outliers : 4.03 % Allowed : 15.38 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.14), residues: 3341 helix: 0.15 (0.15), residues: 1210 sheet: -0.83 (0.26), residues: 384 loop : -1.56 (0.14), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP D 115 HIS 0.023 0.002 HIS C 554 PHE 0.030 0.003 PHE D 719 TYR 0.041 0.003 TYR G 62 ARG 0.011 0.001 ARG A 45 Details of bonding type rmsd hydrogen bonds : bond 0.05075 ( 1198) hydrogen bonds : angle 5.62105 ( 3388) covalent geometry : bond 0.00871 (28042) covalent geometry : angle 0.84149 (38140) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 339 time to evaluate : 2.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 ILE cc_start: 0.7607 (OUTLIER) cc_final: 0.7064 (tt) REVERT: C 177 ILE cc_start: 0.7702 (mm) cc_final: 0.7394 (mt) REVERT: C 191 LYS cc_start: 0.8573 (mmtt) cc_final: 0.8346 (mmmt) REVERT: C 239 MET cc_start: 0.4225 (mmm) cc_final: 0.3862 (mmm) REVERT: C 410 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7598 (tt) REVERT: C 422 LYS cc_start: 0.7387 (mttm) cc_final: 0.6922 (pttp) REVERT: C 454 ARG cc_start: 0.8277 (ttp-110) cc_final: 0.8042 (ttm110) REVERT: C 631 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7462 (mp0) REVERT: C 758 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.7071 (ttt-90) REVERT: C 768 MET cc_start: 0.7545 (tpt) cc_final: 0.7321 (tpt) REVERT: C 805 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7604 (ptt) REVERT: C 830 THR cc_start: 0.6969 (m) cc_final: 0.6694 (p) REVERT: C 946 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8504 (mm) REVERT: C 964 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7517 (tt) REVERT: C 1078 LYS cc_start: 0.7053 (pttt) cc_final: 0.6647 (ptpt) REVERT: C 1079 ILE cc_start: 0.7319 (pt) cc_final: 0.6955 (mt) REVERT: C 1188 ASP cc_start: 0.7666 (t0) cc_final: 0.7412 (t0) REVERT: D 37 GLU cc_start: 0.6827 (tp30) cc_final: 0.6608 (tp30) REVERT: D 193 ASP cc_start: 0.4711 (t70) cc_final: 0.4468 (t0) REVERT: D 298 MET cc_start: 0.5547 (ptm) cc_final: 0.4589 (mmt) REVERT: D 490 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8118 (pt) REVERT: D 822 MET cc_start: 0.6776 (mmm) cc_final: 0.6491 (mmm) REVERT: D 870 ASP cc_start: 0.7130 (OUTLIER) cc_final: 0.6808 (t70) REVERT: D 1040 MET cc_start: 0.2452 (tpt) cc_final: 0.2035 (ttp) REVERT: D 1156 LEU cc_start: 0.5840 (mt) cc_final: 0.4453 (pp) REVERT: D 1361 THR cc_start: 0.9041 (t) cc_final: 0.8705 (p) REVERT: E 73 GLN cc_start: 0.5534 (OUTLIER) cc_final: 0.4846 (mm-40) REVERT: E 74 GLU cc_start: 0.5657 (OUTLIER) cc_final: 0.4588 (tt0) REVERT: A 204 GLU cc_start: 0.6215 (pt0) cc_final: 0.5848 (mt-10) REVERT: B 29 GLU cc_start: 0.6039 (pm20) cc_final: 0.4807 (pm20) REVERT: B 35 PHE cc_start: 0.6556 (OUTLIER) cc_final: 0.6326 (t80) REVERT: B 51 MET cc_start: 0.6715 (tpt) cc_final: 0.6010 (tpt) REVERT: B 90 VAL cc_start: 0.5579 (OUTLIER) cc_final: 0.5368 (m) REVERT: B 214 GLU cc_start: 0.3847 (pt0) cc_final: 0.3420 (pt0) REVERT: B 217 ILE cc_start: 0.6028 (OUTLIER) cc_final: 0.5720 (tp) outliers start: 115 outliers final: 68 residues processed: 429 average time/residue: 0.3860 time to fit residues: 264.5661 Evaluate side-chains 383 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 302 time to evaluate : 2.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 554 HIS Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1080 ASN Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1143 GLU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 653 ILE Chi-restraints excluded: chain D residue 655 SER Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 744 ARG Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 870 ASP Chi-restraints excluded: chain D residue 1190 ILE Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1240 VAL Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain D residue 1370 MET Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 73 GLN Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 217 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 188 optimal weight: 6.9990 chunk 221 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 305 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 chunk 120 optimal weight: 8.9990 chunk 329 optimal weight: 7.9990 chunk 103 optimal weight: 0.0370 chunk 109 optimal weight: 0.9980 chunk 294 optimal weight: 9.9990 chunk 331 optimal weight: 3.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 GLN C 437 ASN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 GLN D 875 ASN D 921 GLN ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN ** G 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 29 GLN ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4888 r_free = 0.4888 target = 0.236104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.191539 restraints weight = 34348.186| |-----------------------------------------------------------------------------| r_work (start): 0.4478 rms_B_bonded: 2.46 r_work: 0.4172 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28042 Z= 0.146 Angle : 0.630 8.739 38140 Z= 0.332 Chirality : 0.044 0.219 4349 Planarity : 0.005 0.056 4796 Dihedral : 13.822 145.399 4363 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.73 % Favored : 95.18 % Rotamer: Outliers : 3.01 % Allowed : 17.06 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.14), residues: 3341 helix: 0.55 (0.15), residues: 1214 sheet: -0.78 (0.26), residues: 391 loop : -1.51 (0.14), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 73 HIS 0.023 0.001 HIS C 554 PHE 0.026 0.001 PHE D 17 TYR 0.021 0.001 TYR D 772 ARG 0.009 0.001 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.03937 ( 1198) hydrogen bonds : angle 5.11935 ( 3388) covalent geometry : bond 0.00329 (28042) covalent geometry : angle 0.62991 (38140) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 341 time to evaluate : 2.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 239 MET cc_start: 0.3973 (mmm) cc_final: 0.3640 (mmm) REVERT: C 410 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7557 (tt) REVERT: C 422 LYS cc_start: 0.7342 (mttm) cc_final: 0.6922 (pttp) REVERT: C 631 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7463 (mp0) REVERT: C 768 MET cc_start: 0.7217 (tpt) cc_final: 0.6967 (tpt) REVERT: C 805 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7559 (ptt) REVERT: C 851 THR cc_start: 0.8136 (t) cc_final: 0.7909 (p) REVERT: C 964 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7373 (tt) REVERT: C 1079 ILE cc_start: 0.6813 (pt) cc_final: 0.6523 (mt) REVERT: C 1188 ASP cc_start: 0.7162 (t0) cc_final: 0.6932 (t0) REVERT: D 283 LEU cc_start: 0.5786 (mt) cc_final: 0.5359 (tt) REVERT: D 298 MET cc_start: 0.5438 (ptm) cc_final: 0.4550 (mmt) REVERT: D 329 ASP cc_start: 0.7315 (m-30) cc_final: 0.6835 (m-30) REVERT: D 822 MET cc_start: 0.6886 (mmm) cc_final: 0.6211 (mmm) REVERT: D 870 ASP cc_start: 0.7044 (OUTLIER) cc_final: 0.6696 (t70) REVERT: D 1040 MET cc_start: 0.2437 (tpt) cc_final: 0.2059 (ttp) REVERT: D 1095 MET cc_start: 0.2077 (tpt) cc_final: -0.0695 (ptt) REVERT: D 1152 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6328 (mp0) REVERT: D 1156 LEU cc_start: 0.5705 (mt) cc_final: 0.4431 (pp) REVERT: D 1191 PRO cc_start: 0.7467 (Cg_exo) cc_final: 0.7109 (Cg_endo) REVERT: E 12 LYS cc_start: 0.6449 (mmtp) cc_final: 0.6129 (mmmm) REVERT: E 73 GLN cc_start: 0.5519 (OUTLIER) cc_final: 0.4875 (mm-40) REVERT: E 74 GLU cc_start: 0.5580 (OUTLIER) cc_final: 0.4604 (tt0) REVERT: A 204 GLU cc_start: 0.6178 (pt0) cc_final: 0.5842 (mt-10) REVERT: G 1 MET cc_start: 0.3563 (mmm) cc_final: 0.1000 (tmm) REVERT: B 29 GLU cc_start: 0.5802 (pm20) cc_final: 0.4826 (pm20) REVERT: B 35 PHE cc_start: 0.6206 (OUTLIER) cc_final: 0.5970 (t80) REVERT: B 51 MET cc_start: 0.6552 (tpt) cc_final: 0.5886 (tpt) REVERT: B 127 GLN cc_start: 0.6902 (mt0) cc_final: 0.6536 (mm110) REVERT: B 217 ILE cc_start: 0.5624 (OUTLIER) cc_final: 0.5379 (tp) REVERT: B 227 GLN cc_start: 0.6788 (OUTLIER) cc_final: 0.6387 (mt0) outliers start: 86 outliers final: 43 residues processed: 408 average time/residue: 0.3913 time to fit residues: 254.6691 Evaluate side-chains 361 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 309 time to evaluate : 2.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 554 HIS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1143 GLU Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 744 ARG Chi-restraints excluded: chain D residue 870 ASP Chi-restraints excluded: chain D residue 875 ASN Chi-restraints excluded: chain D residue 1190 ILE Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1221 LEU Chi-restraints excluded: chain D residue 1240 VAL Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 73 GLN Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 227 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 223 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 180 optimal weight: 0.5980 chunk 122 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 278 optimal weight: 0.7980 chunk 333 optimal weight: 10.0000 chunk 185 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 107 optimal weight: 0.0170 chunk 236 optimal weight: 0.0060 overall best weight: 1.0836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 519 ASN ** D 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 875 ASN A 23 HIS A 41 ASN A 75 GLN ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.235813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.191783 restraints weight = 34126.273| |-----------------------------------------------------------------------------| r_work (start): 0.4487 rms_B_bonded: 2.51 r_work: 0.4162 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 28042 Z= 0.154 Angle : 0.626 10.913 38140 Z= 0.328 Chirality : 0.044 0.213 4349 Planarity : 0.005 0.058 4796 Dihedral : 13.726 146.272 4363 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.97 % Favored : 94.94 % Rotamer: Outliers : 3.12 % Allowed : 17.86 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.14), residues: 3341 helix: 0.65 (0.15), residues: 1224 sheet: -0.75 (0.25), residues: 416 loop : -1.47 (0.14), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 183 HIS 0.017 0.001 HIS C 554 PHE 0.025 0.001 PHE D 17 TYR 0.046 0.002 TYR G 62 ARG 0.007 0.000 ARG C1269 Details of bonding type rmsd hydrogen bonds : bond 0.03840 ( 1198) hydrogen bonds : angle 5.01273 ( 3388) covalent geometry : bond 0.00356 (28042) covalent geometry : angle 0.62627 (38140) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 326 time to evaluate : 2.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 191 LYS cc_start: 0.8523 (mmtt) cc_final: 0.8322 (mmmt) REVERT: C 239 MET cc_start: 0.4337 (mmm) cc_final: 0.3916 (mmm) REVERT: C 347 ILE cc_start: 0.7325 (mm) cc_final: 0.7089 (mm) REVERT: C 410 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7553 (tt) REVERT: C 422 LYS cc_start: 0.7385 (mttm) cc_final: 0.6941 (pttp) REVERT: C 631 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7454 (mp0) REVERT: C 805 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7767 (ptt) REVERT: C 851 THR cc_start: 0.8130 (t) cc_final: 0.7890 (p) REVERT: C 964 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7330 (tt) REVERT: C 1079 ILE cc_start: 0.6898 (pt) cc_final: 0.6613 (mt) REVERT: C 1170 MET cc_start: 0.7815 (tpp) cc_final: 0.7432 (mmt) REVERT: C 1188 ASP cc_start: 0.7157 (t0) cc_final: 0.6908 (t0) REVERT: D 37 GLU cc_start: 0.6609 (tp30) cc_final: 0.6361 (tp30) REVERT: D 180 MET cc_start: 0.2458 (mmp) cc_final: -0.0160 (pmm) REVERT: D 283 LEU cc_start: 0.5706 (mt) cc_final: 0.5332 (tt) REVERT: D 298 MET cc_start: 0.5499 (ptm) cc_final: 0.4554 (mmt) REVERT: D 329 ASP cc_start: 0.7412 (m-30) cc_final: 0.6944 (m-30) REVERT: D 725 MET cc_start: 0.6847 (OUTLIER) cc_final: 0.6115 (mmt) REVERT: D 822 MET cc_start: 0.6817 (mmm) cc_final: 0.6295 (mmm) REVERT: D 870 ASP cc_start: 0.7002 (OUTLIER) cc_final: 0.6661 (t70) REVERT: D 1040 MET cc_start: 0.2415 (tpt) cc_final: 0.2054 (ttp) REVERT: D 1095 MET cc_start: 0.1573 (tpt) cc_final: -0.0708 (ptt) REVERT: D 1152 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6393 (mp0) REVERT: D 1156 LEU cc_start: 0.5727 (mt) cc_final: 0.4440 (pp) REVERT: D 1189 MET cc_start: 0.6715 (tmm) cc_final: 0.6405 (tmm) REVERT: D 1191 PRO cc_start: 0.7449 (Cg_exo) cc_final: 0.6961 (Cg_endo) REVERT: E 12 LYS cc_start: 0.6490 (mmtp) cc_final: 0.6156 (mmmm) REVERT: E 73 GLN cc_start: 0.5497 (OUTLIER) cc_final: 0.4873 (mm-40) REVERT: E 74 GLU cc_start: 0.5553 (OUTLIER) cc_final: 0.4602 (tt0) REVERT: A 204 GLU cc_start: 0.6281 (pt0) cc_final: 0.5906 (mt-10) REVERT: G 1 MET cc_start: 0.3440 (mmm) cc_final: 0.0957 (tmm) REVERT: G 77 MET cc_start: 0.6313 (mpt) cc_final: 0.6084 (mpp) REVERT: B 29 GLU cc_start: 0.5754 (pm20) cc_final: 0.4838 (pm20) REVERT: B 35 PHE cc_start: 0.6142 (OUTLIER) cc_final: 0.5912 (t80) REVERT: B 51 MET cc_start: 0.6513 (tpt) cc_final: 0.5759 (tpt) REVERT: B 127 GLN cc_start: 0.6923 (mt0) cc_final: 0.6546 (mm110) REVERT: B 214 GLU cc_start: 0.3767 (pt0) cc_final: 0.3447 (pt0) REVERT: B 217 ILE cc_start: 0.5821 (OUTLIER) cc_final: 0.5536 (tp) REVERT: B 227 GLN cc_start: 0.6832 (OUTLIER) cc_final: 0.6420 (mt0) outliers start: 89 outliers final: 53 residues processed: 392 average time/residue: 0.3829 time to fit residues: 240.5864 Evaluate side-chains 375 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 312 time to evaluate : 3.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 554 HIS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1143 GLU Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 497 GLU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 744 ARG Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 870 ASP Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1190 ILE Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1221 LEU Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 73 GLN Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 227 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 153 optimal weight: 40.0000 chunk 161 optimal weight: 8.9990 chunk 285 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 222 optimal weight: 2.9990 chunk 295 optimal weight: 3.9990 chunk 308 optimal weight: 20.0000 chunk 235 optimal weight: 30.0000 chunk 218 optimal weight: 9.9990 chunk 214 optimal weight: 0.1980 chunk 96 optimal weight: 8.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 875 ASN ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4846 r_free = 0.4846 target = 0.231300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.185869 restraints weight = 34349.012| |-----------------------------------------------------------------------------| r_work (start): 0.4424 rms_B_bonded: 2.62 r_work: 0.4082 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 28042 Z= 0.230 Angle : 0.701 11.805 38140 Z= 0.365 Chirality : 0.046 0.279 4349 Planarity : 0.005 0.056 4796 Dihedral : 13.790 146.959 4363 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.60 % Favored : 94.31 % Rotamer: Outliers : 3.29 % Allowed : 18.00 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.14), residues: 3341 helix: 0.46 (0.15), residues: 1215 sheet: -0.78 (0.26), residues: 395 loop : -1.49 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 36 HIS 0.023 0.002 HIS C 554 PHE 0.023 0.002 PHE D 17 TYR 0.025 0.002 TYR C 578 ARG 0.008 0.001 ARG A 45 Details of bonding type rmsd hydrogen bonds : bond 0.04202 ( 1198) hydrogen bonds : angle 5.19755 ( 3388) covalent geometry : bond 0.00549 (28042) covalent geometry : angle 0.70115 (38140) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 318 time to evaluate : 2.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 22 LEU cc_start: 0.7977 (tp) cc_final: 0.7745 (tp) REVERT: C 39 ILE cc_start: 0.7531 (OUTLIER) cc_final: 0.6908 (tt) REVERT: C 175 ARG cc_start: 0.7306 (tpp80) cc_final: 0.7105 (tpp80) REVERT: C 191 LYS cc_start: 0.8647 (mmtt) cc_final: 0.8351 (mmmt) REVERT: C 239 MET cc_start: 0.4510 (mmm) cc_final: 0.3931 (mmm) REVERT: C 410 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7583 (tt) REVERT: C 422 LYS cc_start: 0.7437 (mttm) cc_final: 0.6968 (pttp) REVERT: C 631 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7430 (mp0) REVERT: C 805 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7752 (ptt) REVERT: C 964 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7428 (tt) REVERT: C 1079 ILE cc_start: 0.7030 (pt) cc_final: 0.6728 (mt) REVERT: C 1188 ASP cc_start: 0.7466 (t0) cc_final: 0.7193 (t0) REVERT: D 283 LEU cc_start: 0.5767 (mt) cc_final: 0.5355 (tt) REVERT: D 298 MET cc_start: 0.5564 (ptm) cc_final: 0.4531 (mmt) REVERT: D 329 ASP cc_start: 0.7526 (m-30) cc_final: 0.7065 (m-30) REVERT: D 725 MET cc_start: 0.7021 (OUTLIER) cc_final: 0.6324 (mmt) REVERT: D 822 MET cc_start: 0.6721 (mmm) cc_final: 0.6338 (mmm) REVERT: D 870 ASP cc_start: 0.7071 (OUTLIER) cc_final: 0.6758 (t70) REVERT: D 1040 MET cc_start: 0.2360 (tpt) cc_final: 0.2081 (ttp) REVERT: D 1152 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6386 (mp0) REVERT: D 1191 PRO cc_start: 0.7284 (Cg_exo) cc_final: 0.6936 (Cg_endo) REVERT: E 12 LYS cc_start: 0.6522 (mmtp) cc_final: 0.6207 (mmmm) REVERT: E 73 GLN cc_start: 0.5544 (OUTLIER) cc_final: 0.4927 (mm-40) REVERT: E 74 GLU cc_start: 0.5704 (OUTLIER) cc_final: 0.4710 (tt0) REVERT: A 204 GLU cc_start: 0.6342 (pt0) cc_final: 0.5934 (mt-10) REVERT: G 1 MET cc_start: 0.3541 (mmm) cc_final: 0.1006 (tmm) REVERT: B 29 GLU cc_start: 0.5871 (pm20) cc_final: 0.4896 (pm20) REVERT: B 35 PHE cc_start: 0.6143 (OUTLIER) cc_final: 0.5932 (t80) REVERT: B 51 MET cc_start: 0.6504 (tpt) cc_final: 0.5752 (tpt) REVERT: B 227 GLN cc_start: 0.6889 (OUTLIER) cc_final: 0.6442 (mt0) outliers start: 94 outliers final: 65 residues processed: 383 average time/residue: 0.3643 time to fit residues: 223.2288 Evaluate side-chains 378 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 303 time to evaluate : 2.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 554 HIS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1143 GLU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 497 GLU Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 744 ARG Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 870 ASP Chi-restraints excluded: chain D residue 964 LYS Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1190 ILE Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1221 LEU Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 73 GLN Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 227 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 323 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 143 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 146 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 875 ASN ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4879 r_free = 0.4879 target = 0.235120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.189842 restraints weight = 34250.681| |-----------------------------------------------------------------------------| r_work (start): 0.4463 rms_B_bonded: 2.46 r_work: 0.4158 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 28042 Z= 0.155 Angle : 0.640 12.345 38140 Z= 0.334 Chirality : 0.044 0.222 4349 Planarity : 0.005 0.055 4796 Dihedral : 13.706 145.824 4363 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.97 % Favored : 94.94 % Rotamer: Outliers : 2.63 % Allowed : 18.49 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.14), residues: 3341 helix: 0.56 (0.15), residues: 1232 sheet: -0.77 (0.25), residues: 403 loop : -1.50 (0.14), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 73 HIS 0.017 0.001 HIS C 554 PHE 0.023 0.001 PHE D 17 TYR 0.027 0.002 TYR G 61 ARG 0.007 0.000 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.03839 ( 1198) hydrogen bonds : angle 5.06742 ( 3388) covalent geometry : bond 0.00360 (28042) covalent geometry : angle 0.63979 (38140) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 321 time to evaluate : 2.798 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: C 22 LEU cc_start: 0.7888 (tp) cc_final: 0.7682 (tp) REVERT: C 191 LYS cc_start: 0.8606 (mmtt) cc_final: 0.8287 (mmmt) REVERT: C 239 MET cc_start: 0.4352 (mmm) cc_final: 0.3921 (mmm) REVERT: C 410 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7540 (tt) REVERT: C 422 LYS cc_start: 0.7407 (mttm) cc_final: 0.6946 (pttp) REVERT: C 439 LYS cc_start: 0.6451 (mppt) cc_final: 0.6154 (tttt) REVERT: C 631 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7448 (mp0) REVERT: C 805 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7834 (ptt) REVERT: C 851 THR cc_start: 0.8135 (t) cc_final: 0.7891 (p) REVERT: C 964 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7319 (tt) REVERT: C 1079 ILE cc_start: 0.6821 (pt) cc_final: 0.6550 (mt) REVERT: C 1188 ASP cc_start: 0.7260 (t0) cc_final: 0.7026 (t0) REVERT: D 298 MET cc_start: 0.5560 (ptm) cc_final: 0.4570 (mmt) REVERT: D 329 ASP cc_start: 0.7421 (m-30) cc_final: 0.6981 (m-30) REVERT: D 334 LYS cc_start: 0.4394 (mmtt) cc_final: 0.3704 (tptp) REVERT: D 725 MET cc_start: 0.6872 (OUTLIER) cc_final: 0.6144 (mmt) REVERT: D 822 MET cc_start: 0.6720 (mmm) cc_final: 0.6274 (mmm) REVERT: D 870 ASP cc_start: 0.6835 (OUTLIER) cc_final: 0.6517 (t70) REVERT: D 1040 MET cc_start: 0.2300 (tpt) cc_final: 0.2001 (ttp) REVERT: D 1095 MET cc_start: 0.1708 (tpt) cc_final: -0.0309 (ppp) REVERT: D 1152 GLU cc_start: 0.7241 (mt-10) cc_final: 0.6361 (mp0) REVERT: D 1191 PRO cc_start: 0.7365 (Cg_exo) cc_final: 0.7024 (Cg_endo) REVERT: E 12 LYS cc_start: 0.6533 (mmtp) cc_final: 0.6229 (mmmm) REVERT: E 73 GLN cc_start: 0.5547 (OUTLIER) cc_final: 0.4939 (mm-40) REVERT: E 74 GLU cc_start: 0.5733 (OUTLIER) cc_final: 0.4746 (tt0) REVERT: A 33 ARG cc_start: 0.7765 (tmm-80) cc_final: 0.7266 (tpp80) REVERT: A 204 GLU cc_start: 0.6387 (pt0) cc_final: 0.6002 (mt-10) REVERT: G 1 MET cc_start: 0.3390 (mmm) cc_final: 0.0948 (tmm) REVERT: B 29 GLU cc_start: 0.5827 (pm20) cc_final: 0.4975 (pm20) REVERT: B 35 PHE cc_start: 0.6058 (OUTLIER) cc_final: 0.5827 (t80) REVERT: B 51 MET cc_start: 0.6462 (tpt) cc_final: 0.5699 (tpt) REVERT: B 227 GLN cc_start: 0.6813 (OUTLIER) cc_final: 0.6404 (mt0) outliers start: 75 outliers final: 60 residues processed: 374 average time/residue: 0.3801 time to fit residues: 228.4735 Evaluate side-chains 375 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 306 time to evaluate : 2.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 554 HIS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1143 GLU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 497 GLU Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 744 ARG Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 870 ASP Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1190 ILE Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1221 LEU Chi-restraints excluded: chain D residue 1240 VAL Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 73 GLN Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 227 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 272 optimal weight: 1.9990 chunk 141 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 59 optimal weight: 0.2980 chunk 228 optimal weight: 0.8980 chunk 256 optimal weight: 0.6980 chunk 95 optimal weight: 0.4980 chunk 173 optimal weight: 2.9990 chunk 250 optimal weight: 7.9990 chunk 292 optimal weight: 5.9990 chunk 172 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 808 ASN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 875 ASN ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4902 r_free = 0.4902 target = 0.237875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.193300 restraints weight = 34234.159| |-----------------------------------------------------------------------------| r_work (start): 0.4499 rms_B_bonded: 2.47 r_work: 0.4200 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28042 Z= 0.134 Angle : 0.621 13.015 38140 Z= 0.323 Chirality : 0.043 0.217 4349 Planarity : 0.004 0.055 4796 Dihedral : 13.631 146.513 4363 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.79 % Favored : 95.12 % Rotamer: Outliers : 2.45 % Allowed : 19.16 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.14), residues: 3341 helix: 0.73 (0.15), residues: 1229 sheet: -0.69 (0.25), residues: 403 loop : -1.44 (0.14), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP G 73 HIS 0.013 0.001 HIS C 554 PHE 0.023 0.001 PHE D 17 TYR 0.030 0.001 TYR G 61 ARG 0.007 0.000 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.03682 ( 1198) hydrogen bonds : angle 4.98316 ( 3388) covalent geometry : bond 0.00307 (28042) covalent geometry : angle 0.62073 (38140) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 329 time to evaluate : 2.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 37 LYS cc_start: 0.6308 (tptt) cc_final: 0.6023 (tptt) REVERT: C 191 LYS cc_start: 0.8556 (mmtt) cc_final: 0.8232 (mmmt) REVERT: C 239 MET cc_start: 0.4289 (mmm) cc_final: 0.3603 (mmp) REVERT: C 410 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7540 (tt) REVERT: C 422 LYS cc_start: 0.7385 (mttm) cc_final: 0.6944 (pttp) REVERT: C 439 LYS cc_start: 0.6444 (mppt) cc_final: 0.6122 (tttt) REVERT: C 631 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7435 (mp0) REVERT: C 805 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7877 (ptt) REVERT: C 851 THR cc_start: 0.8106 (t) cc_final: 0.7869 (p) REVERT: C 964 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7241 (tt) REVERT: C 1143 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6416 (mp0) REVERT: D 298 MET cc_start: 0.5661 (ptm) cc_final: 0.4619 (mmt) REVERT: D 332 LYS cc_start: 0.7732 (ttpt) cc_final: 0.7361 (mtpp) REVERT: D 334 LYS cc_start: 0.4310 (mmtt) cc_final: 0.3621 (tptp) REVERT: D 725 MET cc_start: 0.6894 (OUTLIER) cc_final: 0.6102 (mmt) REVERT: D 822 MET cc_start: 0.6790 (mmm) cc_final: 0.6342 (mmm) REVERT: D 870 ASP cc_start: 0.6868 (OUTLIER) cc_final: 0.6515 (t70) REVERT: D 1040 MET cc_start: 0.2386 (tpt) cc_final: 0.1987 (ttp) REVERT: D 1191 PRO cc_start: 0.7291 (Cg_exo) cc_final: 0.6936 (Cg_endo) REVERT: E 12 LYS cc_start: 0.6578 (mmtp) cc_final: 0.6304 (mmmm) REVERT: E 28 ARG cc_start: 0.6237 (mtt-85) cc_final: 0.5860 (mtt180) REVERT: E 73 GLN cc_start: 0.5508 (OUTLIER) cc_final: 0.4923 (mm-40) REVERT: E 74 GLU cc_start: 0.5729 (OUTLIER) cc_final: 0.4855 (tt0) REVERT: A 33 ARG cc_start: 0.7763 (tmm-80) cc_final: 0.7260 (tpp80) REVERT: A 204 GLU cc_start: 0.6438 (pt0) cc_final: 0.6066 (mt-10) REVERT: G 1 MET cc_start: 0.3245 (mmm) cc_final: 0.1049 (tmm) REVERT: B 12 ARG cc_start: 0.2854 (mtm180) cc_final: 0.2628 (mtm180) REVERT: B 29 GLU cc_start: 0.5640 (pm20) cc_final: 0.4783 (pm20) REVERT: B 35 PHE cc_start: 0.5919 (OUTLIER) cc_final: 0.5681 (t80) REVERT: B 51 MET cc_start: 0.6436 (tpt) cc_final: 0.5646 (tpt) REVERT: B 227 GLN cc_start: 0.6795 (OUTLIER) cc_final: 0.6387 (mt0) outliers start: 70 outliers final: 52 residues processed: 382 average time/residue: 0.3809 time to fit residues: 232.8720 Evaluate side-chains 364 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 302 time to evaluate : 2.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 554 HIS Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1143 GLU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 490 ILE Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 870 ASP Chi-restraints excluded: chain D residue 875 ASN Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1190 ILE Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1221 LEU Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 73 GLN Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 227 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 157 optimal weight: 0.8980 chunk 267 optimal weight: 3.9990 chunk 271 optimal weight: 0.9980 chunk 297 optimal weight: 0.7980 chunk 33 optimal weight: 20.0000 chunk 286 optimal weight: 4.9990 chunk 246 optimal weight: 0.9980 chunk 182 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 307 optimal weight: 10.0000 chunk 288 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 716 GLN ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4898 r_free = 0.4898 target = 0.237485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.192516 restraints weight = 34236.876| |-----------------------------------------------------------------------------| r_work (start): 0.4492 rms_B_bonded: 2.46 r_work: 0.4192 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28042 Z= 0.144 Angle : 0.630 12.987 38140 Z= 0.328 Chirality : 0.044 0.212 4349 Planarity : 0.005 0.055 4796 Dihedral : 13.642 145.799 4363 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.91 % Favored : 95.00 % Rotamer: Outliers : 2.35 % Allowed : 19.23 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.14), residues: 3341 helix: 0.76 (0.15), residues: 1227 sheet: -0.65 (0.25), residues: 409 loop : -1.43 (0.14), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 73 HIS 0.016 0.001 HIS C 554 PHE 0.023 0.001 PHE D 17 TYR 0.031 0.001 TYR G 61 ARG 0.008 0.000 ARG C 407 Details of bonding type rmsd hydrogen bonds : bond 0.03693 ( 1198) hydrogen bonds : angle 4.94860 ( 3388) covalent geometry : bond 0.00333 (28042) covalent geometry : angle 0.62953 (38140) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15029.74 seconds wall clock time: 260 minutes 46.41 seconds (15646.41 seconds total)