Starting phenix.real_space_refine on Sun Jun 22 18:17:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dr1_47120/06_2025/9dr1_47120.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dr1_47120/06_2025/9dr1_47120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dr1_47120/06_2025/9dr1_47120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dr1_47120/06_2025/9dr1_47120.map" model { file = "/net/cci-nas-00/data/ceres_data/9dr1_47120/06_2025/9dr1_47120.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dr1_47120/06_2025/9dr1_47120.cif" } resolution = 3.7 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= 0.012 sd= 0.096 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: 6 Type Number sf(0) Gaussians P 67 5.49 5 Mg 1 5.21 5 S 105 5.16 5 C 16232 2.51 5 N 4644 2.21 5 O 5196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26245 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 369 Inner-chain residues flagged as termini: ['pdbres=" DG A 17 "'] Classifications: {'DNA': 18} Modifications used: {'5*END': 2} Link IDs: {'rna3p': 17} Chain: "B" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 601 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "G" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1717 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 9, 'TRANS': 212} Chain breaks: 1 Chain: "H" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1702 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 8, 'TRANS': 211} Chain breaks: 1 Chain: "I" Number of atoms: 10381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1316, 10381 Classifications: {'peptide': 1316} Link IDs: {'PTRANS': 55, 'TRANS': 1260} Chain breaks: 1 Chain: "J" Number of atoms: 10397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1336, 10397 Classifications: {'peptide': 1336} Link IDs: {'PTRANS': 55, 'TRANS': 1280} Chain breaks: 3 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 450 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 4, 'rna3p_pur': 11, 'rna3p_pyr': 5} Link IDs: {'rna2p': 5, 'rna3p': 15} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.66, per 1000 atoms: 0.56 Number of scatterers: 26245 At special positions: 0 Unit cell: (138, 153, 165, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 105 16.00 P 67 15.00 Mg 1 11.99 O 5196 8.00 N 4644 7.00 C 16232 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: 6.19 Conformation dependent library (CDL) restraints added in 3.4 seconds 6302 Ramachandran restraints generated. 3151 Oldfield, 0 Emsley, 3151 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5858 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 46 sheets defined 37.9% alpha, 16.8% beta 25 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 9.53 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.715A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER G 50 " --> pdb=" O ILE G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.693A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 212 through 229 removed outlier: 3.549A pdb=" N GLU G 229 " --> pdb=" O ALA G 225 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.619A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 88 Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 212 through 227 Processing helix chain 'I' and resid 4 through 10 removed outlier: 3.914A pdb=" N ARG I 10 " --> pdb=" O THR I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 39 removed outlier: 3.536A pdb=" N LEU I 32 " --> pdb=" O LEU I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 57 removed outlier: 3.835A pdb=" N VAL I 56 " --> pdb=" O ALA I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.948A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 288 through 295 removed outlier: 3.842A pdb=" N ILE I 292 " --> pdb=" O PRO I 288 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA I 293 " --> pdb=" O VAL I 289 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLY I 294 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LYS I 295 " --> pdb=" O TYR I 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 288 through 295' Processing helix chain 'I' and resid 318 through 329 Processing helix chain 'I' and resid 345 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 4.028A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE I 390 " --> pdb=" O GLU I 386 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 455 through 481 removed outlier: 3.922A pdb=" N ARG I 470 " --> pdb=" O VAL I 466 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL I 471 " --> pdb=" O GLY I 467 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU I 481 " --> pdb=" O GLU I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 494 through 508 removed outlier: 4.638A pdb=" N ILE I 498 " --> pdb=" O ASN I 494 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE I 505 " --> pdb=" O ALA I 501 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.757A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 607 through 614 removed outlier: 3.931A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TYR I 614 " --> pdb=" O GLU I 610 " (cutoff:3.500A) Processing helix chain 'I' and resid 656 through 660 removed outlier: 3.518A pdb=" N GLN I 659 " --> pdb=" O SER I 656 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL I 660 " --> pdb=" O THR I 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 656 through 660' Processing helix chain 'I' and resid 662 through 667 removed outlier: 3.542A pdb=" N LEU I 667 " --> pdb=" O VAL I 663 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 removed outlier: 3.892A pdb=" N ASP I 674 " --> pdb=" O LEU I 671 " (cutoff:3.500A) Processing helix chain 'I' and resid 675 through 686 Processing helix chain 'I' and resid 687 through 689 No H-bonds generated for 'chain 'I' and resid 687 through 689' Processing helix chain 'I' and resid 704 through 711 Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 858 through 865 removed outlier: 3.866A pdb=" N LEU I 862 " --> pdb=" O GLY I 858 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS I 864 " --> pdb=" O ALA I 860 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU I 865 " --> pdb=" O ALA I 861 " (cutoff:3.500A) Processing helix chain 'I' and resid 942 through 981 removed outlier: 3.789A pdb=" N ALA I 981 " --> pdb=" O ALA I 977 " (cutoff:3.500A) Processing helix chain 'I' and resid 987 through 992 Processing helix chain 'I' and resid 1006 through 1038 Processing helix chain 'I' and resid 1081 through 1085 removed outlier: 3.541A pdb=" N MET I1085 " --> pdb=" O ILE I1082 " (cutoff:3.500A) Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 4.116A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG I1106 " --> pdb=" O GLY I1102 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1101 through 1106' Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.713A pdb=" N GLN I1134 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1150 removed outlier: 3.558A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 3.776A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1177 Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1260 through 1264 removed outlier: 3.643A pdb=" N GLN I1264 " --> pdb=" O GLY I1261 " (cutoff:3.500A) Processing helix chain 'I' and resid 1271 through 1281 removed outlier: 3.557A pdb=" N TRP I1276 " --> pdb=" O GLU I1272 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA I1277 " --> pdb=" O MET I1273 " (cutoff:3.500A) Processing helix chain 'I' and resid 1284 through 1292 Processing helix chain 'I' and resid 1297 through 1310 removed outlier: 3.513A pdb=" N VAL I1309 " --> pdb=" O TYR I1305 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP I1310 " --> pdb=" O LYS I1306 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1332 removed outlier: 3.665A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 72 through 76 Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.571A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 162 through 172 Processing helix chain 'J' and resid 181 through 192 removed outlier: 3.697A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 209 removed outlier: 3.553A pdb=" N GLU J 197 " --> pdb=" O ASP J 193 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASN J 209 " --> pdb=" O LEU J 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 215 Processing helix chain 'J' and resid 216 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 264 through 286 removed outlier: 3.870A pdb=" N LEU J 268 " --> pdb=" O ASP J 264 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 336 through 341 Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 389 Processing helix chain 'J' and resid 393 through 403 Processing helix chain 'J' and resid 405 through 416 removed outlier: 3.912A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 417 through 419 No H-bonds generated for 'chain 'J' and resid 417 through 419' Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 453 through 458 removed outlier: 3.509A pdb=" N TYR J 457 " --> pdb=" O VAL J 453 " (cutoff:3.500A) Processing helix chain 'J' and resid 473 through 484 Processing helix chain 'J' and resid 504 through 514 removed outlier: 3.740A pdb=" N LEU J 508 " --> pdb=" O GLN J 504 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 580 Processing helix chain 'J' and resid 597 through 613 Processing helix chain 'J' and resid 614 through 636 Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 703 removed outlier: 3.937A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 741 Processing helix chain 'J' and resid 768 through 804 removed outlier: 3.910A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 removed outlier: 3.635A pdb=" N ARG J 838 " --> pdb=" O PRO J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 876 removed outlier: 3.620A pdb=" N ASN J 875 " --> pdb=" O LEU J 871 " (cutoff:3.500A) Processing helix chain 'J' and resid 895 through 900 removed outlier: 3.641A pdb=" N TYR J 899 " --> pdb=" O CYS J 895 " (cutoff:3.500A) Processing helix chain 'J' and resid 914 through 925 Processing helix chain 'J' and resid 926 through 929 Processing helix chain 'J' and resid 1068 through 1074 removed outlier: 3.627A pdb=" N LEU J1074 " --> pdb=" O GLY J1070 " (cutoff:3.500A) Processing helix chain 'J' and resid 1137 through 1147 Processing helix chain 'J' and resid 1216 through 1225 Processing helix chain 'J' and resid 1225 through 1245 removed outlier: 3.512A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU J1243 " --> pdb=" O ASP J1239 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.184A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1318 through 1326 removed outlier: 3.632A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1347 through 1354 Processing helix chain 'J' and resid 1361 through 1373 removed outlier: 4.623A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 11 Processing helix chain 'K' and resid 17 through 33 removed outlier: 3.750A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 57 Processing helix chain 'K' and resid 60 through 80 removed outlier: 3.658A pdb=" N LEU K 80 " --> pdb=" O GLU K 76 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 13 through 15 removed outlier: 4.069A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG G 182 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.546A pdb=" N LYS G 104 " --> pdb=" O ILE G 140 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N SER G 141 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ILE G 61 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AA5, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.555A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 15 through 18 removed outlier: 6.759A pdb=" N GLU H 206 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 15 through 18 Processing sheet with id=AA8, first strand: chain 'H' and resid 97 through 105 removed outlier: 3.677A pdb=" N GLU H 58 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AB1, first strand: chain 'H' and resid 108 through 111 removed outlier: 3.650A pdb=" N GLY H 108 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU H 133 " --> pdb=" O GLY H 108 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB3, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.722A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 66 through 75 removed outlier: 6.838A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU I 100 " --> pdb=" O GLN I 120 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB6, first strand: chain 'I' and resid 451 through 454 removed outlier: 6.516A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 154 through 158 Processing sheet with id=AB8, first strand: chain 'I' and resid 226 through 230 removed outlier: 4.656A pdb=" N GLU I 226 " --> pdb=" O PHE I 337 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 239 through 240 Processing sheet with id=AC1, first strand: chain 'I' and resid 250 through 251 removed outlier: 3.718A pdb=" N ARG I 267 " --> pdb=" O ALA I 251 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 255 through 257 removed outlier: 3.701A pdb=" N VAL I 263 " --> pdb=" O ILE I 255 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 301 through 302 removed outlier: 7.115A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 580 through 581 removed outlier: 6.024A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC6, first strand: chain 'I' and resid 616 through 617 removed outlier: 3.823A pdb=" N ILE I 616 " --> pdb=" O ARG I 637 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.554A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 750 through 752 removed outlier: 6.714A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AD1, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AD2, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.327A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 9.246A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 830 through 841 removed outlier: 4.411A pdb=" N LYS I1048 " --> pdb=" O SER I 840 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 6.435A pdb=" N CYS J 366 " --> pdb=" O VAL J 440 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE J 442 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LEU J 368 " --> pdb=" O ILE J 442 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AD6, first strand: chain 'I' and resid 1335 through 1338 Processing sheet with id=AD7, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.602A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY J 103 " --> pdb=" O VAL J 244 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 10.658A pdb=" N SER J 109 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 10.182A pdb=" N ILE J 238 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 159 through 161 removed outlier: 3.909A pdb=" N VAL J 145 " --> pdb=" O LYS J 179 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 526 through 527 removed outlier: 4.000A pdb=" N ASP J 558 " --> pdb=" O GLU J 562 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLU J 562 " --> pdb=" O ASP J 558 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 706 through 708 Processing sheet with id=AE2, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE3, first strand: chain 'J' and resid 848 through 849 removed outlier: 6.673A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 949 through 951 Processing sheet with id=AE5, first strand: chain 'J' and resid 991 through 997 removed outlier: 4.171A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 965 through 967 Processing sheet with id=AE7, first strand: chain 'J' and resid 1035 through 1038 removed outlier: 4.017A pdb=" N ALA J1077 " --> pdb=" O THR J1038 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 1046 through 1049 Processing sheet with id=AE9, first strand: chain 'J' and resid 1189 through 1190 removed outlier: 3.592A pdb=" N ARG J1173 " --> pdb=" O ILE J1190 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LYS J1167 " --> pdb=" O ARG J1174 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL J1176 " --> pdb=" O PHE J1165 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE J1165 " --> pdb=" O VAL J1176 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR J1178 " --> pdb=" O VAL J1163 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N VAL J1163 " --> pdb=" O THR J1178 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.406A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1026 hydrogen bonds defined for protein. 2910 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 63 hydrogen bonds 126 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 12.78 Time building geometry restraints manager: 7.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.42: 10847 1.42 - 1.63: 15741 1.63 - 1.83: 186 1.83 - 2.04: 0 2.04 - 2.24: 1 Bond restraints: 26775 Sorted by residual: bond pdb=" O3' G R 48 " pdb=" P U R 49 " ideal model delta sigma weight residual 1.607 2.241 -0.634 1.50e-02 4.44e+03 1.79e+03 bond pdb=" O3' U R 61 " pdb=" P A R 62 " ideal model delta sigma weight residual 1.607 1.641 -0.034 1.50e-02 4.44e+03 5.20e+00 bond pdb=" O5' G R 59 " pdb=" C5' G R 59 " ideal model delta sigma weight residual 1.420 1.454 -0.034 1.50e-02 4.44e+03 5.09e+00 bond pdb=" O5' G R 48 " pdb=" C5' G R 48 " ideal model delta sigma weight residual 1.420 1.453 -0.033 1.50e-02 4.44e+03 4.97e+00 bond pdb=" O5' G R 60 " pdb=" C5' G R 60 " ideal model delta sigma weight residual 1.420 1.449 -0.029 1.50e-02 4.44e+03 3.79e+00 ... (remaining 26770 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 36201 2.67 - 5.33: 241 5.33 - 8.00: 10 8.00 - 10.66: 3 10.66 - 13.33: 3 Bond angle restraints: 36458 Sorted by residual: angle pdb=" C3' G R 48 " pdb=" O3' G R 48 " pdb=" P U R 49 " ideal model delta sigma weight residual 120.20 129.68 -9.48 1.50e+00 4.44e-01 3.99e+01 angle pdb=" N ILE J 416 " pdb=" CA ILE J 416 " pdb=" C ILE J 416 " ideal model delta sigma weight residual 112.29 107.03 5.26 9.40e-01 1.13e+00 3.13e+01 angle pdb=" N GLY I1260 " pdb=" CA GLY I1260 " pdb=" C GLY I1260 " ideal model delta sigma weight residual 115.34 107.82 7.52 1.67e+00 3.59e-01 2.03e+01 angle pdb=" CB MET J1095 " pdb=" CG MET J1095 " pdb=" SD MET J1095 " ideal model delta sigma weight residual 112.70 124.67 -11.97 3.00e+00 1.11e-01 1.59e+01 angle pdb=" CB MET J 151 " pdb=" CG MET J 151 " pdb=" SD MET J 151 " ideal model delta sigma weight residual 112.70 124.54 -11.84 3.00e+00 1.11e-01 1.56e+01 ... (remaining 36453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 15555 35.97 - 71.94: 769 71.94 - 107.90: 53 107.90 - 143.87: 2 143.87 - 179.84: 2 Dihedral angle restraints: 16381 sinusoidal: 7276 harmonic: 9105 Sorted by residual: dihedral pdb=" O4' C R 57 " pdb=" C1' C R 57 " pdb=" N1 C R 57 " pdb=" C2 C R 57 " ideal model delta sinusoidal sigma weight residual 232.00 52.16 179.84 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C R 52 " pdb=" C1' C R 52 " pdb=" N1 C R 52 " pdb=" C2 C R 52 " ideal model delta sinusoidal sigma weight residual -160.00 -78.65 -81.35 1 1.50e+01 4.44e-03 3.62e+01 dihedral pdb=" CA HIS J 430 " pdb=" C HIS J 430 " pdb=" N ARG J 431 " pdb=" CA ARG J 431 " ideal model delta harmonic sigma weight residual 180.00 157.79 22.21 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 16378 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3383 0.050 - 0.099: 621 0.099 - 0.149: 159 0.149 - 0.199: 14 0.199 - 0.248: 4 Chirality restraints: 4181 Sorted by residual: chirality pdb=" P G R 48 " pdb=" OP1 G R 48 " pdb=" OP2 G R 48 " pdb=" O5' G R 48 " both_signs ideal model delta sigma weight residual True 2.41 -2.66 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" P G R 59 " pdb=" OP1 G R 59 " pdb=" OP2 G R 59 " pdb=" O5' G R 59 " both_signs ideal model delta sigma weight residual True 2.41 -2.66 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" P G R 60 " pdb=" OP1 G R 60 " pdb=" OP2 G R 60 " pdb=" O5' G R 60 " both_signs ideal model delta sigma weight residual True 2.41 -2.65 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 4178 not shown) Planarity restraints: 4532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS J 216 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.34e+00 pdb=" C LYS J 216 " -0.050 2.00e-02 2.50e+03 pdb=" O LYS J 216 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU J 217 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE I 57 " -0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO I 58 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO I 58 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO I 58 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY J 358 " -0.025 5.00e-02 4.00e+02 3.84e-02 2.35e+00 pdb=" N PRO J 359 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO J 359 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO J 359 " -0.021 5.00e-02 4.00e+02 ... (remaining 4529 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 346 2.65 - 3.21: 24152 3.21 - 3.77: 41810 3.77 - 4.34: 55459 4.34 - 4.90: 91212 Nonbonded interactions: 212979 Sorted by model distance: nonbonded pdb=" OD2 ASP J 464 " pdb="MG MG J1401 " model vdw 2.083 2.170 nonbonded pdb=" OD1 ASP J 464 " pdb="MG MG J1401 " model vdw 2.115 2.170 nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1401 " model vdw 2.127 2.170 nonbonded pdb=" O3' U R 67 " pdb="MG MG J1401 " model vdw 2.137 2.170 nonbonded pdb=" OG SER I1295 " pdb=" O ARG J 346 " model vdw 2.155 3.040 ... (remaining 212974 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'G' and (resid 8 through 158 or resid 170 through 235)) selection = (chain 'H' and resid 8 through 235) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.200 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: 1.050 Check model and map are aligned: 0.210 Set scattering table: 0.230 Process input model: 67.580 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.100 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.634 26775 Z= 0.303 Angle : 0.558 13.331 36458 Z= 0.301 Chirality : 0.043 0.248 4181 Planarity : 0.003 0.044 4532 Dihedral : 19.299 179.839 10523 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.33 % Allowed : 27.35 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.65 (0.15), residues: 3151 helix: 1.81 (0.16), residues: 1089 sheet: 0.61 (0.27), residues: 390 loop : -0.54 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP I 997 HIS 0.005 0.001 HIS J 430 PHE 0.011 0.001 PHE I 57 TYR 0.012 0.001 TYR I 3 ARG 0.005 0.000 ARG J 978 Details of bonding type rmsd hydrogen bonds : bond 0.17617 ( 1075) hydrogen bonds : angle 6.61677 ( 3036) covalent geometry : bond 0.00521 (26775) covalent geometry : angle 0.55760 (36458) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6302 Ramachandran restraints generated. 3151 Oldfield, 0 Emsley, 3151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6302 Ramachandran restraints generated. 3151 Oldfield, 0 Emsley, 3151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 156 time to evaluate : 2.844 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 163 average time/residue: 0.3857 time to fit residues: 101.7384 Evaluate side-chains 154 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 149 time to evaluate : 2.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 1034 ARG Chi-restraints excluded: chain I residue 1154 ASP Chi-restraints excluded: chain I residue 1337 ILE Chi-restraints excluded: chain J residue 506 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 271 optimal weight: 9.9990 chunk 243 optimal weight: 6.9990 chunk 135 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 251 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 chunk 187 optimal weight: 7.9990 chunk 291 optimal weight: 30.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 66 HIS I 519 ASN I 832 HIS ** I1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 907 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.100291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.070919 restraints weight = 58036.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.070847 restraints weight = 62409.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.070961 restraints weight = 61839.482| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 26775 Z= 0.230 Angle : 0.590 10.134 36458 Z= 0.311 Chirality : 0.043 0.245 4181 Planarity : 0.004 0.046 4532 Dihedral : 14.698 174.895 4326 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.15 % Allowed : 24.65 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.50 (0.15), residues: 3151 helix: 1.66 (0.16), residues: 1103 sheet: 0.38 (0.26), residues: 406 loop : -0.59 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 997 HIS 0.006 0.001 HIS H 23 PHE 0.021 0.001 PHE I 57 TYR 0.013 0.002 TYR I 591 ARG 0.006 0.000 ARG K 28 Details of bonding type rmsd hydrogen bonds : bond 0.04580 ( 1075) hydrogen bonds : angle 4.95187 ( 3036) covalent geometry : bond 0.00549 (26775) covalent geometry : angle 0.59041 (36458) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6302 Ramachandran restraints generated. 3151 Oldfield, 0 Emsley, 3151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6302 Ramachandran restraints generated. 3151 Oldfield, 0 Emsley, 3151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 153 time to evaluate : 3.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 194 GLN cc_start: 0.8259 (tm-30) cc_final: 0.7922 (tm-30) REVERT: H 205 MET cc_start: 0.8187 (mmm) cc_final: 0.7974 (mmm) REVERT: I 580 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8772 (pt0) REVERT: I 1134 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.7977 (pt0) REVERT: I 1278 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.8702 (mp) REVERT: J 123 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7496 (mtt-85) REVERT: K 25 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8143 (ttm170) outliers start: 112 outliers final: 43 residues processed: 255 average time/residue: 0.4220 time to fit residues: 172.9547 Evaluate side-chains 191 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 143 time to evaluate : 2.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 68 TYR Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 71 LYS Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 317 LEU Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 580 GLN Chi-restraints excluded: chain I residue 636 CYS Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 782 VAL Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 968 GLU Chi-restraints excluded: chain I residue 1021 LEU Chi-restraints excluded: chain I residue 1047 LEU Chi-restraints excluded: chain I residue 1134 GLN Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1278 LEU Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1337 ILE Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 123 ARG Chi-restraints excluded: chain J residue 137 ARG Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 372 MET Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 1167 LYS Chi-restraints excluded: chain J residue 1230 THR Chi-restraints excluded: chain J residue 1260 MET Chi-restraints excluded: chain K residue 25 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 164 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 134 optimal weight: 7.9990 chunk 229 optimal weight: 0.0870 chunk 154 optimal weight: 0.6980 chunk 174 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 281 optimal weight: 30.0000 chunk 119 optimal weight: 0.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 768 ASN K 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.103166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.073587 restraints weight = 57926.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.074025 restraints weight = 64665.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.073988 restraints weight = 55316.249| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 26775 Z= 0.103 Angle : 0.499 8.731 36458 Z= 0.262 Chirality : 0.040 0.201 4181 Planarity : 0.003 0.042 4532 Dihedral : 14.568 178.179 4320 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.48 % Allowed : 26.42 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.66 (0.15), residues: 3151 helix: 1.90 (0.16), residues: 1101 sheet: 0.29 (0.26), residues: 401 loop : -0.52 (0.15), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 997 HIS 0.005 0.001 HIS J 430 PHE 0.015 0.001 PHE I 57 TYR 0.011 0.001 TYR J 631 ARG 0.004 0.000 ARG I 678 Details of bonding type rmsd hydrogen bonds : bond 0.03624 ( 1075) hydrogen bonds : angle 4.52364 ( 3036) covalent geometry : bond 0.00230 (26775) covalent geometry : angle 0.49874 (36458) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6302 Ramachandran restraints generated. 3151 Oldfield, 0 Emsley, 3151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6302 Ramachandran restraints generated. 3151 Oldfield, 0 Emsley, 3151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 159 time to evaluate : 3.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 205 MET cc_start: 0.8128 (mmm) cc_final: 0.7861 (mmm) REVERT: I 6 THR cc_start: 0.7820 (OUTLIER) cc_final: 0.7618 (t) REVERT: I 30 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8287 (pt) REVERT: I 253 PHE cc_start: 0.6575 (p90) cc_final: 0.6169 (p90) REVERT: I 1134 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7862 (pt0) REVERT: J 123 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.7189 (mmt180) REVERT: J 625 MET cc_start: 0.9006 (ttp) cc_final: 0.8777 (ttt) outliers start: 67 outliers final: 34 residues processed: 222 average time/residue: 0.3919 time to fit residues: 141.3354 Evaluate side-chains 181 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 143 time to evaluate : 2.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 71 LYS Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 545 PHE Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 636 CYS Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 782 VAL Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 927 THR Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 1047 LEU Chi-restraints excluded: chain I residue 1134 GLN Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1337 ILE Chi-restraints excluded: chain J residue 123 ARG Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 209 ASN Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 876 SER Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 1056 LEU Chi-restraints excluded: chain J residue 1167 LYS Chi-restraints excluded: chain J residue 1174 ARG Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 312 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 290 optimal weight: 3.9990 chunk 205 optimal weight: 9.9990 chunk 123 optimal weight: 0.9980 chunk 306 optimal weight: 8.9990 chunk 3 optimal weight: 20.0000 chunk 93 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 204 optimal weight: 0.9980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 93 GLN H 117 HIS I 580 GLN ** I1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1116 HIS ** J 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 266 ASN J 488 ASN J 907 HIS ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.101461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.071568 restraints weight = 58422.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.071572 restraints weight = 67166.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.071703 restraints weight = 59291.392| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26775 Z= 0.161 Angle : 0.524 8.680 36458 Z= 0.275 Chirality : 0.041 0.216 4181 Planarity : 0.003 0.044 4532 Dihedral : 14.598 175.965 4320 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.96 % Allowed : 25.46 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.58 (0.15), residues: 3151 helix: 1.85 (0.16), residues: 1102 sheet: 0.14 (0.26), residues: 411 loop : -0.56 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 997 HIS 0.005 0.001 HIS J 430 PHE 0.015 0.001 PHE J 116 TYR 0.011 0.001 TYR G 68 ARG 0.004 0.000 ARG K 16 Details of bonding type rmsd hydrogen bonds : bond 0.03851 ( 1075) hydrogen bonds : angle 4.41286 ( 3036) covalent geometry : bond 0.00383 (26775) covalent geometry : angle 0.52404 (36458) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6302 Ramachandran restraints generated. 3151 Oldfield, 0 Emsley, 3151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6302 Ramachandran restraints generated. 3151 Oldfield, 0 Emsley, 3151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 147 time to evaluate : 3.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 93 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7550 (pp30) REVERT: I 1134 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7875 (pt0) REVERT: J 123 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7535 (mtt-85) REVERT: J 137 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.7044 (mtm-85) REVERT: J 625 MET cc_start: 0.9056 (ttp) cc_final: 0.8799 (ttt) REVERT: K 16 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8356 (ttm170) REVERT: K 25 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.8194 (ttm170) outliers start: 107 outliers final: 60 residues processed: 243 average time/residue: 0.4109 time to fit residues: 161.8399 Evaluate side-chains 206 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 140 time to evaluate : 2.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 68 TYR Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 93 GLN Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 71 LYS Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 283 LYS Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 565 GLU Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 636 CYS Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 782 VAL Chi-restraints excluded: chain I residue 836 LEU Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 927 THR Chi-restraints excluded: chain I residue 929 ILE Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 1021 LEU Chi-restraints excluded: chain I residue 1047 LEU Chi-restraints excluded: chain I residue 1134 GLN Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain I residue 1337 ILE Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 123 ARG Chi-restraints excluded: chain J residue 137 ARG Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain J residue 372 MET Chi-restraints excluded: chain J residue 415 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 876 SER Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 1016 THR Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1167 LYS Chi-restraints excluded: chain J residue 1174 ARG Chi-restraints excluded: chain J residue 1260 MET Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain J residue 1293 GLU Chi-restraints excluded: chain K residue 16 ARG Chi-restraints excluded: chain K residue 25 ARG Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 208 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 270 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 177 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 256 optimal weight: 1.9990 chunk 170 optimal weight: 0.3980 chunk 179 optimal weight: 6.9990 chunk 224 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 93 GLN H 117 HIS ** I1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 907 HIS ** J1249 ASN ** 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 = 0.3618 r_free = 0.3618 target = 0.102987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.073317 restraints weight = 57719.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.073532 restraints weight = 66048.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.073595 restraints weight = 56743.971| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 26775 Z= 0.102 Angle : 0.497 15.352 36458 Z= 0.258 Chirality : 0.040 0.187 4181 Planarity : 0.003 0.052 4532 Dihedral : 14.542 177.878 4320 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.92 % Allowed : 26.54 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.70 (0.15), residues: 3151 helix: 2.00 (0.16), residues: 1100 sheet: 0.19 (0.26), residues: 404 loop : -0.51 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 997 HIS 0.005 0.001 HIS J 430 PHE 0.010 0.001 PHE I 57 TYR 0.011 0.001 TYR J 631 ARG 0.003 0.000 ARG J 709 Details of bonding type rmsd hydrogen bonds : bond 0.03406 ( 1075) hydrogen bonds : angle 4.26199 ( 3036) covalent geometry : bond 0.00232 (26775) covalent geometry : angle 0.49675 (36458) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6302 Ramachandran restraints generated. 3151 Oldfield, 0 Emsley, 3151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6302 Ramachandran restraints generated. 3151 Oldfield, 0 Emsley, 3151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 146 time to evaluate : 3.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 93 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7515 (pp30) REVERT: I 30 ILE cc_start: 0.8508 (OUTLIER) cc_final: 0.8174 (pt) REVERT: I 253 PHE cc_start: 0.6683 (p90) cc_final: 0.6332 (p90) REVERT: I 1134 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7805 (pt0) REVERT: J 123 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.6979 (mmt180) REVERT: J 137 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.7025 (mtm-85) REVERT: J 625 MET cc_start: 0.9036 (ttp) cc_final: 0.8784 (ttt) REVERT: K 25 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.8100 (ttm170) outliers start: 79 outliers final: 51 residues processed: 218 average time/residue: 0.3713 time to fit residues: 132.2894 Evaluate side-chains 197 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 140 time to evaluate : 3.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 93 GLN Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 71 LYS Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 283 LYS Chi-restraints excluded: chain I residue 565 GLU Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 636 CYS Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 927 THR Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 1021 LEU Chi-restraints excluded: chain I residue 1034 ARG Chi-restraints excluded: chain I residue 1047 LEU Chi-restraints excluded: chain I residue 1134 GLN Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1337 ILE Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 123 ARG Chi-restraints excluded: chain J residue 137 ARG Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 876 SER Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1056 LEU Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain J residue 1167 LYS Chi-restraints excluded: chain J residue 1174 ARG Chi-restraints excluded: chain J residue 1215 GLU Chi-restraints excluded: chain J residue 1293 GLU Chi-restraints excluded: chain K residue 25 ARG Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 255 optimal weight: 5.9990 chunk 173 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 185 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 131 optimal weight: 0.0470 chunk 252 optimal weight: 0.0970 chunk 211 optimal weight: 5.9990 chunk 98 optimal weight: 0.0020 chunk 197 optimal weight: 9.9990 chunk 88 optimal weight: 0.0870 overall best weight: 0.2464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 117 HIS I 519 ASN I 955 GLN ** I1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 157 GLN J 488 ASN J 907 HIS ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.104620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.075382 restraints weight = 57575.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.075508 restraints weight = 65367.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.075782 restraints weight = 54667.381| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 26775 Z= 0.089 Angle : 0.480 15.974 36458 Z= 0.249 Chirality : 0.040 0.179 4181 Planarity : 0.003 0.059 4532 Dihedral : 14.450 179.527 4320 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.85 % Allowed : 26.61 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.82 (0.15), residues: 3151 helix: 2.10 (0.16), residues: 1102 sheet: 0.33 (0.26), residues: 391 loop : -0.47 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 997 HIS 0.004 0.001 HIS J 430 PHE 0.010 0.001 PHE J1037 TYR 0.011 0.001 TYR J 631 ARG 0.004 0.000 ARG J 77 Details of bonding type rmsd hydrogen bonds : bond 0.03057 ( 1075) hydrogen bonds : angle 4.07334 ( 3036) covalent geometry : bond 0.00195 (26775) covalent geometry : angle 0.47998 (36458) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6302 Ramachandran restraints generated. 3151 Oldfield, 0 Emsley, 3151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6302 Ramachandran restraints generated. 3151 Oldfield, 0 Emsley, 3151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 152 time to evaluate : 3.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 30 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8133 (pt) REVERT: I 253 PHE cc_start: 0.6588 (p90) cc_final: 0.6268 (p90) REVERT: I 674 ASP cc_start: 0.8377 (p0) cc_final: 0.8098 (p0) REVERT: I 974 ARG cc_start: 0.3799 (OUTLIER) cc_final: 0.3293 (mmp80) REVERT: I 1134 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7772 (pt0) REVERT: J 123 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.6947 (mmt180) REVERT: J 137 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.7132 (mtp180) REVERT: J 478 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8757 (mm) REVERT: J 625 MET cc_start: 0.9036 (ttp) cc_final: 0.8773 (ttt) REVERT: J 1293 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6926 (mp0) REVERT: K 25 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.8070 (ttm170) outliers start: 77 outliers final: 46 residues processed: 223 average time/residue: 0.3835 time to fit residues: 137.8210 Evaluate side-chains 199 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 145 time to evaluate : 2.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 565 GLU Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 636 CYS Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 927 THR Chi-restraints excluded: chain I residue 929 ILE Chi-restraints excluded: chain I residue 974 ARG Chi-restraints excluded: chain I residue 980 VAL Chi-restraints excluded: chain I residue 1021 LEU Chi-restraints excluded: chain I residue 1034 ARG Chi-restraints excluded: chain I residue 1047 LEU Chi-restraints excluded: chain I residue 1134 GLN Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 123 ARG Chi-restraints excluded: chain J residue 137 ARG Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 767 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 876 SER Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 1016 THR Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain J residue 1167 LYS Chi-restraints excluded: chain J residue 1174 ARG Chi-restraints excluded: chain J residue 1293 GLU Chi-restraints excluded: chain K residue 25 ARG Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 73 optimal weight: 0.2980 chunk 188 optimal weight: 0.2980 chunk 108 optimal weight: 2.9990 chunk 257 optimal weight: 0.8980 chunk 258 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 234 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 93 GLN H 117 HIS I 965 GLN ** I1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** 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 = 0.3610 r_free = 0.3610 target = 0.102384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.072694 restraints weight = 57825.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.073121 restraints weight = 65017.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.073223 restraints weight = 52737.225| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26775 Z= 0.136 Angle : 0.511 16.569 36458 Z= 0.262 Chirality : 0.040 0.197 4181 Planarity : 0.003 0.059 4532 Dihedral : 14.499 177.161 4318 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.44 % Allowed : 26.05 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 (0.15), residues: 3151 helix: 2.08 (0.16), residues: 1102 sheet: 0.24 (0.25), residues: 413 loop : -0.51 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 997 HIS 0.004 0.001 HIS J 907 PHE 0.012 0.001 PHE J1037 TYR 0.010 0.001 TYR J 631 ARG 0.005 0.000 ARG J 77 Details of bonding type rmsd hydrogen bonds : bond 0.03477 ( 1075) hydrogen bonds : angle 4.11266 ( 3036) covalent geometry : bond 0.00321 (26775) covalent geometry : angle 0.51113 (36458) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6302 Ramachandran restraints generated. 3151 Oldfield, 0 Emsley, 3151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6302 Ramachandran restraints generated. 3151 Oldfield, 0 Emsley, 3151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 142 time to evaluate : 3.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 30 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8183 (pt) REVERT: I 965 GLN cc_start: 0.5233 (OUTLIER) cc_final: 0.4885 (tt0) REVERT: I 974 ARG cc_start: 0.3829 (OUTLIER) cc_final: 0.3296 (mmp80) REVERT: I 1134 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7797 (pt0) REVERT: I 1216 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7830 (ptt180) REVERT: J 77 ARG cc_start: 0.7411 (tpm170) cc_final: 0.7177 (tpm170) REVERT: J 123 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7259 (mtt-85) REVERT: J 137 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.7185 (mtp180) REVERT: J 478 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8798 (mm) REVERT: J 625 MET cc_start: 0.9062 (ttp) cc_final: 0.8813 (ttt) REVERT: J 1293 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6968 (mp0) REVERT: K 16 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7682 (ttm170) REVERT: K 25 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.8123 (ttm170) outliers start: 93 outliers final: 61 residues processed: 225 average time/residue: 0.3835 time to fit residues: 139.3116 Evaluate side-chains 208 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 136 time to evaluate : 3.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 93 GLN Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 283 LYS Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 636 CYS Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 927 THR Chi-restraints excluded: chain I residue 929 ILE Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 965 GLN Chi-restraints excluded: chain I residue 974 ARG Chi-restraints excluded: chain I residue 1021 LEU Chi-restraints excluded: chain I residue 1034 ARG Chi-restraints excluded: chain I residue 1047 LEU Chi-restraints excluded: chain I residue 1134 GLN Chi-restraints excluded: chain I residue 1216 ARG Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 123 ARG Chi-restraints excluded: chain J residue 137 ARG Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 876 SER Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1016 THR Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1056 LEU Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain J residue 1167 LYS Chi-restraints excluded: chain J residue 1174 ARG Chi-restraints excluded: chain J residue 1215 GLU Chi-restraints excluded: chain J residue 1260 MET Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain J residue 1293 GLU Chi-restraints excluded: chain J residue 1349 GLU Chi-restraints excluded: chain K residue 16 ARG Chi-restraints excluded: chain K residue 25 ARG Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 241 optimal weight: 7.9990 chunk 157 optimal weight: 0.9980 chunk 195 optimal weight: 9.9990 chunk 311 optimal weight: 1.9990 chunk 217 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 230 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 186 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 93 GLN H 117 HIS ** I1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** 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 = 0.3608 r_free = 0.3608 target = 0.101905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.069438 restraints weight = 58042.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.068598 restraints weight = 40511.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.068725 restraints weight = 40549.129| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26775 Z= 0.139 Angle : 0.515 15.981 36458 Z= 0.263 Chirality : 0.041 0.199 4181 Planarity : 0.003 0.060 4532 Dihedral : 14.504 176.784 4318 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.44 % Allowed : 26.17 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.74 (0.15), residues: 3151 helix: 2.05 (0.16), residues: 1102 sheet: 0.27 (0.26), residues: 401 loop : -0.53 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 997 HIS 0.004 0.001 HIS J 430 PHE 0.036 0.001 PHE I 253 TYR 0.011 0.001 TYR J 631 ARG 0.006 0.000 ARG J 77 Details of bonding type rmsd hydrogen bonds : bond 0.03496 ( 1075) hydrogen bonds : angle 4.12347 ( 3036) covalent geometry : bond 0.00329 (26775) covalent geometry : angle 0.51471 (36458) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6302 Ramachandran restraints generated. 3151 Oldfield, 0 Emsley, 3151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6302 Ramachandran restraints generated. 3151 Oldfield, 0 Emsley, 3151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 138 time to evaluate : 2.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 58 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7209 (mm-30) REVERT: I 30 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8136 (pt) REVERT: I 974 ARG cc_start: 0.3707 (OUTLIER) cc_final: 0.2975 (mmp80) REVERT: I 1064 ASP cc_start: 0.8717 (OUTLIER) cc_final: 0.8332 (m-30) REVERT: I 1134 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.7975 (pt0) REVERT: I 1216 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7925 (ptt180) REVERT: I 1278 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.8632 (mp) REVERT: J 123 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.7096 (mtt-85) REVERT: J 137 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7260 (mtm-85) REVERT: J 478 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8711 (mm) REVERT: J 532 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7489 (tt0) REVERT: J 625 MET cc_start: 0.9097 (ttp) cc_final: 0.8825 (ttt) REVERT: J 1293 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6935 (mp0) REVERT: K 16 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.7775 (ttm170) REVERT: K 25 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.8057 (ttm170) outliers start: 93 outliers final: 67 residues processed: 222 average time/residue: 0.3783 time to fit residues: 135.7042 Evaluate side-chains 217 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 136 time to evaluate : 2.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 93 GLN Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 283 LYS Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 636 CYS Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 927 THR Chi-restraints excluded: chain I residue 929 ILE Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 974 ARG Chi-restraints excluded: chain I residue 1021 LEU Chi-restraints excluded: chain I residue 1034 ARG Chi-restraints excluded: chain I residue 1047 LEU Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1097 VAL Chi-restraints excluded: chain I residue 1134 GLN Chi-restraints excluded: chain I residue 1216 ARG Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1278 LEU Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 123 ARG Chi-restraints excluded: chain J residue 137 ARG Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 517 CYS Chi-restraints excluded: chain J residue 532 GLU Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 876 SER Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 1016 THR Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1056 LEU Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain J residue 1167 LYS Chi-restraints excluded: chain J residue 1174 ARG Chi-restraints excluded: chain J residue 1215 GLU Chi-restraints excluded: chain J residue 1260 MET Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain J residue 1293 GLU Chi-restraints excluded: chain J residue 1349 GLU Chi-restraints excluded: chain K residue 16 ARG Chi-restraints excluded: chain K residue 25 ARG Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 37 optimal weight: 0.0980 chunk 16 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 295 optimal weight: 20.0000 chunk 65 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 107 optimal weight: 0.6980 chunk 304 optimal weight: 9.9990 chunk 166 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 93 GLN H 117 HIS I 965 GLN ** I1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** 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 = 0.3614 r_free = 0.3614 target = 0.102252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.069178 restraints weight = 58271.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.068734 restraints weight = 47679.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.069300 restraints weight = 35319.107| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26775 Z= 0.119 Angle : 0.506 15.589 36458 Z= 0.258 Chirality : 0.040 0.194 4181 Planarity : 0.003 0.059 4532 Dihedral : 14.494 177.340 4318 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.40 % Allowed : 26.20 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 (0.15), residues: 3151 helix: 2.07 (0.16), residues: 1102 sheet: 0.27 (0.26), residues: 401 loop : -0.51 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 997 HIS 0.004 0.001 HIS J 430 PHE 0.035 0.001 PHE I 253 TYR 0.011 0.001 TYR J 631 ARG 0.006 0.000 ARG J 77 Details of bonding type rmsd hydrogen bonds : bond 0.03399 ( 1075) hydrogen bonds : angle 4.09343 ( 3036) covalent geometry : bond 0.00280 (26775) covalent geometry : angle 0.50581 (36458) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6302 Ramachandran restraints generated. 3151 Oldfield, 0 Emsley, 3151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6302 Ramachandran restraints generated. 3151 Oldfield, 0 Emsley, 3151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 136 time to evaluate : 6.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 58 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7171 (mm-30) REVERT: I 30 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8123 (pt) REVERT: I 70 TYR cc_start: 0.6992 (OUTLIER) cc_final: 0.6267 (p90) REVERT: I 974 ARG cc_start: 0.3697 (OUTLIER) cc_final: 0.2973 (mmp80) REVERT: I 1064 ASP cc_start: 0.8732 (OUTLIER) cc_final: 0.8354 (m-30) REVERT: I 1134 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.7961 (pt0) REVERT: I 1278 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.8656 (mp) REVERT: J 123 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.7047 (mtt-85) REVERT: J 137 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7236 (mtm-85) REVERT: J 478 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8688 (mm) REVERT: J 532 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7423 (tt0) REVERT: J 625 MET cc_start: 0.9105 (ttp) cc_final: 0.8829 (ttt) REVERT: J 1293 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.7009 (mp0) REVERT: K 16 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.7701 (ttm170) outliers start: 92 outliers final: 69 residues processed: 218 average time/residue: 0.5739 time to fit residues: 208.4560 Evaluate side-chains 218 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 136 time to evaluate : 4.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 93 GLN Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 565 GLU Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 583 GLU Chi-restraints excluded: chain I residue 636 CYS Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 927 THR Chi-restraints excluded: chain I residue 929 ILE Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 974 ARG Chi-restraints excluded: chain I residue 1021 LEU Chi-restraints excluded: chain I residue 1034 ARG Chi-restraints excluded: chain I residue 1047 LEU Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1097 VAL Chi-restraints excluded: chain I residue 1134 GLN Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain I residue 1278 LEU Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 123 ARG Chi-restraints excluded: chain J residue 137 ARG Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 517 CYS Chi-restraints excluded: chain J residue 532 GLU Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 651 HIS Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 876 SER Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 1016 THR Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1056 LEU Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain J residue 1167 LYS Chi-restraints excluded: chain J residue 1174 ARG Chi-restraints excluded: chain J residue 1215 GLU Chi-restraints excluded: chain J residue 1260 MET Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain J residue 1293 GLU Chi-restraints excluded: chain J residue 1349 GLU Chi-restraints excluded: chain K residue 16 ARG Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 198 optimal weight: 0.2980 chunk 223 optimal weight: 0.0040 chunk 142 optimal weight: 6.9990 chunk 299 optimal weight: 0.7980 chunk 122 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 140 optimal weight: 9.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 117 HIS ** I1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 519 ASN ** J 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** 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 = 0.3637 r_free = 0.3637 target = 0.103670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.070994 restraints weight = 57935.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.070402 restraints weight = 46720.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.070713 restraints weight = 40932.402| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 26775 Z= 0.094 Angle : 0.492 15.298 36458 Z= 0.251 Chirality : 0.040 0.176 4181 Planarity : 0.003 0.059 4532 Dihedral : 14.439 179.512 4318 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.89 % Allowed : 26.65 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.86 (0.15), residues: 3151 helix: 2.15 (0.16), residues: 1104 sheet: 0.37 (0.26), residues: 405 loop : -0.48 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 997 HIS 0.004 0.001 HIS J 430 PHE 0.035 0.001 PHE I 253 TYR 0.011 0.001 TYR J 631 ARG 0.009 0.000 ARG J 77 Details of bonding type rmsd hydrogen bonds : bond 0.03100 ( 1075) hydrogen bonds : angle 4.00095 ( 3036) covalent geometry : bond 0.00211 (26775) covalent geometry : angle 0.49189 (36458) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6302 Ramachandran restraints generated. 3151 Oldfield, 0 Emsley, 3151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6302 Ramachandran restraints generated. 3151 Oldfield, 0 Emsley, 3151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 145 time to evaluate : 3.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 58 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7164 (mm-30) REVERT: H 51 MET cc_start: 0.8517 (mmm) cc_final: 0.8296 (mmt) REVERT: I 30 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.8022 (pt) REVERT: I 965 GLN cc_start: 0.6569 (tt0) cc_final: 0.6281 (tm-30) REVERT: I 974 ARG cc_start: 0.3812 (OUTLIER) cc_final: 0.2984 (mmp80) REVERT: I 1064 ASP cc_start: 0.8692 (OUTLIER) cc_final: 0.8318 (m-30) REVERT: I 1134 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7898 (pt0) REVERT: I 1216 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7914 (ptt180) REVERT: I 1278 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8575 (mp) REVERT: J 123 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.6673 (mmt180) REVERT: J 137 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7116 (mtm-85) REVERT: J 478 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8688 (mm) REVERT: J 532 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7483 (tt0) REVERT: J 625 MET cc_start: 0.9093 (ttp) cc_final: 0.8817 (ttt) REVERT: J 1293 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6938 (mp0) REVERT: K 16 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7122 (ttm170) outliers start: 78 outliers final: 59 residues processed: 216 average time/residue: 0.3878 time to fit residues: 136.9938 Evaluate side-chains 211 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 139 time to evaluate : 3.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 565 GLU Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 636 CYS Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 927 THR Chi-restraints excluded: chain I residue 929 ILE Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 974 ARG Chi-restraints excluded: chain I residue 1021 LEU Chi-restraints excluded: chain I residue 1034 ARG Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1097 VAL Chi-restraints excluded: chain I residue 1134 GLN Chi-restraints excluded: chain I residue 1216 ARG Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain I residue 1278 LEU Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 123 ARG Chi-restraints excluded: chain J residue 137 ARG Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 517 CYS Chi-restraints excluded: chain J residue 532 GLU Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 843 VAL Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 876 SER Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 1016 THR Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1056 LEU Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1120 THR Chi-restraints excluded: chain J residue 1167 LYS Chi-restraints excluded: chain J residue 1174 ARG Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain J residue 1293 GLU Chi-restraints excluded: chain J residue 1349 GLU Chi-restraints excluded: chain K residue 16 ARG Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 219 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 190 optimal weight: 0.8980 chunk 131 optimal weight: 8.9990 chunk 150 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 147 optimal weight: 7.9990 chunk 132 optimal weight: 0.5980 chunk 22 optimal weight: 6.9990 chunk 170 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 117 HIS ** I1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** 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 = 0.3634 r_free = 0.3634 target = 0.103455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.071355 restraints weight = 58113.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.070360 restraints weight = 39781.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.070798 restraints weight = 35936.766| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 26775 Z= 0.099 Angle : 0.499 17.591 36458 Z= 0.252 Chirality : 0.040 0.180 4181 Planarity : 0.003 0.060 4532 Dihedral : 14.405 179.524 4318 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.78 % Allowed : 26.87 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.86 (0.15), residues: 3151 helix: 2.15 (0.16), residues: 1105 sheet: 0.36 (0.26), residues: 410 loop : -0.47 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 997 HIS 0.004 0.001 HIS J 430 PHE 0.034 0.001 PHE I 253 TYR 0.011 0.001 TYR J 631 ARG 0.006 0.000 ARG J 77 Details of bonding type rmsd hydrogen bonds : bond 0.03122 ( 1075) hydrogen bonds : angle 3.95937 ( 3036) covalent geometry : bond 0.00229 (26775) covalent geometry : angle 0.49903 (36458) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7423.32 seconds wall clock time: 132 minutes 47.01 seconds (7967.01 seconds total)