Starting phenix.real_space_refine on Tue Jun 24 05:17:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xue_33466/06_2025/7xue_33466.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xue_33466/06_2025/7xue_33466.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xue_33466/06_2025/7xue_33466.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xue_33466/06_2025/7xue_33466.map" model { file = "/net/cci-nas-00/data/ceres_data/7xue_33466/06_2025/7xue_33466.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xue_33466/06_2025/7xue_33466.cif" } resolution = 3.17 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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 135 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 16985 2.51 5 N 4930 2.21 5 O 5705 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27864 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 438 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain breaks: 1 Chain: "B" Number of atoms: 606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 606 Classifications: {'DNA': 30} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 29} Chain: "R" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1816 Classifications: {'RNA': 85} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 4, 'rna3p_pur': 34, 'rna3p_pyr': 37} Link IDs: {'rna2p': 14, 'rna3p': 70} Chain breaks: 1 Chain: "G" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1694 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1687 Classifications: {'peptide': 219} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Chain: "I" Number of atoms: 10577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10577 Classifications: {'peptide': 1341} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1284} Chain: "J" Number of atoms: 10388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10388 Classifications: {'peptide': 1335} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1279} Chain breaks: 2 Chain: "K" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 655 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 17267 SG CYS J 70 55.521 118.464 60.454 1.00 64.30 S ATOM 17281 SG CYS J 72 56.770 121.832 61.006 1.00 70.96 S ATOM 17389 SG CYS J 85 54.761 120.964 57.866 1.00 71.64 S ATOM 17413 SG CYS J 88 58.210 119.100 58.379 1.00 68.81 S ATOM 23101 SG CYS J 814 51.985 51.698 48.305 1.00 59.73 S ATOM 23666 SG CYS J 888 54.321 54.521 49.379 1.00 54.34 S ATOM 23717 SG CYS J 895 51.771 53.099 51.959 1.00 47.82 S ATOM 23738 SG CYS J 898 54.435 50.929 50.773 1.00 50.69 S Time building chain proxies: 14.76, per 1000 atoms: 0.53 Number of scatterers: 27864 At special positions: 0 Unit cell: (152.64, 159, 146.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 106 16.00 P 135 15.00 Mg 1 11.99 O 5705 8.00 N 4930 7.00 C 16985 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: 6.85 Conformation dependent library (CDL) restraints added in 2.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1501 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 88 " pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 888 " Number of angles added : 12 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5904 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 52 sheets defined 38.0% alpha, 16.9% beta 51 base pairs and 90 stacking pairs defined. Time for finding SS restraints: 10.28 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.757A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 86 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 155 through 159 Processing helix chain 'G' and resid 212 through 229 Processing helix chain 'G' and resid 230 through 232 No H-bonds generated for 'chain 'G' and resid 230 through 232' Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.878A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 removed outlier: 3.558A pdb=" N ILE H 81 " --> pdb=" O ASP H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 115 removed outlier: 4.123A pdb=" N ASP H 114 " --> pdb=" O THR H 111 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE H 115 " --> pdb=" O ALA H 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 111 through 115' Processing helix chain 'H' and resid 212 through 228 Processing helix chain 'I' and resid 4 through 9 removed outlier: 3.775A pdb=" N LYS I 9 " --> pdb=" O TYR I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 39 removed outlier: 3.926A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 57 removed outlier: 3.809A pdb=" N ALA I 51 " --> pdb=" O TYR I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 163 through 167 removed outlier: 3.724A pdb=" N SER I 166 " --> pdb=" O LYS I 163 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER I 167 " --> pdb=" O THR I 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 163 through 167' Processing helix chain 'I' and resid 206 through 213 removed outlier: 4.334A 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 289 through 294 removed outlier: 4.101A pdb=" N GLY I 294 " --> pdb=" O GLU I 290 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 327 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 389 removed outlier: 3.971A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (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: 3.685A pdb=" N LEU I 481 " --> pdb=" O GLU I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 508 Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.712A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 608 through 612 removed outlier: 3.856A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 612' Processing helix chain 'I' and resid 648 through 650 No H-bonds generated for 'chain 'I' and resid 648 through 650' Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 686 Processing helix chain 'I' and resid 704 through 711 Processing helix chain 'I' and resid 738 through 741 Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 896 through 906 removed outlier: 3.597A pdb=" N LYS I 900 " --> pdb=" O THR I 896 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU I 901 " --> pdb=" O PRO I 897 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU I 902 " --> pdb=" O GLU I 898 " (cutoff:3.500A) Processing helix chain 'I' and resid 942 through 979 Processing helix chain 'I' and resid 985 through 990 removed outlier: 4.006A pdb=" N ASP I 990 " --> pdb=" O ALA I 986 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1038 Processing helix chain 'I' and resid 1081 through 1085 Processing helix chain 'I' and resid 1099 through 1103 removed outlier: 3.587A pdb=" N GLY I1102 " --> pdb=" O ASN I1099 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 Processing helix chain 'I' and resid 1137 through 1150 removed outlier: 3.649A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 3.810A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1176 removed outlier: 3.716A pdb=" N ARG I1171 " --> pdb=" O GLU I1167 " (cutoff:3.500A) Processing helix chain 'I' and resid 1191 through 1202 removed outlier: 3.514A pdb=" N GLY I1202 " --> pdb=" O LEU I1198 " (cutoff:3.500A) Processing helix chain 'I' and resid 1238 through 1243 Processing helix chain 'I' and resid 1271 through 1281 removed outlier: 3.509A pdb=" N TYR I1281 " --> pdb=" O ALA I1277 " (cutoff:3.500A) Processing helix chain 'I' and resid 1283 through 1292 removed outlier: 3.720A pdb=" N LEU I1287 " --> pdb=" O ALA I1283 " (cutoff:3.500A) Processing helix chain 'I' and resid 1297 through 1310 Processing helix chain 'I' and resid 1320 through 1332 removed outlier: 3.622A 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 58 through 63 Processing helix chain 'J' and resid 77 through 81 removed outlier: 3.713A pdb=" N ARG J 81 " --> pdb=" O LEU J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 100 Processing helix chain 'J' and resid 113 through 118 Processing helix chain 'J' and resid 124 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 181 through 192 Processing helix chain 'J' and resid 193 through 206 removed outlier: 3.860A pdb=" N GLU J 197 " --> pdb=" O ASP J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 230 removed outlier: 4.386A pdb=" N LYS J 215 " --> pdb=" O GLU J 211 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS J 216 " --> pdb=" O THR J 212 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS J 222 " --> pdb=" O THR J 218 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER J 230 " --> pdb=" O ALA J 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 285 removed outlier: 3.883A pdb=" N ASP J 267 " --> pdb=" O SER J 263 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 removed outlier: 3.602A pdb=" N VAL J 292 " --> pdb=" O PRO J 288 " (cutoff:3.500A) Processing helix chain 'J' and resid 326 through 332 Processing helix chain 'J' and resid 336 through 342 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 407 through 415 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 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 504 through 514 Processing helix chain 'J' and resid 529 through 540 Processing helix chain 'J' and resid 574 through 580 Processing helix chain 'J' and resid 597 through 612 removed outlier: 3.692A pdb=" N ILE J 601 " --> pdb=" O GLY J 597 " (cutoff:3.500A) Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.620A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 644 Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 703 removed outlier: 3.594A pdb=" N ARG J 678 " --> pdb=" O THR J 674 " (cutoff:3.500A) removed outlier: 3.862A 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 742 Processing helix chain 'J' and resid 768 through 805 removed outlier: 4.977A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 839 removed outlier: 3.562A pdb=" N ARG J 838 " --> pdb=" O PRO J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 876 Processing helix chain 'J' and resid 896 through 900 Processing helix chain 'J' and resid 914 through 925 removed outlier: 4.026A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 929 Processing helix chain 'J' and resid 1068 through 1073 removed outlier: 4.246A pdb=" N ASP J1073 " --> pdb=" O ALA J1069 " (cutoff:3.500A) Processing helix chain 'J' and resid 1137 through 1147 removed outlier: 3.707A pdb=" N VAL J1141 " --> pdb=" O GLY J1137 " (cutoff:3.500A) Processing helix chain 'J' and resid 1216 through 1223 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 3.682A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL J1240 " --> pdb=" O GLU J1236 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.429A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1293 Processing helix chain 'J' and resid 1310 through 1315 Processing helix chain 'J' and resid 1318 through 1326 removed outlier: 3.596A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1353 removed outlier: 3.774A pdb=" N ASN J1350 " --> pdb=" O GLY J1346 " (cutoff:3.500A) Processing helix chain 'J' and resid 1362 through 1372 Processing helix chain 'K' and resid 6 through 12 removed outlier: 3.696A pdb=" N LYS K 12 " --> pdb=" O ASP K 8 " (cutoff:3.500A) Processing helix chain 'K' and resid 17 through 32 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 84 Processing sheet with id=AA1, first strand: chain 'G' and resid 12 through 17 removed outlier: 5.231A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 4.083A 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: 7.493A pdb=" N SER G 141 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ILE G 61 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 108 through 111 removed outlier: 6.329A pdb=" N GLY G 108 " --> pdb=" O HIS G 132 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N HIS G 132 " --> pdb=" O GLY G 108 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL G 110 " --> pdb=" O ILE G 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 12 through 16 removed outlier: 5.864A pdb=" N LEU H 13 " --> pdb=" O GLU H 29 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N GLU H 29 " --> pdb=" O LEU H 13 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASP H 15 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG H 182 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 12 through 16 removed outlier: 5.864A pdb=" N LEU H 13 " --> pdb=" O GLU H 29 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N GLU H 29 " --> pdb=" O LEU H 13 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASP H 15 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 98 through 105 removed outlier: 3.700A pdb=" N VAL H 98 " --> pdb=" O VAL H 146 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AA9, first strand: chain 'H' and resid 108 through 110 Processing sheet with id=AB1, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.280A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 66 through 75 removed outlier: 5.323A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET I 124 " --> pdb=" O LEU I 96 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE I 104 " --> pdb=" O ASP I 116 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB5, first strand: chain 'I' and resid 451 through 454 Processing sheet with id=AB6, first strand: chain 'I' and resid 154 through 158 removed outlier: 3.523A pdb=" N ASN I 173 " --> pdb=" O ASP I 158 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 195 through 196 Processing sheet with id=AB8, first strand: chain 'I' and resid 227 through 231 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 255 through 257 removed outlier: 6.767A pdb=" N ILE I 255 " --> pdb=" O TYR I 262 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 301 through 302 removed outlier: 3.617A pdb=" N TYR I 301 " --> pdb=" O CYS I 311 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.696A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N THR I 595 " --> pdb=" O THR I 600 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N THR I 600 " --> pdb=" O THR I 595 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC5, first strand: chain 'I' and resid 616 through 617 Processing sheet with id=AC6, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.453A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 749 through 752 removed outlier: 6.432A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AC9, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AD1, first strand: chain 'I' and resid 1066 through 1068 removed outlier: 4.569A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 9.064A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE I 816 " --> pdb=" O LYS I1078 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ASN I1080 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL I 818 " --> pdb=" O ASN I1080 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 1066 through 1068 Processing sheet with id=AD3, first strand: chain 'I' and resid 830 through 833 removed outlier: 6.831A pdb=" N SER I 840 " --> pdb=" O LEU I1047 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ILE I1049 " --> pdb=" O CYS I 838 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N CYS I 838 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LYS I1051 " --> pdb=" O LEU I 836 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU I 836 " --> pdb=" O LYS I1051 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 830 through 833 removed outlier: 3.873A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.764A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 887 through 889 Processing sheet with id=AD7, first strand: chain 'I' and resid 1087 through 1088 Processing sheet with id=AD8, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 3.595A pdb=" N CYS J 366 " --> pdb=" O GLU J 438 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 1268 through 1270 removed outlier: 3.599A pdb=" N GLN I1268 " --> pdb=" O VAL J 347 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 1335 through 1339 Processing sheet with id=AE2, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.696A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 9.877A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.586A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 159 through 160 removed outlier: 3.631A pdb=" N TYR J 144 " --> pdb=" O LEU J 160 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 253 through 254 removed outlier: 3.746A pdb=" N VAL J 253 " --> pdb=" O ALA J 261 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 526 through 527 removed outlier: 3.638A pdb=" N SER J 568 " --> pdb=" O ILE J 552 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 706 through 708 Processing sheet with id=AE7, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AE8, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE9, first strand: chain 'J' and resid 848 through 849 removed outlier: 7.391A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 949 through 951 removed outlier: 6.891A pdb=" N ILE J 950 " --> pdb=" O VAL J1017 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 957 through 961 removed outlier: 4.163A pdb=" N SER J 961 " --> pdb=" O GLU J 981 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU J 981 " --> pdb=" O SER J 961 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 965 through 967 Processing sheet with id=AF4, first strand: chain 'J' and resid 1034 through 1036 removed outlier: 3.824A pdb=" N LYS J1079 " --> pdb=" O ARG J1036 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 1059 through 1060 removed outlier: 3.742A pdb=" N LEU J1059 " --> pdb=" O VAL J1107 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 1163 through 1165 Processing sheet with id=AF7, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.519A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP J1305 " --> pdb=" O LYS J1263 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1020 hydrogen bonds defined for protein. 2874 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 126 hydrogen bonds 244 hydrogen bond angles 0 basepair planarities 51 basepair parallelities 90 stacking parallelities Total time for adding SS restraints: 15.28 Time building geometry restraints manager: 7.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8654 1.34 - 1.46: 4454 1.46 - 1.57: 15009 1.57 - 1.69: 266 1.69 - 1.81: 184 Bond restraints: 28567 Sorted by residual: bond pdb=" C THR J1178 " pdb=" N PRO J1179 " ideal model delta sigma weight residual 1.328 1.350 -0.022 1.26e-02 6.30e+03 2.94e+00 bond pdb=" C1' DC A 94 " pdb=" N1 DC A 94 " ideal model delta sigma weight residual 1.490 1.540 -0.050 3.00e-02 1.11e+03 2.73e+00 bond pdb=" N LYS J 79 " pdb=" CA LYS J 79 " ideal model delta sigma weight residual 1.456 1.478 -0.022 1.32e-02 5.74e+03 2.67e+00 bond pdb=" N GLN I 894 " pdb=" CA GLN I 894 " ideal model delta sigma weight residual 1.465 1.487 -0.021 1.31e-02 5.83e+03 2.65e+00 bond pdb=" CA ASP I1166 " pdb=" CB ASP I1166 " ideal model delta sigma weight residual 1.530 1.558 -0.027 1.69e-02 3.50e+03 2.64e+00 ... (remaining 28562 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 37134 1.53 - 3.07: 1719 3.07 - 4.60: 297 4.60 - 6.13: 56 6.13 - 7.67: 9 Bond angle restraints: 39215 Sorted by residual: angle pdb=" N LYS J 79 " pdb=" CA LYS J 79 " pdb=" C LYS J 79 " ideal model delta sigma weight residual 113.16 107.80 5.36 1.24e+00 6.50e-01 1.87e+01 angle pdb=" N LYS I 161 " pdb=" CA LYS I 161 " pdb=" C LYS I 161 " ideal model delta sigma weight residual 111.03 115.80 -4.77 1.11e+00 8.12e-01 1.85e+01 angle pdb=" N ILE H 115 " pdb=" CA ILE H 115 " pdb=" C ILE H 115 " ideal model delta sigma weight residual 110.21 105.87 4.34 1.13e+00 7.83e-01 1.48e+01 angle pdb=" CA VAL J 858 " pdb=" C VAL J 858 " pdb=" N PRO J 859 " ideal model delta sigma weight residual 116.57 120.31 -3.74 9.80e-01 1.04e+00 1.46e+01 angle pdb=" N CYS H 131 " pdb=" CA CYS H 131 " pdb=" C CYS H 131 " ideal model delta sigma weight residual 108.46 113.73 -5.27 1.51e+00 4.39e-01 1.22e+01 ... (remaining 39210 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.74: 16796 34.74 - 69.48: 711 69.48 - 104.22: 67 104.22 - 138.96: 1 138.96 - 173.70: 2 Dihedral angle restraints: 17577 sinusoidal: 8398 harmonic: 9179 Sorted by residual: dihedral pdb=" CA ARG J 352 " pdb=" C ARG J 352 " pdb=" N SER J 353 " pdb=" CA SER J 353 " ideal model delta harmonic sigma weight residual 180.00 153.90 26.10 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA GLU I 631 " pdb=" C GLU I 631 " pdb=" N ASP I 632 " pdb=" CA ASP I 632 " ideal model delta harmonic sigma weight residual -180.00 -154.01 -25.99 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA LYS I 755 " pdb=" C LYS I 755 " pdb=" N TYR I 756 " pdb=" CA TYR I 756 " ideal model delta harmonic sigma weight residual -180.00 -154.30 -25.70 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 17574 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 3261 0.042 - 0.084: 921 0.084 - 0.126: 294 0.126 - 0.169: 61 0.169 - 0.211: 5 Chirality restraints: 4542 Sorted by residual: chirality pdb=" C3' A R 54 " pdb=" C4' A R 54 " pdb=" O3' A R 54 " pdb=" C2' A R 54 " both_signs ideal model delta sigma weight residual False -2.74 -2.53 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB ILE H 183 " pdb=" CA ILE H 183 " pdb=" CG1 ILE H 183 " pdb=" CG2 ILE H 183 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CB VAL H 192 " pdb=" CA VAL H 192 " pdb=" CG1 VAL H 192 " pdb=" CG2 VAL H 192 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.96e-01 ... (remaining 4539 not shown) Planarity restraints: 4633 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU J 78 " 0.015 2.00e-02 2.50e+03 2.95e-02 8.71e+00 pdb=" C LEU J 78 " -0.051 2.00e-02 2.50e+03 pdb=" O LEU J 78 " 0.019 2.00e-02 2.50e+03 pdb=" N LYS J 79 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP I 42 " 0.043 5.00e-02 4.00e+02 6.50e-02 6.75e+00 pdb=" N PRO I 43 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO I 43 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO I 43 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP I1166 " -0.012 2.00e-02 2.50e+03 2.47e-02 6.12e+00 pdb=" C ASP I1166 " 0.043 2.00e-02 2.50e+03 pdb=" O ASP I1166 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU I1167 " -0.014 2.00e-02 2.50e+03 ... (remaining 4630 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 215 2.57 - 3.15: 22517 3.15 - 3.73: 42372 3.73 - 4.32: 59103 4.32 - 4.90: 98071 Nonbonded interactions: 222278 Sorted by model distance: nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1503 " model vdw 1.985 2.170 nonbonded pdb=" OP1 U R 95 " pdb="MG MG J1503 " model vdw 1.987 2.170 nonbonded pdb=" OG SER I 93 " pdb=" OE1 GLU I 126 " model vdw 2.015 3.040 nonbonded pdb=" OH TYR I 591 " pdb=" OE2 GLU I 611 " model vdw 2.021 3.040 nonbonded pdb=" O2' A R 22 " pdb=" O5' A R 23 " model vdw 2.056 3.040 ... (remaining 222273 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'G' and (resid 7 through 158 or resid 169 through 232)) selection = (chain 'H' and (resid 7 through 190 or (resid 191 through 192 and (name N or nam \ e CA or name C or name O or name CB )) or resid 193 or (resid 194 and (name N or \ name CA or name C or name O or name CB )) or resid 195 through 232)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.020 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: 0.030 Extract box with map and model: 0.950 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 75.220 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:2.900 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 28575 Z= 0.207 Angle : 0.774 13.080 39227 Z= 0.425 Chirality : 0.045 0.211 4542 Planarity : 0.005 0.065 4633 Dihedral : 17.671 173.697 11673 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.04 % Allowed : 0.11 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % 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: -1.87 (0.14), residues: 3181 helix: 0.05 (0.16), residues: 1086 sheet: -1.45 (0.25), residues: 376 loop : -2.12 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 997 HIS 0.007 0.001 HIS J 104 PHE 0.019 0.002 PHE I 514 TYR 0.020 0.002 TYR I 70 ARG 0.021 0.001 ARG I 779 Details of bonding type rmsd hydrogen bonds : bond 0.14705 ( 1131) hydrogen bonds : angle 6.25539 ( 3118) metal coordination : bond 0.01387 ( 8) metal coordination : angle 6.95004 ( 12) covalent geometry : bond 0.00444 (28567) covalent geometry : angle 0.76425 (39215) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 498 time to evaluate : 2.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 95 LYS cc_start: 0.7742 (mtmm) cc_final: 0.7477 (mttp) REVERT: G 120 ASP cc_start: 0.7239 (t70) cc_final: 0.6675 (t70) REVERT: G 170 ARG cc_start: 0.7171 (tpp80) cc_final: 0.6924 (ttp-170) REVERT: G 208 ASN cc_start: 0.8537 (p0) cc_final: 0.8182 (p0) REVERT: H 84 ASN cc_start: 0.9030 (m110) cc_final: 0.8812 (m110) REVERT: H 185 TYR cc_start: 0.9030 (p90) cc_final: 0.8619 (p90) REVERT: I 70 TYR cc_start: 0.7928 (t80) cc_final: 0.7555 (t80) REVERT: I 189 ASP cc_start: 0.6521 (p0) cc_final: 0.6084 (p0) REVERT: I 193 ASN cc_start: 0.8713 (m-40) cc_final: 0.8010 (m110) REVERT: I 195 PHE cc_start: 0.8168 (m-80) cc_final: 0.7282 (m-80) REVERT: I 490 GLN cc_start: 0.6825 (tm-30) cc_final: 0.6555 (tm-30) REVERT: I 696 ASP cc_start: 0.8100 (t70) cc_final: 0.7432 (t70) REVERT: I 955 GLN cc_start: 0.7977 (tp40) cc_final: 0.7564 (tp40) REVERT: J 37 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7687 (tm-30) REVERT: J 133 ARG cc_start: 0.6930 (mtm110) cc_final: 0.6564 (mtm-85) REVERT: J 200 GLN cc_start: 0.8179 (tm-30) cc_final: 0.7933 (tm-30) REVERT: J 714 GLU cc_start: 0.5985 (mp0) cc_final: 0.5653 (mp0) REVERT: J 873 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7633 (tm-30) REVERT: J 918 ILE cc_start: 0.8764 (tt) cc_final: 0.8318 (mt) REVERT: J 983 LYS cc_start: 0.7961 (mppt) cc_final: 0.7647 (mmtm) REVERT: J 1196 LEU cc_start: 0.7831 (mp) cc_final: 0.7240 (tp) REVERT: J 1334 GLU cc_start: 0.7525 (tt0) cc_final: 0.7314 (mt-10) REVERT: K 11 GLU cc_start: 0.7894 (tp30) cc_final: 0.7613 (mm-30) outliers start: 1 outliers final: 0 residues processed: 499 average time/residue: 0.5183 time to fit residues: 392.1808 Evaluate side-chains 414 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 414 time to evaluate : 2.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 279 optimal weight: 0.4980 chunk 250 optimal weight: 0.9980 chunk 139 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 169 optimal weight: 0.2980 chunk 134 optimal weight: 4.9990 chunk 259 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 157 optimal weight: 5.9990 chunk 193 optimal weight: 0.6980 chunk 300 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 127 GLN ** I 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 865 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.177543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.121617 restraints weight = 34289.301| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.30 r_work: 0.3047 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28575 Z= 0.143 Angle : 0.620 9.845 39227 Z= 0.326 Chirality : 0.043 0.219 4542 Planarity : 0.005 0.055 4633 Dihedral : 16.737 164.058 5427 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.18 % Allowed : 6.58 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % 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: -1.24 (0.14), residues: 3181 helix: 0.68 (0.16), residues: 1110 sheet: -1.11 (0.25), residues: 376 loop : -1.85 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J1193 HIS 0.005 0.001 HIS H 66 PHE 0.016 0.001 PHE J 260 TYR 0.033 0.002 TYR J1186 ARG 0.011 0.001 ARG J1148 Details of bonding type rmsd hydrogen bonds : bond 0.04467 ( 1131) hydrogen bonds : angle 4.66330 ( 3118) metal coordination : bond 0.00892 ( 8) metal coordination : angle 4.46800 ( 12) covalent geometry : bond 0.00319 (28567) covalent geometry : angle 0.61528 (39215) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 450 time to evaluate : 3.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 95 LYS cc_start: 0.7737 (mtmm) cc_final: 0.7237 (mttp) REVERT: G 97 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8052 (tt0) REVERT: G 120 ASP cc_start: 0.7696 (t70) cc_final: 0.6984 (t70) REVERT: G 145 LYS cc_start: 0.8815 (tttt) cc_final: 0.8583 (ttmm) REVERT: G 208 ASN cc_start: 0.8518 (p0) cc_final: 0.8186 (p0) REVERT: H 51 MET cc_start: 0.9336 (mmm) cc_final: 0.9092 (mmm) REVERT: H 104 LYS cc_start: 0.7801 (tttp) cc_final: 0.7241 (tttm) REVERT: H 142 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7631 (mtm) REVERT: H 185 TYR cc_start: 0.9253 (p90) cc_final: 0.8821 (p90) REVERT: I 189 ASP cc_start: 0.7192 (p0) cc_final: 0.6939 (p0) REVERT: I 191 LYS cc_start: 0.8631 (mmtp) cc_final: 0.8420 (mmtm) REVERT: I 193 ASN cc_start: 0.8618 (m-40) cc_final: 0.8068 (m110) REVERT: I 211 ARG cc_start: 0.8585 (mtt180) cc_final: 0.8378 (mtt180) REVERT: I 392 GLU cc_start: 0.8501 (mp0) cc_final: 0.8297 (mp0) REVERT: I 461 GLU cc_start: 0.8288 (tt0) cc_final: 0.7970 (tt0) REVERT: I 488 MET cc_start: 0.6690 (mmp) cc_final: 0.6407 (mmp) REVERT: I 490 GLN cc_start: 0.7336 (tm-30) cc_final: 0.6914 (tm-30) REVERT: I 859 GLU cc_start: 0.7127 (tm-30) cc_final: 0.6788 (tm-30) REVERT: I 955 GLN cc_start: 0.8356 (tp40) cc_final: 0.7682 (tp40) REVERT: I 960 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7874 (tp) REVERT: I 1230 MET cc_start: 0.9281 (ttp) cc_final: 0.8762 (ttp) REVERT: J 37 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7810 (tm-30) REVERT: J 129 ASP cc_start: 0.7994 (OUTLIER) cc_final: 0.7776 (m-30) REVERT: J 133 ARG cc_start: 0.7778 (mtm110) cc_final: 0.7404 (mtm-85) REVERT: J 200 GLN cc_start: 0.8250 (tm-30) cc_final: 0.7965 (tm-30) REVERT: J 466 MET cc_start: 0.8976 (ttm) cc_final: 0.8640 (ttm) REVERT: J 714 GLU cc_start: 0.6403 (mp0) cc_final: 0.6187 (mp0) REVERT: J 873 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8189 (tm-30) REVERT: J 992 LYS cc_start: 0.8446 (mmmm) cc_final: 0.7626 (mmtt) REVERT: J 1040 MET cc_start: 0.7389 (mpp) cc_final: 0.7086 (mpp) REVERT: J 1196 LEU cc_start: 0.7805 (mp) cc_final: 0.6971 (tp) REVERT: J 1334 GLU cc_start: 0.8440 (tt0) cc_final: 0.8204 (tt0) REVERT: K 11 GLU cc_start: 0.8757 (tp30) cc_final: 0.8374 (mm-30) REVERT: K 12 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8228 (mtpp) outliers start: 32 outliers final: 16 residues processed: 463 average time/residue: 0.6426 time to fit residues: 470.6023 Evaluate side-chains 415 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 394 time to evaluate : 4.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 725 GLN Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 129 ASP Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 820 ILE Chi-restraints excluded: chain K residue 12 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 45 optimal weight: 0.2980 chunk 253 optimal weight: 2.9990 chunk 330 optimal weight: 4.9990 chunk 141 optimal weight: 10.0000 chunk 295 optimal weight: 9.9990 chunk 230 optimal weight: 2.9990 chunk 175 optimal weight: 0.8980 chunk 245 optimal weight: 1.9990 chunk 268 optimal weight: 1.9990 chunk 298 optimal weight: 30.0000 chunk 192 optimal weight: 0.0020 overall best weight: 1.0392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 84 ASN J 157 GLN J 865 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.176719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.121038 restraints weight = 34465.467| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.24 r_work: 0.3039 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28575 Z= 0.148 Angle : 0.581 11.993 39227 Z= 0.304 Chirality : 0.042 0.218 4542 Planarity : 0.004 0.050 4633 Dihedral : 16.570 166.041 5427 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.66 % Allowed : 9.67 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % 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: -0.95 (0.14), residues: 3181 helix: 0.96 (0.16), residues: 1114 sheet: -0.80 (0.26), residues: 375 loop : -1.76 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J1193 HIS 0.005 0.001 HIS I 554 PHE 0.014 0.001 PHE I 389 TYR 0.013 0.001 TYR G 177 ARG 0.009 0.000 ARG J1148 Details of bonding type rmsd hydrogen bonds : bond 0.04258 ( 1131) hydrogen bonds : angle 4.41668 ( 3118) metal coordination : bond 0.00988 ( 8) metal coordination : angle 4.05974 ( 12) covalent geometry : bond 0.00345 (28567) covalent geometry : angle 0.57669 (39215) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 420 time to evaluate : 2.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 95 LYS cc_start: 0.7687 (mtmm) cc_final: 0.7123 (mttp) REVERT: G 97 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7964 (tt0) REVERT: G 120 ASP cc_start: 0.7796 (t70) cc_final: 0.7094 (t70) REVERT: G 145 LYS cc_start: 0.8862 (tttt) cc_final: 0.8637 (ttmm) REVERT: G 208 ASN cc_start: 0.8513 (p0) cc_final: 0.8187 (p0) REVERT: H 104 LYS cc_start: 0.7802 (tttp) cc_final: 0.7319 (tttm) REVERT: H 142 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7706 (mtm) REVERT: H 185 TYR cc_start: 0.9263 (p90) cc_final: 0.8849 (p90) REVERT: I 99 LYS cc_start: 0.8535 (tppt) cc_final: 0.8285 (tppt) REVERT: I 145 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8800 (mp) REVERT: I 193 ASN cc_start: 0.8523 (m-40) cc_final: 0.7995 (m110) REVERT: I 239 MET cc_start: 0.4755 (tmm) cc_final: 0.4549 (tmm) REVERT: I 392 GLU cc_start: 0.8502 (mp0) cc_final: 0.8289 (mp0) REVERT: I 490 GLN cc_start: 0.7270 (tm-30) cc_final: 0.6789 (tm-30) REVERT: I 633 LEU cc_start: 0.6688 (OUTLIER) cc_final: 0.6380 (pp) REVERT: I 779 ARG cc_start: 0.8522 (mtp-110) cc_final: 0.8260 (ttm110) REVERT: I 951 MET cc_start: 0.8573 (tpp) cc_final: 0.8359 (tpp) REVERT: I 955 GLN cc_start: 0.8337 (tp40) cc_final: 0.7656 (tp40) REVERT: I 1216 ARG cc_start: 0.8397 (ptt180) cc_final: 0.7730 (mtm180) REVERT: I 1230 MET cc_start: 0.9278 (ttp) cc_final: 0.8774 (ttp) REVERT: J 37 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7701 (tm-30) REVERT: J 133 ARG cc_start: 0.7780 (mtm110) cc_final: 0.7371 (mtm-85) REVERT: J 200 GLN cc_start: 0.8245 (tm-30) cc_final: 0.8012 (tm-30) REVERT: J 222 LYS cc_start: 0.9127 (mmmt) cc_final: 0.8844 (mmmm) REVERT: J 466 MET cc_start: 0.8984 (ttm) cc_final: 0.8714 (ttm) REVERT: J 714 GLU cc_start: 0.6342 (mp0) cc_final: 0.6117 (mp0) REVERT: J 873 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8218 (tm-30) REVERT: J 918 ILE cc_start: 0.9013 (tt) cc_final: 0.8643 (mt) REVERT: J 992 LYS cc_start: 0.8445 (mmmm) cc_final: 0.7591 (mmtt) REVERT: J 1040 MET cc_start: 0.7093 (mpp) cc_final: 0.6711 (mpp) REVERT: J 1334 GLU cc_start: 0.8477 (tt0) cc_final: 0.8241 (tt0) REVERT: J 1361 THR cc_start: 0.9317 (OUTLIER) cc_final: 0.8762 (p) REVERT: J 1371 ARG cc_start: 0.6613 (mtp-110) cc_final: 0.6286 (mtp-110) REVERT: K 12 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8308 (mtpp) REVERT: K 65 ASP cc_start: 0.8708 (OUTLIER) cc_final: 0.8440 (t0) outliers start: 45 outliers final: 29 residues processed: 440 average time/residue: 0.4360 time to fit residues: 294.4172 Evaluate side-chains 433 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 397 time to evaluate : 2.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 348 SER Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 725 GLN Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 946 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 820 ILE Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1361 THR Chi-restraints excluded: chain K residue 12 LYS Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 65 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 77 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 329 optimal weight: 1.9990 chunk 261 optimal weight: 5.9990 chunk 187 optimal weight: 5.9990 chunk 175 optimal weight: 0.7980 chunk 238 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 305 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1227 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.175566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.119605 restraints weight = 34820.642| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.33 r_work: 0.3002 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 28575 Z= 0.200 Angle : 0.607 14.423 39227 Z= 0.315 Chirality : 0.043 0.216 4542 Planarity : 0.004 0.048 4633 Dihedral : 16.529 166.047 5427 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.21 % Allowed : 11.29 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % 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: -0.90 (0.14), residues: 3181 helix: 0.97 (0.16), residues: 1111 sheet: -0.67 (0.25), residues: 386 loop : -1.73 (0.14), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J1193 HIS 0.006 0.001 HIS I 554 PHE 0.014 0.001 PHE I1265 TYR 0.017 0.001 TYR J 679 ARG 0.008 0.000 ARG H 143 Details of bonding type rmsd hydrogen bonds : bond 0.04487 ( 1131) hydrogen bonds : angle 4.38468 ( 3118) metal coordination : bond 0.01277 ( 8) metal coordination : angle 4.23835 ( 12) covalent geometry : bond 0.00479 (28567) covalent geometry : angle 0.60304 (39215) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 421 time to evaluate : 2.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 95 LYS cc_start: 0.7709 (mtmm) cc_final: 0.7331 (mttp) REVERT: G 97 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8100 (tt0) REVERT: G 120 ASP cc_start: 0.7768 (t70) cc_final: 0.7208 (t0) REVERT: G 208 ASN cc_start: 0.8583 (p0) cc_final: 0.8261 (p0) REVERT: H 17 GLU cc_start: 0.8434 (tt0) cc_final: 0.8160 (tt0) REVERT: H 104 LYS cc_start: 0.7829 (tttp) cc_final: 0.7613 (tttm) REVERT: H 142 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7677 (mtm) REVERT: H 185 TYR cc_start: 0.9280 (p90) cc_final: 0.8894 (p90) REVERT: I 145 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8837 (mp) REVERT: I 193 ASN cc_start: 0.8507 (m-40) cc_final: 0.8122 (m110) REVERT: I 239 MET cc_start: 0.4821 (tmm) cc_final: 0.4588 (tmm) REVERT: I 461 GLU cc_start: 0.8279 (tt0) cc_final: 0.8030 (tt0) REVERT: I 490 GLN cc_start: 0.7380 (tm-30) cc_final: 0.6857 (tm-30) REVERT: I 853 ASP cc_start: 0.8384 (t0) cc_final: 0.8154 (p0) REVERT: I 859 GLU cc_start: 0.7149 (tm-30) cc_final: 0.6878 (tm-30) REVERT: I 951 MET cc_start: 0.8638 (tpp) cc_final: 0.8424 (tpp) REVERT: I 955 GLN cc_start: 0.8368 (tp40) cc_final: 0.7625 (tp40) REVERT: I 1216 ARG cc_start: 0.8462 (ptt180) cc_final: 0.7828 (mtm180) REVERT: I 1227 VAL cc_start: 0.9349 (OUTLIER) cc_final: 0.9013 (t) REVERT: J 37 GLU cc_start: 0.8299 (tm-30) cc_final: 0.7724 (tm-30) REVERT: J 133 ARG cc_start: 0.7785 (mtm110) cc_final: 0.7318 (mtt180) REVERT: J 200 GLN cc_start: 0.8225 (tm-30) cc_final: 0.7986 (tm-30) REVERT: J 279 LEU cc_start: 0.8057 (tp) cc_final: 0.7806 (tp) REVERT: J 714 GLU cc_start: 0.6322 (mp0) cc_final: 0.6096 (mp0) REVERT: J 873 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8238 (tm-30) REVERT: J 875 ASN cc_start: 0.6509 (m-40) cc_final: 0.6199 (m-40) REVERT: J 918 ILE cc_start: 0.9059 (tt) cc_final: 0.8808 (mt) REVERT: J 992 LYS cc_start: 0.8489 (mmmm) cc_final: 0.7649 (mmtt) REVERT: J 1025 MET cc_start: 0.7942 (tpt) cc_final: 0.7248 (mmt) REVERT: J 1027 VAL cc_start: 0.9237 (OUTLIER) cc_final: 0.9021 (p) REVERT: J 1040 MET cc_start: 0.7100 (mpp) cc_final: 0.6853 (mpp) REVERT: J 1196 LEU cc_start: 0.7809 (mp) cc_final: 0.7019 (tp) REVERT: J 1334 GLU cc_start: 0.8447 (tt0) cc_final: 0.8222 (tt0) REVERT: J 1361 THR cc_start: 0.9365 (OUTLIER) cc_final: 0.8782 (p) REVERT: J 1371 ARG cc_start: 0.6667 (mtp-110) cc_final: 0.6303 (mtp-110) REVERT: K 12 LYS cc_start: 0.8591 (mtpp) cc_final: 0.8360 (mtpp) outliers start: 60 outliers final: 40 residues processed: 455 average time/residue: 0.4433 time to fit residues: 311.1808 Evaluate side-chains 458 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 412 time to evaluate : 2.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 348 SER Chi-restraints excluded: chain I residue 374 GLU Chi-restraints excluded: chain I residue 488 MET Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 725 GLN Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 946 LEU Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 820 ILE Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1292 LEU Chi-restraints excluded: chain J residue 1361 THR Chi-restraints excluded: chain K residue 58 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 320 optimal weight: 4.9990 chunk 117 optimal weight: 0.7980 chunk 276 optimal weight: 4.9990 chunk 159 optimal weight: 0.0670 chunk 317 optimal weight: 2.9990 chunk 283 optimal weight: 20.0000 chunk 239 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 225 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 513 GLN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1227 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.176526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.120434 restraints weight = 34534.334| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.36 r_work: 0.3025 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 28575 Z= 0.150 Angle : 0.571 13.724 39227 Z= 0.296 Chirality : 0.042 0.214 4542 Planarity : 0.004 0.049 4633 Dihedral : 16.432 166.613 5427 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.13 % Allowed : 13.42 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % 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: -0.72 (0.15), residues: 3181 helix: 1.12 (0.16), residues: 1114 sheet: -0.51 (0.26), residues: 376 loop : -1.63 (0.14), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J1193 HIS 0.004 0.001 HIS I 554 PHE 0.012 0.001 PHE I 405 TYR 0.015 0.001 TYR J 679 ARG 0.008 0.000 ARG H 143 Details of bonding type rmsd hydrogen bonds : bond 0.04044 ( 1131) hydrogen bonds : angle 4.24590 ( 3118) metal coordination : bond 0.01005 ( 8) metal coordination : angle 3.83763 ( 12) covalent geometry : bond 0.00352 (28567) covalent geometry : angle 0.56728 (39215) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 445 time to evaluate : 2.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 97 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7939 (tt0) REVERT: G 208 ASN cc_start: 0.8547 (p0) cc_final: 0.8223 (p0) REVERT: H 17 GLU cc_start: 0.8490 (tt0) cc_final: 0.8269 (tt0) REVERT: H 84 ASN cc_start: 0.8935 (m-40) cc_final: 0.8648 (m110) REVERT: H 142 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7696 (mtm) REVERT: H 185 TYR cc_start: 0.9273 (p90) cc_final: 0.8882 (p90) REVERT: I 145 ILE cc_start: 0.9159 (OUTLIER) cc_final: 0.8772 (mp) REVERT: I 193 ASN cc_start: 0.8568 (m-40) cc_final: 0.8241 (m110) REVERT: I 239 MET cc_start: 0.4830 (tmm) cc_final: 0.4528 (tmm) REVERT: I 371 ARG cc_start: 0.7913 (ttm-80) cc_final: 0.7615 (ptp-110) REVERT: I 394 ARG cc_start: 0.8253 (tpp80) cc_final: 0.7873 (mmm-85) REVERT: I 429 MET cc_start: 0.8114 (mtt) cc_final: 0.7912 (mtt) REVERT: I 461 GLU cc_start: 0.8222 (tt0) cc_final: 0.7983 (tt0) REVERT: I 490 GLN cc_start: 0.7392 (tm-30) cc_final: 0.6796 (tm-30) REVERT: I 628 HIS cc_start: 0.7744 (m-70) cc_final: 0.7393 (m90) REVERT: I 672 GLU cc_start: 0.8808 (pm20) cc_final: 0.8454 (pm20) REVERT: I 725 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8084 (tp40) REVERT: I 779 ARG cc_start: 0.8490 (mtp-110) cc_final: 0.8164 (ttm110) REVERT: I 853 ASP cc_start: 0.8380 (t0) cc_final: 0.8134 (p0) REVERT: I 951 MET cc_start: 0.8631 (tpp) cc_final: 0.8404 (tpp) REVERT: I 955 GLN cc_start: 0.8401 (tp40) cc_final: 0.7640 (tp40) REVERT: I 1216 ARG cc_start: 0.8386 (ptt180) cc_final: 0.7850 (mtm180) REVERT: J 37 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7779 (tm-30) REVERT: J 42 GLU cc_start: 0.8198 (tt0) cc_final: 0.7985 (tt0) REVERT: J 133 ARG cc_start: 0.7827 (mtm110) cc_final: 0.7324 (mtt180) REVERT: J 200 GLN cc_start: 0.8199 (tm-30) cc_final: 0.7956 (tm-30) REVERT: J 279 LEU cc_start: 0.8086 (tp) cc_final: 0.7834 (tp) REVERT: J 399 LYS cc_start: 0.8872 (ttpp) cc_final: 0.8613 (mmtt) REVERT: J 714 GLU cc_start: 0.6305 (mp0) cc_final: 0.6091 (mp0) REVERT: J 873 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8266 (tm-30) REVERT: J 892 PHE cc_start: 0.8208 (m-80) cc_final: 0.7925 (m-80) REVERT: J 992 LYS cc_start: 0.8490 (mmmm) cc_final: 0.7667 (mmtt) REVERT: J 1025 MET cc_start: 0.8032 (tpt) cc_final: 0.7287 (mmt) REVERT: J 1040 MET cc_start: 0.7118 (mpp) cc_final: 0.6838 (mpp) REVERT: J 1196 LEU cc_start: 0.7937 (mp) cc_final: 0.7125 (tp) REVERT: J 1334 GLU cc_start: 0.8476 (tt0) cc_final: 0.8262 (tt0) REVERT: J 1361 THR cc_start: 0.9268 (OUTLIER) cc_final: 0.8708 (p) REVERT: J 1371 ARG cc_start: 0.6676 (mtp-110) cc_final: 0.6364 (mtp-110) REVERT: K 21 LEU cc_start: 0.8770 (mt) cc_final: 0.8538 (mt) outliers start: 58 outliers final: 38 residues processed: 475 average time/residue: 0.4346 time to fit residues: 318.1499 Evaluate side-chains 459 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 416 time to evaluate : 2.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 348 SER Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 725 GLN Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 820 ILE Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1352 ILE Chi-restraints excluded: chain J residue 1361 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 102 optimal weight: 1.9990 chunk 295 optimal weight: 10.0000 chunk 170 optimal weight: 1.9990 chunk 53 optimal weight: 0.0020 chunk 232 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 279 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 248 optimal weight: 0.5980 chunk 311 optimal weight: 0.9980 chunk 126 optimal weight: 0.8980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN I 165 HIS I 628 HIS ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1227 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.178181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.122473 restraints weight = 34698.026| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.30 r_work: 0.3051 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28575 Z= 0.121 Angle : 0.555 13.162 39227 Z= 0.287 Chirality : 0.041 0.213 4542 Planarity : 0.004 0.047 4633 Dihedral : 16.367 166.789 5427 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.43 % Allowed : 14.23 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % 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: 3181 helix: 1.26 (0.16), residues: 1115 sheet: -0.63 (0.25), residues: 400 loop : -1.53 (0.14), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J1193 HIS 0.004 0.001 HIS H 66 PHE 0.015 0.001 PHE I 389 TYR 0.015 0.001 TYR J 679 ARG 0.011 0.000 ARG H 143 Details of bonding type rmsd hydrogen bonds : bond 0.03767 ( 1131) hydrogen bonds : angle 4.12571 ( 3118) metal coordination : bond 0.00782 ( 8) metal coordination : angle 3.38339 ( 12) covalent geometry : bond 0.00278 (28567) covalent geometry : angle 0.55207 (39215) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 431 time to evaluate : 2.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 120 ASP cc_start: 0.7767 (t70) cc_final: 0.7222 (t0) REVERT: G 208 ASN cc_start: 0.8522 (p0) cc_final: 0.8221 (p0) REVERT: H 17 GLU cc_start: 0.8488 (tt0) cc_final: 0.8258 (tt0) REVERT: H 84 ASN cc_start: 0.8956 (m-40) cc_final: 0.8719 (m110) REVERT: H 104 LYS cc_start: 0.7730 (tttp) cc_final: 0.7136 (tttm) REVERT: H 142 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.7582 (mtm) REVERT: H 185 TYR cc_start: 0.9240 (p90) cc_final: 0.8858 (p90) REVERT: I 119 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8391 (pp20) REVERT: I 193 ASN cc_start: 0.8489 (m-40) cc_final: 0.8173 (m110) REVERT: I 239 MET cc_start: 0.4913 (tmm) cc_final: 0.4627 (tmm) REVERT: I 315 MET cc_start: 0.8121 (ppp) cc_final: 0.7812 (ppp) REVERT: I 393 ASP cc_start: 0.8504 (m-30) cc_final: 0.7895 (t70) REVERT: I 473 ARG cc_start: 0.8068 (tmm-80) cc_final: 0.7854 (tmm-80) REVERT: I 490 GLN cc_start: 0.7398 (tm-30) cc_final: 0.6818 (tm-30) REVERT: I 672 GLU cc_start: 0.8794 (pm20) cc_final: 0.8469 (pm20) REVERT: I 725 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8032 (tp40) REVERT: I 779 ARG cc_start: 0.8443 (mtp-110) cc_final: 0.8148 (ttm-80) REVERT: I 853 ASP cc_start: 0.8309 (t0) cc_final: 0.8101 (p0) REVERT: I 859 GLU cc_start: 0.7101 (tm-30) cc_final: 0.6892 (tm-30) REVERT: I 951 MET cc_start: 0.8621 (tpp) cc_final: 0.8397 (tpp) REVERT: I 955 GLN cc_start: 0.8393 (tp40) cc_final: 0.7673 (tp40) REVERT: I 1216 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7830 (mtm180) REVERT: I 1227 VAL cc_start: 0.9340 (OUTLIER) cc_final: 0.9060 (t) REVERT: J 37 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7461 (tm-30) REVERT: J 42 GLU cc_start: 0.8188 (tt0) cc_final: 0.7973 (tt0) REVERT: J 133 ARG cc_start: 0.7834 (mtm110) cc_final: 0.7325 (mtt180) REVERT: J 200 GLN cc_start: 0.8194 (tm-30) cc_final: 0.7948 (tm-30) REVERT: J 279 LEU cc_start: 0.8103 (tp) cc_final: 0.7859 (tp) REVERT: J 873 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8224 (tm-30) REVERT: J 892 PHE cc_start: 0.8085 (m-80) cc_final: 0.7852 (m-80) REVERT: J 992 LYS cc_start: 0.8527 (mmmm) cc_final: 0.7699 (mmtt) REVERT: J 1025 MET cc_start: 0.7996 (tpt) cc_final: 0.7294 (mmt) REVERT: J 1040 MET cc_start: 0.7156 (mpp) cc_final: 0.6823 (mpp) REVERT: J 1148 ARG cc_start: 0.7655 (mtt90) cc_final: 0.7428 (mtm-85) REVERT: J 1189 MET cc_start: 0.8403 (mmm) cc_final: 0.7778 (tmm) REVERT: J 1196 LEU cc_start: 0.7826 (mp) cc_final: 0.6945 (tp) REVERT: J 1305 ASP cc_start: 0.8660 (m-30) cc_final: 0.8217 (t70) REVERT: J 1334 GLU cc_start: 0.8516 (tt0) cc_final: 0.8298 (tt0) REVERT: J 1361 THR cc_start: 0.9179 (OUTLIER) cc_final: 0.8463 (p) REVERT: J 1371 ARG cc_start: 0.6660 (mtp-110) cc_final: 0.6345 (mtp-110) REVERT: K 21 LEU cc_start: 0.8752 (mt) cc_final: 0.8550 (mt) REVERT: K 65 ASP cc_start: 0.8692 (OUTLIER) cc_final: 0.8424 (t0) REVERT: K 72 GLN cc_start: 0.8205 (tm-30) cc_final: 0.7903 (tm-30) outliers start: 66 outliers final: 40 residues processed: 468 average time/residue: 0.4235 time to fit residues: 307.7450 Evaluate side-chains 456 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 409 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 122 GLU Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 119 GLU Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 348 SER Chi-restraints excluded: chain I residue 488 MET Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 725 GLN Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1216 ARG Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 681 LYS Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 817 HIS Chi-restraints excluded: chain J residue 820 ILE Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1361 THR Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 65 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 192 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 280 optimal weight: 0.6980 chunk 174 optimal weight: 0.5980 chunk 150 optimal weight: 0.4980 chunk 17 optimal weight: 3.9990 chunk 290 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 248 optimal weight: 0.4980 chunk 67 optimal weight: 9.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 513 GLN J 777 HIS ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1227 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.179592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.122941 restraints weight = 34596.990| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.30 r_work: 0.3066 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28575 Z= 0.115 Angle : 0.553 12.515 39227 Z= 0.285 Chirality : 0.041 0.212 4542 Planarity : 0.004 0.047 4633 Dihedral : 16.293 167.041 5427 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.24 % Allowed : 14.75 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % 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: -0.40 (0.15), residues: 3181 helix: 1.41 (0.16), residues: 1114 sheet: -0.38 (0.26), residues: 387 loop : -1.46 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J1193 HIS 0.004 0.001 HIS H 66 PHE 0.013 0.001 PHE I 389 TYR 0.014 0.001 TYR J 679 ARG 0.011 0.000 ARG H 143 Details of bonding type rmsd hydrogen bonds : bond 0.03545 ( 1131) hydrogen bonds : angle 4.01849 ( 3118) metal coordination : bond 0.00677 ( 8) metal coordination : angle 2.84182 ( 12) covalent geometry : bond 0.00264 (28567) covalent geometry : angle 0.55121 (39215) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 428 time to evaluate : 3.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 120 ASP cc_start: 0.7772 (t70) cc_final: 0.7397 (t0) REVERT: G 208 ASN cc_start: 0.8435 (p0) cc_final: 0.8179 (p0) REVERT: H 17 GLU cc_start: 0.8527 (tt0) cc_final: 0.8313 (tt0) REVERT: H 142 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7597 (mtm) REVERT: H 185 TYR cc_start: 0.9209 (p90) cc_final: 0.8845 (p90) REVERT: I 99 LYS cc_start: 0.8436 (tppt) cc_final: 0.8155 (tppt) REVERT: I 104 ILE cc_start: 0.7772 (OUTLIER) cc_final: 0.7560 (mt) REVERT: I 119 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8297 (pp20) REVERT: I 145 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8750 (mp) REVERT: I 193 ASN cc_start: 0.8433 (m-40) cc_final: 0.8113 (m110) REVERT: I 211 ARG cc_start: 0.8549 (mtt180) cc_final: 0.7987 (ttt180) REVERT: I 239 MET cc_start: 0.4925 (tmm) cc_final: 0.4631 (tmm) REVERT: I 393 ASP cc_start: 0.8608 (m-30) cc_final: 0.7916 (t70) REVERT: I 473 ARG cc_start: 0.8073 (tmm-80) cc_final: 0.7867 (tmm-80) REVERT: I 490 GLN cc_start: 0.7281 (tm-30) cc_final: 0.6706 (tm-30) REVERT: I 672 GLU cc_start: 0.8803 (pm20) cc_final: 0.8487 (pm20) REVERT: I 725 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8129 (tp40) REVERT: I 779 ARG cc_start: 0.8467 (mtp-110) cc_final: 0.8145 (ttm-80) REVERT: I 799 ASN cc_start: 0.8721 (OUTLIER) cc_final: 0.8494 (m110) REVERT: I 853 ASP cc_start: 0.8316 (t0) cc_final: 0.8085 (p0) REVERT: I 951 MET cc_start: 0.8614 (tpp) cc_final: 0.8389 (tpp) REVERT: I 955 GLN cc_start: 0.8385 (tp40) cc_final: 0.7642 (tp40) REVERT: I 1216 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7815 (mtm180) REVERT: I 1227 VAL cc_start: 0.9323 (OUTLIER) cc_final: 0.9041 (t) REVERT: J 37 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7406 (tm-30) REVERT: J 200 GLN cc_start: 0.8128 (tm-30) cc_final: 0.7812 (pp30) REVERT: J 275 ARG cc_start: 0.7986 (mmp80) cc_final: 0.7774 (mmp80) REVERT: J 279 LEU cc_start: 0.8055 (tp) cc_final: 0.7788 (tp) REVERT: J 399 LYS cc_start: 0.8843 (ttpp) cc_final: 0.8578 (mmtt) REVERT: J 403 ARG cc_start: 0.8145 (ttp-110) cc_final: 0.7903 (mtm-85) REVERT: J 873 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8276 (tm-30) REVERT: J 992 LYS cc_start: 0.8522 (mmmm) cc_final: 0.7721 (mmtt) REVERT: J 1025 MET cc_start: 0.8075 (tpt) cc_final: 0.7391 (mmt) REVERT: J 1040 MET cc_start: 0.7253 (mpp) cc_final: 0.6867 (mpp) REVERT: J 1148 ARG cc_start: 0.7653 (mtt90) cc_final: 0.7287 (mtm-85) REVERT: J 1189 MET cc_start: 0.8347 (mmm) cc_final: 0.7876 (tmm) REVERT: J 1196 LEU cc_start: 0.7859 (mp) cc_final: 0.6968 (tp) REVERT: J 1305 ASP cc_start: 0.8651 (m-30) cc_final: 0.8215 (t70) REVERT: J 1334 GLU cc_start: 0.8487 (tt0) cc_final: 0.8277 (tt0) REVERT: J 1361 THR cc_start: 0.9058 (OUTLIER) cc_final: 0.8525 (p) REVERT: J 1370 MET cc_start: 0.7053 (mmp) cc_final: 0.6780 (mmt) REVERT: J 1371 ARG cc_start: 0.6705 (mtp-110) cc_final: 0.6373 (mtp-110) REVERT: K 65 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.8400 (t0) REVERT: K 72 GLN cc_start: 0.8215 (tm-30) cc_final: 0.7894 (tm-30) outliers start: 61 outliers final: 38 residues processed: 463 average time/residue: 0.4322 time to fit residues: 310.0364 Evaluate side-chains 453 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 405 time to evaluate : 2.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 119 GLU Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 348 SER Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 725 GLN Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1216 ARG Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 820 ILE Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1361 THR Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 65 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 71 optimal weight: 4.9990 chunk 132 optimal weight: 0.5980 chunk 269 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 229 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 309 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 278 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 84 ASN I1146 GLN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1227 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.179660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.122571 restraints weight = 34586.431| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.35 r_work: 0.3051 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28575 Z= 0.132 Angle : 0.568 13.227 39227 Z= 0.291 Chirality : 0.041 0.218 4542 Planarity : 0.004 0.053 4633 Dihedral : 16.259 167.078 5427 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.24 % Allowed : 14.97 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % 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: -0.39 (0.15), residues: 3181 helix: 1.43 (0.16), residues: 1116 sheet: -0.42 (0.26), residues: 388 loop : -1.46 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J1193 HIS 0.005 0.001 HIS H 66 PHE 0.012 0.001 PHE I 389 TYR 0.024 0.001 TYR I 367 ARG 0.014 0.000 ARG H 143 Details of bonding type rmsd hydrogen bonds : bond 0.03672 ( 1131) hydrogen bonds : angle 4.01228 ( 3118) metal coordination : bond 0.00772 ( 8) metal coordination : angle 2.90476 ( 12) covalent geometry : bond 0.00309 (28567) covalent geometry : angle 0.56545 (39215) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 418 time to evaluate : 2.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 60 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7122 (mp0) REVERT: G 120 ASP cc_start: 0.7777 (t70) cc_final: 0.7355 (t0) REVERT: G 208 ASN cc_start: 0.8486 (p0) cc_final: 0.8211 (p0) REVERT: H 17 GLU cc_start: 0.8515 (tt0) cc_final: 0.8287 (tt0) REVERT: H 142 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7527 (mtm) REVERT: H 185 TYR cc_start: 0.9199 (p90) cc_final: 0.8883 (p90) REVERT: I 36 GLN cc_start: 0.8514 (tp40) cc_final: 0.8308 (tp40) REVERT: I 99 LYS cc_start: 0.8464 (tppt) cc_final: 0.8236 (tppt) REVERT: I 145 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8759 (mp) REVERT: I 193 ASN cc_start: 0.8542 (m-40) cc_final: 0.8158 (m110) REVERT: I 211 ARG cc_start: 0.8576 (mtt180) cc_final: 0.7995 (ttt180) REVERT: I 239 MET cc_start: 0.4972 (tmm) cc_final: 0.4648 (tmm) REVERT: I 392 GLU cc_start: 0.8569 (mp0) cc_final: 0.8275 (mp0) REVERT: I 393 ASP cc_start: 0.8624 (m-30) cc_final: 0.7996 (t70) REVERT: I 461 GLU cc_start: 0.8335 (tt0) cc_final: 0.7998 (mt-10) REVERT: I 473 ARG cc_start: 0.8136 (tmm-80) cc_final: 0.7915 (tmm-80) REVERT: I 490 GLN cc_start: 0.7283 (tm-30) cc_final: 0.6650 (tm-30) REVERT: I 631 GLU cc_start: 0.6543 (OUTLIER) cc_final: 0.6176 (tm-30) REVERT: I 672 GLU cc_start: 0.8818 (pm20) cc_final: 0.8501 (pm20) REVERT: I 725 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8152 (tp40) REVERT: I 779 ARG cc_start: 0.8497 (mtp-110) cc_final: 0.8156 (ttm-80) REVERT: I 853 ASP cc_start: 0.8313 (t0) cc_final: 0.8064 (p0) REVERT: I 951 MET cc_start: 0.8651 (tpp) cc_final: 0.8409 (tpp) REVERT: I 955 GLN cc_start: 0.8399 (tp40) cc_final: 0.7661 (tp40) REVERT: I 1216 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7816 (mtm180) REVERT: I 1227 VAL cc_start: 0.9328 (OUTLIER) cc_final: 0.9023 (t) REVERT: J 37 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7389 (tm-30) REVERT: J 200 GLN cc_start: 0.8148 (tm-30) cc_final: 0.7829 (pp30) REVERT: J 275 ARG cc_start: 0.7957 (mmp80) cc_final: 0.7710 (mmp80) REVERT: J 279 LEU cc_start: 0.8092 (tp) cc_final: 0.7830 (tp) REVERT: J 399 LYS cc_start: 0.8850 (ttpp) cc_final: 0.8613 (mmtt) REVERT: J 873 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8209 (tm-30) REVERT: J 875 ASN cc_start: 0.6498 (m-40) cc_final: 0.6242 (m-40) REVERT: J 992 LYS cc_start: 0.8524 (mmmm) cc_final: 0.7726 (mmtt) REVERT: J 1025 MET cc_start: 0.8090 (tpt) cc_final: 0.7388 (mmt) REVERT: J 1040 MET cc_start: 0.7240 (mpp) cc_final: 0.6842 (mpp) REVERT: J 1148 ARG cc_start: 0.7640 (mtt90) cc_final: 0.7355 (mtm-85) REVERT: J 1189 MET cc_start: 0.8348 (mmm) cc_final: 0.7890 (tmm) REVERT: J 1196 LEU cc_start: 0.7869 (mp) cc_final: 0.6985 (tp) REVERT: J 1278 GLU cc_start: 0.7240 (tt0) cc_final: 0.6873 (pt0) REVERT: J 1305 ASP cc_start: 0.8621 (OUTLIER) cc_final: 0.8192 (t70) REVERT: J 1334 GLU cc_start: 0.8492 (tt0) cc_final: 0.8276 (tt0) REVERT: J 1371 ARG cc_start: 0.6843 (mtp-110) cc_final: 0.6501 (mtp-110) REVERT: K 65 ASP cc_start: 0.8676 (OUTLIER) cc_final: 0.8410 (t0) REVERT: K 72 GLN cc_start: 0.8283 (tm-30) cc_final: 0.7930 (tm-30) outliers start: 61 outliers final: 44 residues processed: 450 average time/residue: 0.4328 time to fit residues: 299.0974 Evaluate side-chains 464 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 412 time to evaluate : 2.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 122 GLU Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 348 SER Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 631 GLU Chi-restraints excluded: chain I residue 725 GLN Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1216 ARG Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 820 ILE Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1305 ASP Chi-restraints excluded: chain J residue 1361 THR Chi-restraints excluded: chain K residue 65 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 9 optimal weight: 10.0000 chunk 112 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 252 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 254 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 156 optimal weight: 20.0000 chunk 71 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1227 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.178141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.121734 restraints weight = 34649.763| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.33 r_work: 0.3037 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28575 Z= 0.148 Angle : 0.579 13.972 39227 Z= 0.296 Chirality : 0.041 0.233 4542 Planarity : 0.004 0.056 4633 Dihedral : 16.256 167.120 5427 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.24 % Allowed : 15.23 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % 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: -0.40 (0.15), residues: 3181 helix: 1.41 (0.16), residues: 1116 sheet: -0.33 (0.26), residues: 383 loop : -1.47 (0.14), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J1193 HIS 0.005 0.001 HIS H 66 PHE 0.012 0.001 PHE J 260 TYR 0.013 0.001 TYR J 631 ARG 0.014 0.000 ARG H 143 Details of bonding type rmsd hydrogen bonds : bond 0.03779 ( 1131) hydrogen bonds : angle 4.04617 ( 3118) metal coordination : bond 0.00861 ( 8) metal coordination : angle 3.05405 ( 12) covalent geometry : bond 0.00352 (28567) covalent geometry : angle 0.57683 (39215) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 426 time to evaluate : 2.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 60 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7134 (mp0) REVERT: G 120 ASP cc_start: 0.7787 (t70) cc_final: 0.7416 (t0) REVERT: G 135 ASP cc_start: 0.8303 (t0) cc_final: 0.8038 (t0) REVERT: G 199 ASP cc_start: 0.8257 (m-30) cc_final: 0.7995 (m-30) REVERT: G 208 ASN cc_start: 0.8533 (p0) cc_final: 0.8252 (p0) REVERT: H 17 GLU cc_start: 0.8553 (tt0) cc_final: 0.8329 (tt0) REVERT: H 142 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7456 (mtm) REVERT: H 185 TYR cc_start: 0.9198 (p90) cc_final: 0.8889 (p90) REVERT: I 99 LYS cc_start: 0.8431 (tppt) cc_final: 0.8043 (tppt) REVERT: I 145 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8794 (mp) REVERT: I 193 ASN cc_start: 0.8570 (m-40) cc_final: 0.8178 (m110) REVERT: I 211 ARG cc_start: 0.8559 (mtt180) cc_final: 0.7977 (ttt180) REVERT: I 239 MET cc_start: 0.4951 (tmm) cc_final: 0.4602 (tmm) REVERT: I 315 MET cc_start: 0.7859 (ppp) cc_final: 0.7230 (ppp) REVERT: I 443 ASP cc_start: 0.7493 (m-30) cc_final: 0.7249 (m-30) REVERT: I 461 GLU cc_start: 0.8316 (tt0) cc_final: 0.8000 (mt-10) REVERT: I 473 ARG cc_start: 0.8152 (tmm-80) cc_final: 0.7929 (tmm-80) REVERT: I 490 GLN cc_start: 0.7244 (tm-30) cc_final: 0.6674 (tm-30) REVERT: I 631 GLU cc_start: 0.6535 (OUTLIER) cc_final: 0.6018 (tm-30) REVERT: I 672 GLU cc_start: 0.8834 (pm20) cc_final: 0.8510 (pm20) REVERT: I 725 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8165 (tp40) REVERT: I 779 ARG cc_start: 0.8520 (mtp-110) cc_final: 0.8186 (ttm-80) REVERT: I 853 ASP cc_start: 0.8334 (t0) cc_final: 0.7992 (p0) REVERT: I 859 GLU cc_start: 0.6831 (tp30) cc_final: 0.6450 (tm-30) REVERT: I 951 MET cc_start: 0.8658 (tpp) cc_final: 0.8411 (tpp) REVERT: I 955 GLN cc_start: 0.8420 (tp40) cc_final: 0.7915 (tm-30) REVERT: I 1216 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7910 (mtm180) REVERT: I 1227 VAL cc_start: 0.9342 (OUTLIER) cc_final: 0.9028 (t) REVERT: J 37 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7448 (tm-30) REVERT: J 42 GLU cc_start: 0.8077 (pm20) cc_final: 0.7836 (pm20) REVERT: J 53 ARG cc_start: 0.7461 (ptm-80) cc_final: 0.6978 (ptm160) REVERT: J 200 GLN cc_start: 0.8179 (tm-30) cc_final: 0.7853 (pp30) REVERT: J 279 LEU cc_start: 0.8116 (tp) cc_final: 0.7875 (tp) REVERT: J 399 LYS cc_start: 0.8852 (ttpp) cc_final: 0.8642 (mmtt) REVERT: J 737 ILE cc_start: 0.9133 (mm) cc_final: 0.8924 (mm) REVERT: J 873 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8260 (tm-30) REVERT: J 875 ASN cc_start: 0.6562 (m-40) cc_final: 0.6302 (m-40) REVERT: J 992 LYS cc_start: 0.8526 (mmmm) cc_final: 0.7722 (mmtt) REVERT: J 1025 MET cc_start: 0.8077 (tpt) cc_final: 0.7393 (mmt) REVERT: J 1040 MET cc_start: 0.7224 (mpp) cc_final: 0.6823 (mpp) REVERT: J 1148 ARG cc_start: 0.7720 (mtt90) cc_final: 0.7407 (mtm-85) REVERT: J 1189 MET cc_start: 0.8341 (mmm) cc_final: 0.7901 (tmm) REVERT: J 1196 LEU cc_start: 0.7885 (mp) cc_final: 0.7006 (tp) REVERT: J 1278 GLU cc_start: 0.7159 (tt0) cc_final: 0.6771 (pt0) REVERT: J 1305 ASP cc_start: 0.8629 (OUTLIER) cc_final: 0.8202 (t70) REVERT: J 1370 MET cc_start: 0.7111 (mmp) cc_final: 0.6809 (mmt) REVERT: J 1371 ARG cc_start: 0.6888 (mtp-110) cc_final: 0.6550 (mtp-110) REVERT: K 65 ASP cc_start: 0.8692 (OUTLIER) cc_final: 0.8429 (t0) REVERT: K 72 GLN cc_start: 0.8281 (tm-30) cc_final: 0.7934 (tm-30) outliers start: 61 outliers final: 47 residues processed: 459 average time/residue: 0.4229 time to fit residues: 299.8977 Evaluate side-chains 466 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 411 time to evaluate : 2.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 348 SER Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 631 GLU Chi-restraints excluded: chain I residue 725 GLN Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 946 LEU Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1216 ARG Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 177 ASP Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 592 VAL Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 820 ILE Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1305 ASP Chi-restraints excluded: chain J residue 1361 THR Chi-restraints excluded: chain K residue 65 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 45 optimal weight: 5.9990 chunk 200 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 273 optimal weight: 7.9990 chunk 15 optimal weight: 0.5980 chunk 41 optimal weight: 0.0000 chunk 222 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 287 optimal weight: 20.0000 chunk 260 optimal weight: 2.9990 chunk 263 optimal weight: 0.0970 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1227 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.179882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.123828 restraints weight = 34637.558| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.32 r_work: 0.3077 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28575 Z= 0.113 Angle : 0.563 12.902 39227 Z= 0.288 Chirality : 0.040 0.237 4542 Planarity : 0.004 0.057 4633 Dihedral : 16.199 167.286 5427 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.77 % Allowed : 15.70 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % 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: -0.25 (0.15), residues: 3181 helix: 1.49 (0.16), residues: 1123 sheet: -0.20 (0.27), residues: 379 loop : -1.37 (0.14), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J1193 HIS 0.004 0.001 HIS H 66 PHE 0.016 0.001 PHE J 141 TYR 0.018 0.001 TYR I 367 ARG 0.014 0.000 ARG H 143 Details of bonding type rmsd hydrogen bonds : bond 0.03402 ( 1131) hydrogen bonds : angle 3.96517 ( 3118) metal coordination : bond 0.00574 ( 8) metal coordination : angle 2.58675 ( 12) covalent geometry : bond 0.00259 (28567) covalent geometry : angle 0.56128 (39215) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 421 time to evaluate : 2.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 60 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7044 (mp0) REVERT: G 120 ASP cc_start: 0.7785 (t70) cc_final: 0.7447 (t0) REVERT: G 208 ASN cc_start: 0.8458 (p0) cc_final: 0.8136 (p0) REVERT: H 17 GLU cc_start: 0.8564 (tt0) cc_final: 0.8333 (tt0) REVERT: H 142 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7625 (mtm) REVERT: H 185 TYR cc_start: 0.9117 (p90) cc_final: 0.8813 (p90) REVERT: I 36 GLN cc_start: 0.8580 (tp40) cc_final: 0.8256 (tp-100) REVERT: I 99 LYS cc_start: 0.8441 (tppt) cc_final: 0.8007 (tppt) REVERT: I 104 ILE cc_start: 0.7743 (OUTLIER) cc_final: 0.7519 (mt) REVERT: I 145 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8727 (mp) REVERT: I 193 ASN cc_start: 0.8591 (m-40) cc_final: 0.8173 (m110) REVERT: I 239 MET cc_start: 0.4852 (tmm) cc_final: 0.4433 (tmm) REVERT: I 315 MET cc_start: 0.7827 (ppp) cc_final: 0.7186 (ppp) REVERT: I 443 ASP cc_start: 0.7550 (m-30) cc_final: 0.7296 (m-30) REVERT: I 461 GLU cc_start: 0.8288 (tt0) cc_final: 0.7981 (mt-10) REVERT: I 473 ARG cc_start: 0.8118 (tmm-80) cc_final: 0.7906 (tmm-80) REVERT: I 490 GLN cc_start: 0.7159 (tm-30) cc_final: 0.6573 (tm-30) REVERT: I 631 GLU cc_start: 0.6516 (OUTLIER) cc_final: 0.6124 (tm-30) REVERT: I 672 GLU cc_start: 0.8731 (pm20) cc_final: 0.8428 (pm20) REVERT: I 725 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8218 (tp40) REVERT: I 853 ASP cc_start: 0.8328 (t0) cc_final: 0.7996 (p0) REVERT: I 859 GLU cc_start: 0.6817 (tp30) cc_final: 0.6354 (tm-30) REVERT: I 951 MET cc_start: 0.8623 (tpp) cc_final: 0.8374 (tpp) REVERT: I 955 GLN cc_start: 0.8408 (tp40) cc_final: 0.7957 (tm-30) REVERT: I 1216 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7759 (mtm180) REVERT: I 1227 VAL cc_start: 0.9314 (OUTLIER) cc_final: 0.9014 (t) REVERT: J 37 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7357 (tm-30) REVERT: J 53 ARG cc_start: 0.7308 (ptm-80) cc_final: 0.6736 (ttp-170) REVERT: J 133 ARG cc_start: 0.7780 (mtm110) cc_final: 0.7323 (mtt180) REVERT: J 200 GLN cc_start: 0.8193 (tm-30) cc_final: 0.7884 (pp30) REVERT: J 279 LEU cc_start: 0.8045 (tp) cc_final: 0.7772 (tp) REVERT: J 311 ARG cc_start: 0.8625 (mmt90) cc_final: 0.7871 (mtt90) REVERT: J 322 ARG cc_start: 0.8583 (mpp-170) cc_final: 0.8309 (mpp-170) REVERT: J 399 LYS cc_start: 0.8821 (ttpp) cc_final: 0.8610 (mmtt) REVERT: J 485 MET cc_start: 0.9176 (tpt) cc_final: 0.8689 (tpt) REVERT: J 873 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8220 (tm-30) REVERT: J 875 ASN cc_start: 0.6449 (m-40) cc_final: 0.6178 (m-40) REVERT: J 992 LYS cc_start: 0.8509 (mmmm) cc_final: 0.7818 (mptt) REVERT: J 1025 MET cc_start: 0.8080 (tpt) cc_final: 0.7439 (mmt) REVERT: J 1040 MET cc_start: 0.7161 (mpp) cc_final: 0.6763 (mpp) REVERT: J 1148 ARG cc_start: 0.7692 (mtt90) cc_final: 0.7408 (mtm-85) REVERT: J 1189 MET cc_start: 0.8304 (mmm) cc_final: 0.7833 (tmm) REVERT: J 1196 LEU cc_start: 0.7839 (mp) cc_final: 0.6995 (tp) REVERT: J 1278 GLU cc_start: 0.7132 (tt0) cc_final: 0.6898 (tt0) REVERT: J 1305 ASP cc_start: 0.8548 (m-30) cc_final: 0.8290 (t0) REVERT: J 1361 THR cc_start: 0.9073 (OUTLIER) cc_final: 0.8489 (p) REVERT: J 1371 ARG cc_start: 0.6840 (mtp-110) cc_final: 0.6511 (mtp-110) REVERT: K 72 GLN cc_start: 0.8283 (tm-30) cc_final: 0.7957 (tm-30) outliers start: 48 outliers final: 35 residues processed: 445 average time/residue: 0.4396 time to fit residues: 302.7592 Evaluate side-chains 455 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 412 time to evaluate : 3.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 348 SER Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 631 GLU Chi-restraints excluded: chain I residue 725 GLN Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 946 LEU Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1216 ARG Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 592 VAL Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1361 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 179 optimal weight: 0.8980 chunk 157 optimal weight: 5.9990 chunk 219 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 171 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 315 optimal weight: 0.7980 chunk 268 optimal weight: 0.8980 chunk 254 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN I 799 ASN I1017 GLN J 777 HIS ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1227 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.178821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.122705 restraints weight = 34549.282| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.38 r_work: 0.3051 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28575 Z= 0.132 Angle : 0.574 13.289 39227 Z= 0.293 Chirality : 0.041 0.225 4542 Planarity : 0.004 0.060 4633 Dihedral : 16.163 167.193 5427 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.02 % Allowed : 15.81 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % 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: -0.25 (0.15), residues: 3181 helix: 1.50 (0.16), residues: 1121 sheet: -0.15 (0.26), residues: 385 loop : -1.39 (0.14), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J1193 HIS 0.005 0.001 HIS H 66 PHE 0.011 0.001 PHE I 389 TYR 0.013 0.001 TYR I 367 ARG 0.014 0.000 ARG H 143 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 1131) hydrogen bonds : angle 3.97869 ( 3118) metal coordination : bond 0.00744 ( 8) metal coordination : angle 2.75249 ( 12) covalent geometry : bond 0.00312 (28567) covalent geometry : angle 0.57210 (39215) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19910.67 seconds wall clock time: 346 minutes 39.19 seconds (20799.19 seconds total)