Starting phenix.real_space_refine on Fri Mar 6 02:37:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uwe_26830/03_2026/7uwe_26830.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uwe_26830/03_2026/7uwe_26830.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7uwe_26830/03_2026/7uwe_26830.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uwe_26830/03_2026/7uwe_26830.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uwe_26830/03_2026/7uwe_26830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uwe_26830/03_2026/7uwe_26830.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 55 5.49 5 Mg 1 5.21 5 S 112 5.16 5 C 16965 2.51 5 N 4844 2.21 5 O 5348 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 138 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27327 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 413 Classifications: {'DNA': 20} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 19} Chain breaks: 1 Chain: "B" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 520 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "R" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 221 Classifications: {'RNA': 10} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 8} Chain: "G" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1698 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} Chain breaks: 1 Chain: "H" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1683 Classifications: {'peptide': 218} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 209} Chain breaks: 1 Chain: "I" Number of atoms: 10407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1319, 10407 Classifications: {'peptide': 1319} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1263} Chain breaks: 1 Chain: "J" Number of atoms: 10352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1330, 10352 Classifications: {'peptide': 1330} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1274} Chain breaks: 3 Chain: "K" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "C" Number of atoms: 1448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1448 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 13, 'TRANS': 175} 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 15391 SG CYS J 70 106.631 75.891 26.167 1.00 58.13 S ATOM 15405 SG CYS J 72 106.235 75.954 22.858 1.00 59.71 S ATOM 21225 SG CYS J 814 108.267 87.899 93.260 1.00 22.17 S ATOM 21790 SG CYS J 888 105.934 87.832 90.203 1.00 15.87 S ATOM 21841 SG CYS J 895 107.042 84.581 91.826 1.00 10.26 S ATOM 21862 SG CYS J 898 104.698 86.683 93.680 1.00 10.05 S Time building chain proxies: 5.63, per 1000 atoms: 0.21 Number of scatterers: 27327 At special positions: 0 Unit cell: (142.284, 165.288, 148.248, 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 112 16.00 P 55 15.00 Mg 1 11.99 O 5348 8.00 N 4844 7.00 C 16965 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 911.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " Number of angles added : 6 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6186 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 50 sheets defined 38.2% alpha, 15.6% beta 11 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 3.03 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 Processing helix chain 'G' and resid 77 through 87 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 154 through 159 removed outlier: 3.979A pdb=" N ARG G 158 " --> pdb=" O PRO G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 228 Processing helix chain 'G' and resid 229 through 231 No H-bonds generated for 'chain 'G' and resid 229 through 231' Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.787A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 88 Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 212 through 226 removed outlier: 3.543A pdb=" N ALA H 225 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 39 Processing helix chain 'I' and resid 48 through 57 removed outlier: 3.518A pdb=" N ALA I 52 " --> pdb=" O GLY I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.640A pdb=" N LEU I 213 " --> pdb=" O ILE I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 219 through 224 removed outlier: 4.268A pdb=" N LEU I 223 " --> pdb=" O GLN I 219 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE I 224 " --> pdb=" O ILE I 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 219 through 224' Processing helix chain 'I' and resid 242 through 247 removed outlier: 4.393A pdb=" N ARG I 247 " --> pdb=" O GLU I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 288 through 293 removed outlier: 4.230A pdb=" N ILE I 292 " --> pdb=" O PRO I 288 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA I 293 " --> pdb=" O VAL I 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 288 through 293' Processing helix chain 'I' and resid 318 through 328 removed outlier: 3.952A pdb=" N SER I 328 " --> pdb=" O LYS I 324 " (cutoff:3.500A) Processing helix chain 'I' and resid 345 through 354 Processing helix chain 'I' and resid 358 through 371 removed outlier: 3.604A pdb=" N ALA I 362 " --> pdb=" O ASP I 358 " (cutoff:3.500A) Processing helix chain 'I' and resid 377 through 387 Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 447 through 449 No H-bonds generated for 'chain 'I' and resid 447 through 449' Processing helix chain 'I' and resid 455 through 480 Processing helix chain 'I' and resid 494 through 508 removed outlier: 4.630A pdb=" N ILE I 498 " --> pdb=" O ASN I 494 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 544 through 549 Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.864A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 607 through 614 removed outlier: 3.901A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR I 614 " --> pdb=" O GLU I 610 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 688 Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 820 through 826 Processing helix chain 'I' and resid 858 through 863 Processing helix chain 'I' and resid 942 through 979 Processing helix chain 'I' and resid 985 through 990 removed outlier: 4.194A pdb=" N ASP I 990 " --> pdb=" O ALA I 986 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1038 removed outlier: 4.145A pdb=" N ASN I1009 " --> pdb=" O GLU I1005 " (cutoff:3.500A) Processing helix chain 'I' and resid 1081 through 1085 Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 4.311A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.936A pdb=" N LEU I1113 " --> pdb=" O ILE I1109 " (cutoff:3.500A) Processing helix chain 'I' and resid 1138 through 1151 Processing helix chain 'I' and resid 1165 through 1176 removed outlier: 3.510A pdb=" N LEU I1172 " --> pdb=" O GLU I1168 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA I1173 " --> pdb=" O VAL I1169 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU I1174 " --> pdb=" O MET I1170 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASN I1175 " --> pdb=" O ARG I1171 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU I1176 " --> pdb=" O LEU I1172 " (cutoff:3.500A) Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1243 Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1284 through 1292 Processing helix chain 'I' and resid 1297 through 1310 Processing helix chain 'I' and resid 1320 through 1333 removed outlier: 3.813A 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 77 through 81 Processing helix chain 'J' and resid 96 through 101 Processing helix chain 'J' and resid 113 through 118 Processing helix chain 'J' and resid 122 through 128 Processing helix chain 'J' and resid 131 through 139 removed outlier: 3.508A pdb=" N ARG J 137 " --> pdb=" O ARG J 133 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU J 139 " --> pdb=" O ILE J 135 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 169 Processing helix chain 'J' and resid 181 through 191 Processing helix chain 'J' and resid 194 through 204 Processing helix chain 'J' and resid 210 through 230 removed outlier: 3.704A pdb=" N LEU J 223 " --> pdb=" O LYS J 219 " (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: 4.497A pdb=" N ASP J 267 " --> pdb=" O SER J 263 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP J 284 " --> pdb=" O LYS J 280 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU J 285 " --> pdb=" O ARG J 281 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 326 through 332 Processing helix chain 'J' and resid 336 through 341 Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 389 Processing helix chain 'J' and resid 393 through 404 removed outlier: 3.893A pdb=" N ALA J 397 " --> pdb=" O THR J 393 " (cutoff:3.500A) Processing helix chain 'J' and resid 405 through 417 removed outlier: 4.353A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG J 417 " --> pdb=" O ASP J 413 " (cutoff:3.500A) 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 589 through 593 removed outlier: 3.557A pdb=" N VAL J 592 " --> pdb=" O TYR J 589 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 613 Processing helix chain 'J' and resid 614 through 636 Processing helix chain 'J' and resid 640 through 644 Processing helix chain 'J' and resid 649 through 671 Processing helix chain 'J' and resid 674 through 702 Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 737 through 742 removed outlier: 3.877A pdb=" N ALA J 741 " --> pdb=" O ILE J 737 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 773 Processing helix chain 'J' and resid 775 through 789 removed outlier: 3.788A pdb=" N ALA J 779 " --> pdb=" O SER J 775 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG J 780 " --> pdb=" O THR J 776 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS J 781 " --> pdb=" O HIS J 777 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA J 787 " --> pdb=" O LEU J 783 " (cutoff:3.500A) Processing helix chain 'J' and resid 789 through 802 Processing helix chain 'J' and resid 834 through 840 removed outlier: 3.535A pdb=" N ARG J 838 " --> pdb=" O PRO J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 915 through 925 Processing helix chain 'J' and resid 1068 through 1074 removed outlier: 3.620A pdb=" N LYS J1072 " --> pdb=" O THR J1068 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASP J1073 " --> pdb=" O ALA J1069 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU J1074 " --> pdb=" O GLY J1070 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 1068 through 1074' Processing helix chain 'J' and resid 1137 through 1147 Processing helix chain 'J' and resid 1216 through 1224 Processing helix chain 'J' and resid 1225 through 1244 Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.370A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 removed outlier: 3.561A pdb=" N GLU J1291 " --> pdb=" O ILE J1287 " (cutoff:3.500A) Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1319 through 1325 Processing helix chain 'J' and resid 1328 through 1339 Processing helix chain 'J' and resid 1347 through 1354 Processing helix chain 'J' and resid 1362 through 1373 removed outlier: 3.562A pdb=" N HIS J1366 " --> pdb=" O GLY J1362 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 17 through 33 removed outlier: 4.150A pdb=" N GLY K 33 " --> pdb=" O GLN K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 57 Processing helix chain 'K' and resid 60 through 74 Processing helix chain 'C' and resid 50 through 65 removed outlier: 3.805A pdb=" N GLU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU C 60 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU C 63 " --> pdb=" O GLU C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 97 removed outlier: 7.062A pdb=" N ILE C 83 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 9.209A pdb=" N LEU C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N HIS C 85 " --> pdb=" O LEU C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 128 Processing helix chain 'C' and resid 129 through 154 removed outlier: 3.543A pdb=" N VAL C 153 " --> pdb=" O ALA C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 157 No H-bonds generated for 'chain 'C' and resid 155 through 157' Processing helix chain 'C' and resid 158 through 163 removed outlier: 3.510A pdb=" N HIS C 162 " --> pdb=" O GLY C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 178 Processing helix chain 'C' and resid 187 through 194 Processing sheet with id=AA1, first strand: chain 'G' and resid 12 through 17 removed outlier: 5.720A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) removed outlier: 3.628A 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 removed outlier: 3.655A pdb=" N VAL G 153 " --> pdb=" O ALA G 175 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 97 through 104 removed outlier: 6.352A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 90 through 91 Processing sheet with id=AA5, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.587A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 12 through 18 removed outlier: 5.690A pdb=" N LEU H 13 " --> pdb=" O GLU H 29 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N GLU H 29 " --> pdb=" O LEU H 13 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASP H 15 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR H 27 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 6.631A 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 101 removed outlier: 4.012A pdb=" N VAL H 98 " --> pdb=" O VAL H 146 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 7.314A 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 removed outlier: 3.524A pdb=" N ARG H 91 " --> pdb=" O GLU H 122 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU H 122 " --> pdb=" O ARG H 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AB1, first strand: chain 'H' and resid 108 through 111 Processing sheet with id=AB2, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB3, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.812A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 59 through 60 removed outlier: 4.683A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET I 124 " --> pdb=" O LEU I 96 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN I 120 " --> pdb=" O LEU I 100 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 136 through 137 removed outlier: 3.532A pdb=" N VAL I 144 " --> pdb=" O GLN I 513 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN I 513 " --> pdb=" O VAL I 144 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 451 through 453 removed outlier: 6.241A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 154 through 158 removed outlier: 3.671A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 180 through 181 Processing sheet with id=AB9, first strand: chain 'I' and resid 284 through 285 removed outlier: 3.526A pdb=" N ILE I 285 " --> pdb=" O MET I 239 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ILE I 229 " --> pdb=" O GLU I 240 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 249 through 250 removed outlier: 4.317A pdb=" N GLU I 249 " --> pdb=" O ILE I 269 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.869A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 296 through 297 removed outlier: 3.715A pdb=" N MET I 315 " --> pdb=" O VAL I 297 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 580 through 581 removed outlier: 6.928A pdb=" N LEU I 587 " --> pdb=" O LEU I 606 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU I 606 " --> pdb=" O LEU I 587 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N THR I 589 " --> pdb=" O HIS I 604 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N HIS I 604 " --> pdb=" O THR I 589 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR I 591 " --> pdb=" O GLU I 602 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLU I 602 " --> pdb=" O TYR I 591 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS I 593 " --> pdb=" O THR I 600 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 580 through 581 removed outlier: 3.610A pdb=" N ASP I 654 " --> pdb=" O ALA I 617 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 634 through 637 removed outlier: 3.593A pdb=" N VAL I 634 " --> pdb=" O PHE I 645 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 717 through 718 removed outlier: 3.800A pdb=" N ASP I 781 " --> pdb=" O ALA I 718 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 749 through 752 removed outlier: 3.540A pdb=" N TYR I 726 " --> pdb=" O VAL I 733 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AD1, first strand: chain 'I' and resid 768 through 769 Processing sheet with id=AD2, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AD3, first strand: chain 'I' and resid 1066 through 1067 removed outlier: 4.544A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 9.519A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 1066 through 1067 Processing sheet with id=AD5, first strand: chain 'I' and resid 846 through 847 removed outlier: 3.830A pdb=" N GLY I 846 " --> pdb=" O THR I 843 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR I 843 " --> pdb=" O GLY I 846 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR I 830 " --> pdb=" O LYS I1057 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LYS I1057 " --> pdb=" O THR I 830 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N HIS I 832 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA I1055 " --> pdb=" O HIS I 832 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLN I 834 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N TYR I1053 " --> pdb=" O GLN I 834 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU I 836 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LYS I1051 " --> pdb=" O LEU I 836 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N CYS I 838 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ILE I1049 " --> pdb=" O CYS I 838 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N SER I 840 " --> pdb=" O LEU I1047 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 882 through 884 removed outlier: 7.135A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 887 through 888 Processing sheet with id=AD8, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 3.555A pdb=" N SER J 353 " --> pdb=" O MET J 466 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AE1, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AE2, first strand: chain 'I' and resid 1335 through 1338 Processing sheet with id=AE3, first strand: chain 'J' and resid 34 through 37 removed outlier: 5.011A pdb=" N SER J 34 " --> pdb=" O MET J 102 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N HIS J 104 " --> pdb=" O SER J 34 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLY J 36 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N GLU J 106 " --> pdb=" O GLY J 36 " (cutoff:3.500A) removed outlier: 10.604A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.960A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 526 through 527 removed outlier: 3.562A pdb=" N LEU J 527 " --> pdb=" O LYS J 549 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG J 551 " --> pdb=" O LEU J 527 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR J 572 " --> pdb=" O VAL J 548 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL J 550 " --> pdb=" O LYS J 570 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS J 570 " --> pdb=" O VAL J 550 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE J 552 " --> pdb=" O SER J 568 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER J 568 " --> pdb=" O ILE J 552 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AE6, first strand: chain 'J' and resid 820 through 822 removed outlier: 3.541A pdb=" N VAL J 880 " --> pdb=" O MET J 822 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 949 through 950 removed outlier: 3.981A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 957 through 961 removed outlier: 4.356A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 965 through 967 Processing sheet with id=AF1, first strand: chain 'J' and resid 1098 through 1100 removed outlier: 3.501A pdb=" N GLY J1033 " --> pdb=" O ILE J1115 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 1046 through 1049 removed outlier: 3.900A pdb=" N GLN J1049 " --> pdb=" O SER J1058 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 1187 through 1190 removed outlier: 3.510A pdb=" N LEU J1175 " --> pdb=" O GLU J1188 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL J1204 " --> pdb=" O GLY J1161 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 6.871A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 67 through 73 removed outlier: 6.416A pdb=" N ALA C 13 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ASP C 108 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL C 15 " --> pdb=" O ASP C 108 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL C 105 " --> pdb=" O MET C 120 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N VAL C 122 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ILE C 107 " --> pdb=" O VAL C 122 " (cutoff:3.500A) 1051 hydrogen bonds defined for protein. 2952 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 6.24 Time building geometry restraints manager: 3.04 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: 9033 1.34 - 1.46: 4380 1.46 - 1.58: 14140 1.58 - 1.70: 107 1.70 - 1.82: 195 Bond restraints: 27855 Sorted by residual: bond pdb=" C GLY C 21 " pdb=" N PRO C 22 " ideal model delta sigma weight residual 1.332 1.391 -0.059 1.33e-02 5.65e+03 2.00e+01 bond pdb=" O3' DC A 4 " pdb=" P DT A 5 " ideal model delta sigma weight residual 1.607 1.658 -0.051 1.50e-02 4.44e+03 1.15e+01 bond pdb=" CA THR I 635 " pdb=" C THR I 635 " ideal model delta sigma weight residual 1.524 1.566 -0.042 1.26e-02 6.30e+03 1.13e+01 bond pdb=" CA ARG J 731 " pdb=" C ARG J 731 " ideal model delta sigma weight residual 1.519 1.555 -0.036 1.14e-02 7.69e+03 9.77e+00 bond pdb=" C ILE I1109 " pdb=" N GLY I1110 " ideal model delta sigma weight residual 1.334 1.372 -0.038 1.27e-02 6.20e+03 8.74e+00 ... (remaining 27850 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 36705 1.97 - 3.93: 1007 3.93 - 5.90: 120 5.90 - 7.87: 24 7.87 - 9.83: 7 Bond angle restraints: 37863 Sorted by residual: angle pdb=" N ARG J 156 " pdb=" CA ARG J 156 " pdb=" C ARG J 156 " ideal model delta sigma weight residual 111.07 118.98 -7.91 1.07e+00 8.73e-01 5.46e+01 angle pdb=" N LYS J1170 " pdb=" CA LYS J1170 " pdb=" C LYS J1170 " ideal model delta sigma weight residual 111.24 102.74 8.50 1.29e+00 6.01e-01 4.34e+01 angle pdb=" C ALA J 328 " pdb=" N ASP J 329 " pdb=" CA ASP J 329 " ideal model delta sigma weight residual 120.38 128.72 -8.34 1.37e+00 5.33e-01 3.71e+01 angle pdb=" N THR J1169 " pdb=" CA THR J1169 " pdb=" C THR J1169 " ideal model delta sigma weight residual 112.58 119.64 -7.06 1.22e+00 6.72e-01 3.35e+01 angle pdb=" C ARG J 322 " pdb=" N PRO J 323 " pdb=" CA PRO J 323 " ideal model delta sigma weight residual 119.76 125.64 -5.88 1.03e+00 9.43e-01 3.26e+01 ... (remaining 37858 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 15472 17.89 - 35.78: 1130 35.78 - 53.67: 327 53.67 - 71.56: 81 71.56 - 89.45: 15 Dihedral angle restraints: 17025 sinusoidal: 7412 harmonic: 9613 Sorted by residual: dihedral pdb=" CA GLU I1137 " pdb=" C GLU I1137 " pdb=" N VAL I1138 " pdb=" CA VAL I1138 " ideal model delta harmonic sigma weight residual -180.00 -151.25 -28.75 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA ALA C 26 " pdb=" C ALA C 26 " pdb=" N VAL C 27 " pdb=" CA VAL C 27 " ideal model delta harmonic sigma weight residual 180.00 152.86 27.14 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA LEU C 81 " pdb=" C LEU C 81 " pdb=" N ASN C 82 " pdb=" CA ASN C 82 " ideal model delta harmonic sigma weight residual -180.00 -158.85 -21.15 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 17022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 3934 0.084 - 0.168: 368 0.168 - 0.252: 19 0.252 - 0.336: 4 0.336 - 0.420: 2 Chirality restraints: 4327 Sorted by residual: chirality pdb=" CA ILE J1248 " pdb=" N ILE J1248 " pdb=" C ILE J1248 " pdb=" CB ILE J1248 " both_signs ideal model delta sigma weight residual False 2.43 2.85 -0.42 2.00e-01 2.50e+01 4.41e+00 chirality pdb=" CG LEU I 468 " pdb=" CB LEU I 468 " pdb=" CD1 LEU I 468 " pdb=" CD2 LEU I 468 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" CA ASN C 82 " pdb=" N ASN C 82 " pdb=" C ASN C 82 " pdb=" CB ASN C 82 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.79e+00 ... (remaining 4324 not shown) Planarity restraints: 4761 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP J 751 " 0.026 2.00e-02 2.50e+03 5.14e-02 2.64e+01 pdb=" C ASP J 751 " -0.089 2.00e-02 2.50e+03 pdb=" O ASP J 751 " 0.033 2.00e-02 2.50e+03 pdb=" N GLY J 752 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 19 " -0.022 2.00e-02 2.50e+03 4.67e-02 2.18e+01 pdb=" C GLY C 19 " 0.081 2.00e-02 2.50e+03 pdb=" O GLY C 19 " -0.032 2.00e-02 2.50e+03 pdb=" N ARG C 20 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 45 " -0.015 2.00e-02 2.50e+03 3.15e-02 9.92e+00 pdb=" CG ASP C 45 " 0.054 2.00e-02 2.50e+03 pdb=" OD1 ASP C 45 " -0.020 2.00e-02 2.50e+03 pdb=" OD2 ASP C 45 " -0.019 2.00e-02 2.50e+03 ... (remaining 4758 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 365 2.66 - 3.22: 24302 3.22 - 3.78: 39745 3.78 - 4.34: 54244 4.34 - 4.90: 89628 Nonbonded interactions: 208284 Sorted by model distance: nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1501 " model vdw 2.097 2.170 nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1501 " model vdw 2.097 2.170 nonbonded pdb=" OG SER J 119 " pdb=" O PRO J 121 " model vdw 2.201 3.040 nonbonded pdb=" OG SER J 977 " pdb=" OG1 THR J 980 " model vdw 2.208 3.040 nonbonded pdb=" OG SER I 318 " pdb=" OD1 ASP I 320 " model vdw 2.231 3.040 ... (remaining 208279 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 170 through 232)) selection = (chain 'H' and resid 7 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: 2.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 29.360 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 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:7.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 39.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 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 0.059 27861 Z= 0.233 Angle : 0.746 9.832 37869 Z= 0.477 Chirality : 0.048 0.420 4327 Planarity : 0.005 0.092 4761 Dihedral : 14.004 89.445 10839 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.42 % Favored : 95.46 % Rotamer: Outliers : 0.67 % Allowed : 2.43 % Favored : 96.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.14), residues: 3325 helix: 0.96 (0.16), residues: 1156 sheet: -0.07 (0.25), residues: 414 loop : -1.67 (0.13), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 28 TYR 0.024 0.001 TYR C 157 PHE 0.018 0.001 PHE J 35 TRP 0.033 0.002 TRP C 68 HIS 0.011 0.001 HIS C 177 Details of bonding type rmsd covalent geometry : bond 0.00384 (27855) covalent geometry : angle 0.74558 (37863) hydrogen bonds : bond 0.18459 ( 1068) hydrogen bonds : angle 6.88619 ( 3002) metal coordination : bond 0.00483 ( 6) metal coordination : angle 2.73145 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 538 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 208 THR cc_start: 0.5961 (m) cc_final: 0.5154 (t) REVERT: J 932 MET cc_start: 0.6556 (tpt) cc_final: 0.6342 (tpp) REVERT: C 159 PHE cc_start: 0.6096 (m-80) cc_final: 0.5299 (m-10) outliers start: 19 outliers final: 6 residues processed: 552 average time/residue: 0.8089 time to fit residues: 507.9646 Evaluate side-chains 302 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 296 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 849 GLU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 744 ARG Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain C residue 183 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.2980 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 84 ASN ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 330 HIS I 834 GLN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 164 GLN J 320 ASN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN C 177 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.138304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.087832 restraints weight = 58406.470| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 3.10 r_work: 0.3105 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27861 Z= 0.126 Angle : 0.625 9.642 37869 Z= 0.319 Chirality : 0.043 0.203 4327 Planarity : 0.005 0.089 4761 Dihedral : 11.726 73.270 4320 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.15 % Allowed : 11.69 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.14), residues: 3325 helix: 1.20 (0.15), residues: 1184 sheet: -0.03 (0.26), residues: 410 loop : -1.50 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 271 TYR 0.013 0.001 TYR J1365 PHE 0.016 0.001 PHE C 154 TRP 0.009 0.001 TRP J1020 HIS 0.009 0.001 HIS J 651 Details of bonding type rmsd covalent geometry : bond 0.00285 (27855) covalent geometry : angle 0.62362 (37863) hydrogen bonds : bond 0.03838 ( 1068) hydrogen bonds : angle 4.83918 ( 3002) metal coordination : bond 0.00421 ( 6) metal coordination : angle 2.85100 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 338 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 102 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8095 (tm) REVERT: H 117 HIS cc_start: 0.7982 (p-80) cc_final: 0.7696 (p-80) REVERT: H 181 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8045 (mp0) REVERT: H 228 LEU cc_start: 0.9685 (OUTLIER) cc_final: 0.9345 (pp) REVERT: I 6 THR cc_start: 0.8141 (p) cc_final: 0.7906 (t) REVERT: I 7 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7746 (tm-30) REVERT: I 202 ARG cc_start: 0.7873 (ptt180) cc_final: 0.7224 (ptt-90) REVERT: I 337 PHE cc_start: 0.7741 (t80) cc_final: 0.7116 (t80) REVERT: I 635 THR cc_start: 0.7616 (p) cc_final: 0.7411 (p) REVERT: I 951 MET cc_start: 0.8696 (mmm) cc_final: 0.8374 (mmt) REVERT: I 952 GLN cc_start: 0.8772 (tp-100) cc_final: 0.8557 (tp-100) REVERT: I 1232 MET cc_start: 0.9178 (mmm) cc_final: 0.8927 (mmm) REVERT: J 133 ARG cc_start: 0.8800 (tpm-80) cc_final: 0.8567 (tpm-80) REVERT: J 151 MET cc_start: 0.7516 (tpp) cc_final: 0.7166 (tpp) REVERT: J 289 ASP cc_start: 0.8230 (m-30) cc_final: 0.7840 (p0) REVERT: J 298 MET cc_start: 0.8342 (ptm) cc_final: 0.8133 (ppp) REVERT: J 932 MET cc_start: 0.8381 (tpt) cc_final: 0.7756 (tpp) REVERT: J 1189 MET cc_start: 0.4163 (tpt) cc_final: 0.3646 (tpt) REVERT: K 54 ILE cc_start: 0.9495 (OUTLIER) cc_final: 0.9252 (mp) REVERT: K 69 ARG cc_start: 0.8760 (ttp80) cc_final: 0.8302 (mtm110) REVERT: K 70 GLN cc_start: 0.8524 (tm-30) cc_final: 0.8296 (tm-30) REVERT: C 68 TRP cc_start: 0.8887 (p-90) cc_final: 0.8441 (p90) REVERT: C 147 MET cc_start: 0.9021 (tpp) cc_final: 0.8710 (tpp) REVERT: C 154 PHE cc_start: 0.9032 (m-80) cc_final: 0.8365 (m-80) REVERT: C 159 PHE cc_start: 0.8893 (m-80) cc_final: 0.7999 (m-80) outliers start: 61 outliers final: 24 residues processed: 371 average time/residue: 0.6857 time to fit residues: 295.0430 Evaluate side-chains 310 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 283 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 398 SER Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 873 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 134 ASP Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 153 ASN Chi-restraints excluded: chain J residue 213 LYS Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain C residue 58 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 99 optimal weight: 2.9990 chunk 184 optimal weight: 0.0980 chunk 230 optimal weight: 0.8980 chunk 74 optimal weight: 20.0000 chunk 318 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 240 optimal weight: 0.7980 chunk 219 optimal weight: 0.9990 chunk 185 optimal weight: 7.9990 chunk 136 optimal weight: 9.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 127 GLN G 132 HIS I 86 GLN I 622 ASN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 200 GLN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1218 HIS C 82 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.136198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.085444 restraints weight = 58446.750| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 3.08 r_work: 0.3061 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27861 Z= 0.117 Angle : 0.593 10.361 37869 Z= 0.302 Chirality : 0.042 0.168 4327 Planarity : 0.004 0.052 4761 Dihedral : 11.506 73.302 4309 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.11 % Allowed : 14.01 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.14), residues: 3325 helix: 1.36 (0.15), residues: 1177 sheet: 0.12 (0.26), residues: 414 loop : -1.43 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 407 TYR 0.012 0.001 TYR J1365 PHE 0.013 0.001 PHE I 514 TRP 0.024 0.001 TRP I 997 HIS 0.008 0.001 HIS J 651 Details of bonding type rmsd covalent geometry : bond 0.00266 (27855) covalent geometry : angle 0.59263 (37863) hydrogen bonds : bond 0.03537 ( 1068) hydrogen bonds : angle 4.46866 ( 3002) metal coordination : bond 0.00410 ( 6) metal coordination : angle 2.28639 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 319 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 197 ASP cc_start: 0.7062 (OUTLIER) cc_final: 0.6625 (m-30) REVERT: H 95 LYS cc_start: 0.7414 (tptp) cc_final: 0.6872 (mtmt) REVERT: H 102 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8060 (tm) REVERT: H 117 HIS cc_start: 0.8036 (p-80) cc_final: 0.7723 (p-80) REVERT: H 158 ARG cc_start: 0.6856 (OUTLIER) cc_final: 0.5986 (mpp80) REVERT: H 228 LEU cc_start: 0.9685 (OUTLIER) cc_final: 0.9350 (pp) REVERT: I 7 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7727 (tm-30) REVERT: I 59 ILE cc_start: 0.8849 (pp) cc_final: 0.7824 (pp) REVERT: I 191 LYS cc_start: 0.9418 (mmmt) cc_final: 0.8730 (tmmt) REVERT: I 200 ARG cc_start: 0.7630 (mtm180) cc_final: 0.7386 (mtm180) REVERT: I 337 PHE cc_start: 0.7903 (t80) cc_final: 0.6905 (t80) REVERT: I 504 GLU cc_start: 0.8912 (tt0) cc_final: 0.8594 (pp20) REVERT: I 516 ASP cc_start: 0.8252 (p0) cc_final: 0.8020 (p0) REVERT: I 542 ARG cc_start: 0.6836 (ttt180) cc_final: 0.6142 (ttt180) REVERT: I 635 THR cc_start: 0.7933 (p) cc_final: 0.7719 (p) REVERT: I 952 GLN cc_start: 0.8793 (tp-100) cc_final: 0.8540 (tp-100) REVERT: I 1304 MET cc_start: 0.9202 (OUTLIER) cc_final: 0.7996 (tpt) REVERT: J 151 MET cc_start: 0.8249 (tpp) cc_final: 0.7976 (tpp) REVERT: J 152 THR cc_start: 0.8965 (OUTLIER) cc_final: 0.8654 (p) REVERT: J 204 GLU cc_start: 0.9467 (OUTLIER) cc_final: 0.9113 (mm-30) REVERT: J 289 ASP cc_start: 0.8175 (m-30) cc_final: 0.7926 (p0) REVERT: J 591 ILE cc_start: 0.7841 (tp) cc_final: 0.7560 (tp) REVERT: J 599 LYS cc_start: 0.7155 (pmtt) cc_final: 0.6711 (ptpp) REVERT: J 932 MET cc_start: 0.8511 (tpt) cc_final: 0.7740 (tpp) REVERT: J 1040 MET cc_start: 0.7522 (OUTLIER) cc_final: 0.7115 (ppp) REVERT: J 1189 MET cc_start: 0.4007 (tpt) cc_final: 0.3503 (tpt) REVERT: K 70 GLN cc_start: 0.8667 (tm-30) cc_final: 0.8383 (tm-30) REVERT: C 68 TRP cc_start: 0.8963 (p-90) cc_final: 0.8441 (p90) REVERT: C 114 LYS cc_start: 0.8267 (pmtt) cc_final: 0.8016 (pmtt) REVERT: C 137 ILE cc_start: 0.9016 (pp) cc_final: 0.8643 (pp) REVERT: C 147 MET cc_start: 0.9055 (tpp) cc_final: 0.8677 (tpp) REVERT: C 154 PHE cc_start: 0.9038 (m-80) cc_final: 0.8512 (m-80) REVERT: C 159 PHE cc_start: 0.8857 (m-80) cc_final: 0.8109 (m-80) REVERT: C 161 GLN cc_start: 0.8536 (pp30) cc_final: 0.8314 (pp30) REVERT: C 173 LYS cc_start: 0.9775 (mmtm) cc_final: 0.9519 (tppp) outliers start: 60 outliers final: 24 residues processed: 355 average time/residue: 0.7142 time to fit residues: 292.1525 Evaluate side-chains 303 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 271 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 158 ARG Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 398 SER Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1304 MET Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 152 THR Chi-restraints excluded: chain J residue 204 GLU Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 1040 MET Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain C residue 58 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 62 optimal weight: 5.9990 chunk 213 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 250 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 179 optimal weight: 8.9990 chunk 215 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 120 GLN I 150 HIS I 622 ASN I1299 ASN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 465 GLN ** J 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 792 ASN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.127331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.074468 restraints weight = 57043.135| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 3.01 r_work: 0.2851 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 27861 Z= 0.211 Angle : 0.696 12.941 37869 Z= 0.359 Chirality : 0.045 0.181 4327 Planarity : 0.005 0.068 4761 Dihedral : 11.667 73.333 4309 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.89 % Allowed : 15.77 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.14), residues: 3325 helix: 1.10 (0.15), residues: 1176 sheet: 0.02 (0.24), residues: 447 loop : -1.47 (0.14), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 133 TYR 0.021 0.002 TYR J 46 PHE 0.028 0.002 PHE I 972 TRP 0.028 0.002 TRP I 997 HIS 0.012 0.002 HIS C 162 Details of bonding type rmsd covalent geometry : bond 0.00498 (27855) covalent geometry : angle 0.69540 (37863) hydrogen bonds : bond 0.05278 ( 1068) hydrogen bonds : angle 4.62987 ( 3002) metal coordination : bond 0.00840 ( 6) metal coordination : angle 2.14202 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 302 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 145 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8554 (tptm) REVERT: H 13 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7982 (tt) REVERT: H 28 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8701 (tt) REVERT: H 95 LYS cc_start: 0.7864 (tptp) cc_final: 0.7588 (mtmt) REVERT: H 102 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7869 (tm) REVERT: H 117 HIS cc_start: 0.8157 (p-80) cc_final: 0.7939 (p-80) REVERT: H 144 ILE cc_start: 0.9486 (mt) cc_final: 0.9253 (pp) REVERT: H 158 ARG cc_start: 0.7540 (OUTLIER) cc_final: 0.6694 (mpp80) REVERT: H 212 ASP cc_start: 0.7905 (t0) cc_final: 0.7688 (t0) REVERT: H 228 LEU cc_start: 0.9672 (OUTLIER) cc_final: 0.9355 (pp) REVERT: I 200 ARG cc_start: 0.7706 (mtm180) cc_final: 0.7480 (mtp-110) REVERT: I 337 PHE cc_start: 0.8115 (t80) cc_final: 0.7554 (t80) REVERT: I 370 MET cc_start: 0.8978 (mmm) cc_final: 0.8371 (pp-130) REVERT: I 371 ARG cc_start: 0.9241 (ttm-80) cc_final: 0.8518 (ttm-80) REVERT: I 542 ARG cc_start: 0.6936 (ttt180) cc_final: 0.6237 (ttt180) REVERT: I 951 MET cc_start: 0.9162 (tpp) cc_final: 0.8933 (ttp) REVERT: I 952 GLN cc_start: 0.8918 (tp-100) cc_final: 0.8640 (tp-100) REVERT: I 1304 MET cc_start: 0.9413 (OUTLIER) cc_final: 0.8193 (tpt) REVERT: J 100 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8450 (mp0) REVERT: J 134 ASP cc_start: 0.9485 (m-30) cc_final: 0.9171 (p0) REVERT: J 204 GLU cc_start: 0.9273 (OUTLIER) cc_final: 0.9024 (mm-30) REVERT: J 289 ASP cc_start: 0.8462 (m-30) cc_final: 0.7988 (p0) REVERT: J 591 ILE cc_start: 0.9334 (tp) cc_final: 0.8975 (tp) REVERT: J 932 MET cc_start: 0.8895 (tpt) cc_final: 0.7924 (tpp) REVERT: J 1189 MET cc_start: 0.4526 (tpt) cc_final: 0.3930 (tpp) REVERT: K 15 ASN cc_start: 0.8599 (t0) cc_final: 0.7811 (t160) REVERT: K 70 GLN cc_start: 0.8638 (tm-30) cc_final: 0.8343 (tm-30) REVERT: C 147 MET cc_start: 0.9028 (tpp) cc_final: 0.8638 (tpp) REVERT: C 154 PHE cc_start: 0.9005 (m-80) cc_final: 0.8502 (m-80) REVERT: C 159 PHE cc_start: 0.8944 (m-80) cc_final: 0.8138 (m-80) outliers start: 82 outliers final: 27 residues processed: 358 average time/residue: 0.7238 time to fit residues: 299.1664 Evaluate side-chains 268 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 233 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 145 LYS Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 158 ARG Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 86 GLN Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 873 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain I residue 1304 MET Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 153 ASN Chi-restraints excluded: chain J residue 204 GLU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 58 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 254 optimal weight: 1.9990 chunk 221 optimal weight: 0.8980 chunk 152 optimal weight: 0.9980 chunk 292 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 298 optimal weight: 0.9990 chunk 206 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 chunk 286 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 117 HIS I 622 ASN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 465 GLN ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.129526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.078134 restraints weight = 56730.479| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.96 r_work: 0.2938 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27861 Z= 0.114 Angle : 0.601 12.252 37869 Z= 0.304 Chirality : 0.042 0.227 4327 Planarity : 0.004 0.059 4761 Dihedral : 11.390 74.443 4309 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.08 % Allowed : 18.44 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.14), residues: 3325 helix: 1.35 (0.16), residues: 1165 sheet: 0.17 (0.26), residues: 423 loop : -1.41 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 473 TYR 0.014 0.001 TYR G 177 PHE 0.011 0.001 PHE I 224 TRP 0.034 0.001 TRP I 997 HIS 0.006 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00258 (27855) covalent geometry : angle 0.60038 (37863) hydrogen bonds : bond 0.03575 ( 1068) hydrogen bonds : angle 4.34132 ( 3002) metal coordination : bond 0.00330 ( 6) metal coordination : angle 1.84563 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 276 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 145 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8312 (tptm) REVERT: G 168 ILE cc_start: 0.8103 (pt) cc_final: 0.7778 (mt) REVERT: H 95 LYS cc_start: 0.8003 (tptp) cc_final: 0.7722 (mtmt) REVERT: H 144 ILE cc_start: 0.9504 (mt) cc_final: 0.9293 (pp) REVERT: H 158 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.6872 (mpp80) REVERT: I 191 LYS cc_start: 0.9540 (mmmt) cc_final: 0.8888 (tmmt) REVERT: I 200 ARG cc_start: 0.7755 (mtm180) cc_final: 0.7505 (mtp-110) REVERT: I 202 ARG cc_start: 0.7846 (pmt170) cc_final: 0.7639 (pmt170) REVERT: I 337 PHE cc_start: 0.8174 (t80) cc_final: 0.7370 (t80) REVERT: I 429 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8674 (mtm) REVERT: I 542 ARG cc_start: 0.6940 (ttt180) cc_final: 0.6208 (ttt180) REVERT: I 741 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7452 (ptp) REVERT: I 742 TYR cc_start: 0.7182 (OUTLIER) cc_final: 0.6942 (p90) REVERT: I 951 MET cc_start: 0.9164 (tpp) cc_final: 0.8947 (ttp) REVERT: I 952 GLN cc_start: 0.8942 (tp-100) cc_final: 0.8648 (tp-100) REVERT: I 1304 MET cc_start: 0.9427 (OUTLIER) cc_final: 0.8147 (tpt) REVERT: J 100 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8378 (mp0) REVERT: J 134 ASP cc_start: 0.9465 (m-30) cc_final: 0.9206 (p0) REVERT: J 151 MET cc_start: 0.7930 (tpp) cc_final: 0.7589 (tpp) REVERT: J 204 GLU cc_start: 0.9185 (OUTLIER) cc_final: 0.8901 (mm-30) REVERT: J 289 ASP cc_start: 0.8493 (m-30) cc_final: 0.8052 (p0) REVERT: J 591 ILE cc_start: 0.9302 (tp) cc_final: 0.9076 (tp) REVERT: J 932 MET cc_start: 0.8927 (tpt) cc_final: 0.8054 (tpp) REVERT: K 56 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7623 (mp0) REVERT: K 62 GLN cc_start: 0.8172 (pm20) cc_final: 0.7785 (pm20) REVERT: C 154 PHE cc_start: 0.9087 (m-80) cc_final: 0.8642 (m-80) REVERT: C 159 PHE cc_start: 0.8895 (m-80) cc_final: 0.8292 (m-80) REVERT: C 187 PHE cc_start: 0.9113 (m-80) cc_final: 0.8807 (m-80) outliers start: 59 outliers final: 21 residues processed: 320 average time/residue: 0.7230 time to fit residues: 267.7114 Evaluate side-chains 270 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 241 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 145 LYS Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 158 ARG Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 429 MET Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 741 MET Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 1042 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain I residue 1304 MET Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 204 GLU Chi-restraints excluded: chain J residue 394 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 58 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 280 optimal weight: 0.3980 chunk 170 optimal weight: 0.8980 chunk 74 optimal weight: 20.0000 chunk 296 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 273 optimal weight: 9.9990 chunk 209 optimal weight: 3.9990 chunk 259 optimal weight: 7.9990 chunk 187 optimal weight: 10.0000 chunk 333 optimal weight: 1.9990 chunk 318 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 622 ASN I1129 ASN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1259 GLN ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.127642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.075895 restraints weight = 56793.499| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.94 r_work: 0.2893 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.4924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27861 Z= 0.138 Angle : 0.622 12.104 37869 Z= 0.315 Chirality : 0.043 0.167 4327 Planarity : 0.004 0.070 4761 Dihedral : 11.303 76.275 4309 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.29 % Allowed : 19.15 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.14), residues: 3325 helix: 1.33 (0.16), residues: 1170 sheet: 0.27 (0.25), residues: 431 loop : -1.38 (0.14), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG I 371 TYR 0.013 0.001 TYR G 177 PHE 0.016 0.001 PHE I 514 TRP 0.018 0.001 TRP J1020 HIS 0.006 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00323 (27855) covalent geometry : angle 0.62212 (37863) hydrogen bonds : bond 0.04006 ( 1068) hydrogen bonds : angle 4.33410 ( 3002) metal coordination : bond 0.00468 ( 6) metal coordination : angle 1.63649 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 257 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 33 ARG cc_start: 0.7691 (mmp80) cc_final: 0.7485 (mmp-170) REVERT: G 145 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8299 (tptm) REVERT: G 168 ILE cc_start: 0.8151 (pt) cc_final: 0.7800 (mt) REVERT: H 28 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8773 (tt) REVERT: H 95 LYS cc_start: 0.8116 (tptp) cc_final: 0.7914 (mtmt) REVERT: H 117 HIS cc_start: 0.8066 (p-80) cc_final: 0.7840 (p-80) REVERT: H 137 ASN cc_start: 0.9445 (p0) cc_final: 0.9178 (p0) REVERT: H 158 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7136 (mpp80) REVERT: I 191 LYS cc_start: 0.9534 (mmmt) cc_final: 0.8801 (tmmt) REVERT: I 200 ARG cc_start: 0.7805 (mtm180) cc_final: 0.7443 (mtm180) REVERT: I 337 PHE cc_start: 0.8172 (t80) cc_final: 0.7465 (t80) REVERT: I 340 ASP cc_start: 0.8742 (m-30) cc_final: 0.8535 (p0) REVERT: I 542 ARG cc_start: 0.6935 (ttt180) cc_final: 0.6132 (ttt180) REVERT: I 741 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.7570 (ptp) REVERT: I 742 TYR cc_start: 0.7560 (OUTLIER) cc_final: 0.7262 (p90) REVERT: I 952 GLN cc_start: 0.8954 (tp-100) cc_final: 0.8661 (tp-100) REVERT: I 1304 MET cc_start: 0.9452 (OUTLIER) cc_final: 0.8307 (tpt) REVERT: J 100 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8428 (mp0) REVERT: J 134 ASP cc_start: 0.9456 (m-30) cc_final: 0.9186 (p0) REVERT: J 151 MET cc_start: 0.7996 (tpp) cc_final: 0.7630 (tpp) REVERT: J 204 GLU cc_start: 0.9147 (OUTLIER) cc_final: 0.8880 (mm-30) REVERT: J 289 ASP cc_start: 0.8612 (m-30) cc_final: 0.8135 (p0) REVERT: J 932 MET cc_start: 0.8907 (tpt) cc_final: 0.8054 (tpp) REVERT: J 990 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8378 (pmm-80) REVERT: J 1040 MET cc_start: 0.7234 (ppp) cc_final: 0.6315 (ppp) REVERT: J 1189 MET cc_start: 0.4039 (tpp) cc_final: 0.3472 (tpp) REVERT: J 1278 GLU cc_start: 0.8481 (tt0) cc_final: 0.8124 (pt0) REVERT: J 1334 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8252 (mp0) REVERT: K 35 LYS cc_start: 0.8794 (mmmt) cc_final: 0.8584 (mmmm) REVERT: K 41 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8302 (tm-30) REVERT: K 56 GLU cc_start: 0.8068 (mp0) cc_final: 0.7580 (mp0) REVERT: K 67 ARG cc_start: 0.8830 (mmm160) cc_final: 0.8548 (tpp80) REVERT: C 154 PHE cc_start: 0.9111 (m-80) cc_final: 0.8675 (m-80) REVERT: C 159 PHE cc_start: 0.8860 (m-80) cc_final: 0.8511 (m-80) REVERT: C 187 PHE cc_start: 0.9093 (m-80) cc_final: 0.8771 (m-80) outliers start: 65 outliers final: 29 residues processed: 310 average time/residue: 0.6785 time to fit residues: 244.5784 Evaluate side-chains 280 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 242 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 145 LYS Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 158 ARG Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 741 MET Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain I residue 1304 MET Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 153 ASN Chi-restraints excluded: chain J residue 204 GLU Chi-restraints excluded: chain J residue 356 THR Chi-restraints excluded: chain J residue 394 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain J residue 990 ARG Chi-restraints excluded: chain J residue 1072 LYS Chi-restraints excluded: chain J residue 1177 ILE Chi-restraints excluded: chain J residue 1334 GLU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 58 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 153 optimal weight: 0.2980 chunk 211 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 328 optimal weight: 50.0000 chunk 35 optimal weight: 5.9990 chunk 272 optimal weight: 10.0000 chunk 297 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 97 optimal weight: 0.8980 chunk 332 optimal weight: 9.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 622 ASN I 628 HIS ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 465 GLN J1126 GLN K 31 GLN ** C 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.125473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.073671 restraints weight = 56576.345| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.89 r_work: 0.2842 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.5401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27861 Z= 0.173 Angle : 0.652 13.299 37869 Z= 0.331 Chirality : 0.044 0.196 4327 Planarity : 0.005 0.066 4761 Dihedral : 11.361 78.704 4309 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.64 % Allowed : 19.68 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.14), residues: 3325 helix: 1.25 (0.15), residues: 1172 sheet: 0.32 (0.26), residues: 406 loop : -1.39 (0.14), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I1033 TYR 0.014 0.001 TYR G 177 PHE 0.018 0.001 PHE I 514 TRP 0.017 0.001 TRP J1020 HIS 0.005 0.001 HIS G 23 Details of bonding type rmsd covalent geometry : bond 0.00413 (27855) covalent geometry : angle 0.65183 (37863) hydrogen bonds : bond 0.04549 ( 1068) hydrogen bonds : angle 4.42368 ( 3002) metal coordination : bond 0.00610 ( 6) metal coordination : angle 1.71171 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 246 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 28 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8930 (tt) REVERT: H 117 HIS cc_start: 0.8100 (p-80) cc_final: 0.7893 (p-80) REVERT: H 137 ASN cc_start: 0.9423 (p0) cc_final: 0.9220 (p0) REVERT: H 158 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7585 (mpp80) REVERT: H 193 GLU cc_start: 0.8303 (mp0) cc_final: 0.8019 (tm-30) REVERT: I 59 ILE cc_start: 0.9151 (pp) cc_final: 0.8909 (pp) REVERT: I 200 ARG cc_start: 0.7814 (mtm180) cc_final: 0.7467 (mtm180) REVERT: I 230 PHE cc_start: 0.6485 (OUTLIER) cc_final: 0.5812 (t80) REVERT: I 337 PHE cc_start: 0.8216 (t80) cc_final: 0.7697 (t80) REVERT: I 340 ASP cc_start: 0.8790 (m-30) cc_final: 0.8559 (p0) REVERT: I 488 MET cc_start: 0.8740 (mmp) cc_final: 0.8429 (tpt) REVERT: I 542 ARG cc_start: 0.7031 (ttt180) cc_final: 0.6214 (ttt180) REVERT: I 742 TYR cc_start: 0.7917 (OUTLIER) cc_final: 0.7641 (p90) REVERT: I 952 GLN cc_start: 0.8922 (tp-100) cc_final: 0.8704 (tp-100) REVERT: I 1304 MET cc_start: 0.9490 (OUTLIER) cc_final: 0.8320 (tpt) REVERT: J 100 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8462 (mp0) REVERT: J 134 ASP cc_start: 0.9500 (m-30) cc_final: 0.9256 (p0) REVERT: J 151 MET cc_start: 0.8318 (tpp) cc_final: 0.7867 (tpp) REVERT: J 156 ARG cc_start: 0.9212 (tpp80) cc_final: 0.8883 (tpp80) REVERT: J 204 GLU cc_start: 0.9120 (OUTLIER) cc_final: 0.8832 (mm-30) REVERT: J 217 LEU cc_start: 0.9466 (pp) cc_final: 0.9258 (pt) REVERT: J 289 ASP cc_start: 0.8706 (m-30) cc_final: 0.8234 (p0) REVERT: J 990 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8718 (pmm-80) REVERT: J 1189 MET cc_start: 0.4713 (tpp) cc_final: 0.4479 (mmm) REVERT: J 1334 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8235 (mp0) REVERT: J 1343 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7800 (mm-30) REVERT: K 42 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8160 (mp0) REVERT: K 56 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7751 (mp0) REVERT: K 73 GLN cc_start: 0.8145 (pp30) cc_final: 0.7899 (pp30) REVERT: C 154 PHE cc_start: 0.9156 (m-80) cc_final: 0.8772 (m-80) REVERT: C 159 PHE cc_start: 0.9298 (m-80) cc_final: 0.8420 (m-80) REVERT: C 187 PHE cc_start: 0.9095 (m-80) cc_final: 0.8767 (m-80) outliers start: 75 outliers final: 34 residues processed: 308 average time/residue: 0.7089 time to fit residues: 252.1393 Evaluate side-chains 270 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 227 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain H residue 25 LYS Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 158 ARG Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 230 PHE Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 1042 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain I residue 1304 MET Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 204 GLU Chi-restraints excluded: chain J residue 356 THR Chi-restraints excluded: chain J residue 394 ILE Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 990 ARG Chi-restraints excluded: chain J residue 1334 GLU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 58 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 19 optimal weight: 0.7980 chunk 192 optimal weight: 30.0000 chunk 50 optimal weight: 2.9990 chunk 299 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 190 optimal weight: 0.0010 chunk 118 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 254 optimal weight: 0.8980 chunk 140 optimal weight: 7.9990 chunk 263 optimal weight: 6.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 273 HIS I 622 ASN I 628 HIS ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 465 GLN J1126 GLN ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.126985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.075745 restraints weight = 56744.419| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.91 r_work: 0.2894 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.5479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 27861 Z= 0.117 Angle : 0.629 12.357 37869 Z= 0.315 Chirality : 0.042 0.218 4327 Planarity : 0.004 0.059 4761 Dihedral : 11.211 80.473 4309 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.94 % Allowed : 21.01 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.14), residues: 3325 helix: 1.40 (0.16), residues: 1163 sheet: 0.39 (0.26), residues: 418 loop : -1.32 (0.14), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG I 371 TYR 0.013 0.001 TYR G 177 PHE 0.013 0.001 PHE I 972 TRP 0.016 0.001 TRP I 997 HIS 0.006 0.001 HIS C 177 Details of bonding type rmsd covalent geometry : bond 0.00271 (27855) covalent geometry : angle 0.62862 (37863) hydrogen bonds : bond 0.03569 ( 1068) hydrogen bonds : angle 4.27517 ( 3002) metal coordination : bond 0.00344 ( 6) metal coordination : angle 1.62945 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 244 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 137 ASN cc_start: 0.9262 (OUTLIER) cc_final: 0.9058 (p0) REVERT: G 168 ILE cc_start: 0.8244 (pt) cc_final: 0.7894 (mt) REVERT: H 117 HIS cc_start: 0.8112 (p-80) cc_final: 0.7892 (p-80) REVERT: H 137 ASN cc_start: 0.9456 (p0) cc_final: 0.9221 (p0) REVERT: H 158 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7693 (mpp80) REVERT: I 59 ILE cc_start: 0.9102 (pp) cc_final: 0.8858 (pp) REVERT: I 191 LYS cc_start: 0.9607 (mmmt) cc_final: 0.9014 (tmtt) REVERT: I 200 ARG cc_start: 0.7785 (mtm180) cc_final: 0.7377 (mtm180) REVERT: I 230 PHE cc_start: 0.6258 (OUTLIER) cc_final: 0.5587 (t80) REVERT: I 337 PHE cc_start: 0.8316 (t80) cc_final: 0.7721 (t80) REVERT: I 340 ASP cc_start: 0.8874 (m-30) cc_final: 0.8598 (p0) REVERT: I 407 ARG cc_start: 0.8856 (ttm-80) cc_final: 0.8580 (mtm110) REVERT: I 429 MET cc_start: 0.9119 (mtm) cc_final: 0.8800 (mtm) REVERT: I 488 MET cc_start: 0.8732 (mmp) cc_final: 0.8493 (tpt) REVERT: I 542 ARG cc_start: 0.7005 (ttt180) cc_final: 0.6169 (ttt180) REVERT: I 952 GLN cc_start: 0.8919 (tp-100) cc_final: 0.8682 (tp-100) REVERT: J 134 ASP cc_start: 0.9523 (m-30) cc_final: 0.9276 (p0) REVERT: J 156 ARG cc_start: 0.9251 (tpp80) cc_final: 0.8953 (tpp80) REVERT: J 204 GLU cc_start: 0.9111 (OUTLIER) cc_final: 0.8836 (mm-30) REVERT: J 289 ASP cc_start: 0.8707 (m-30) cc_final: 0.8290 (p0) REVERT: J 802 ASP cc_start: 0.8749 (t70) cc_final: 0.8420 (t0) REVERT: J 932 MET cc_start: 0.8767 (tpp) cc_final: 0.8536 (tpp) REVERT: J 990 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.8724 (pmm-80) REVERT: J 1189 MET cc_start: 0.4666 (tpp) cc_final: 0.4408 (mmm) REVERT: J 1343 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7718 (mm-30) REVERT: K 56 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7651 (mp0) REVERT: K 67 ARG cc_start: 0.8794 (mmp80) cc_final: 0.8217 (tpp80) REVERT: C 68 TRP cc_start: 0.9069 (p-90) cc_final: 0.8581 (p90) REVERT: C 154 PHE cc_start: 0.9087 (m-80) cc_final: 0.8853 (m-80) REVERT: C 159 PHE cc_start: 0.9197 (m-80) cc_final: 0.8438 (m-80) REVERT: C 187 PHE cc_start: 0.9047 (m-80) cc_final: 0.8724 (m-80) outliers start: 55 outliers final: 32 residues processed: 289 average time/residue: 0.7232 time to fit residues: 241.6900 Evaluate side-chains 265 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 227 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 158 ARG Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 230 PHE Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 1042 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 153 ASN Chi-restraints excluded: chain J residue 204 GLU Chi-restraints excluded: chain J residue 394 ILE Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 990 ARG Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 58 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 237 optimal weight: 1.9990 chunk 195 optimal weight: 4.9990 chunk 139 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 63 optimal weight: 0.6980 chunk 309 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 206 optimal weight: 20.0000 chunk 21 optimal weight: 5.9990 chunk 222 optimal weight: 3.9990 chunk 180 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1126 GLN ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.127432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.075361 restraints weight = 56642.751| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.93 r_work: 0.2893 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.5564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27861 Z= 0.123 Angle : 0.647 13.304 37869 Z= 0.323 Chirality : 0.042 0.228 4327 Planarity : 0.004 0.074 4761 Dihedral : 11.152 81.930 4309 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.61 % Favored : 96.36 % Rotamer: Outliers : 1.76 % Allowed : 21.54 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.14), residues: 3325 helix: 1.40 (0.16), residues: 1161 sheet: 0.42 (0.26), residues: 418 loop : -1.29 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG K 69 TYR 0.013 0.001 TYR G 177 PHE 0.012 0.001 PHE I 195 TRP 0.019 0.001 TRP I 997 HIS 0.006 0.001 HIS C 177 Details of bonding type rmsd covalent geometry : bond 0.00289 (27855) covalent geometry : angle 0.64664 (37863) hydrogen bonds : bond 0.03641 ( 1068) hydrogen bonds : angle 4.27694 ( 3002) metal coordination : bond 0.00389 ( 6) metal coordination : angle 1.60155 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 236 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 137 ASN cc_start: 0.9451 (p0) cc_final: 0.9194 (p0) REVERT: H 158 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7647 (mpp80) REVERT: H 228 LEU cc_start: 0.9647 (OUTLIER) cc_final: 0.9335 (pp) REVERT: I 59 ILE cc_start: 0.9095 (pp) cc_final: 0.8816 (pp) REVERT: I 191 LYS cc_start: 0.9600 (mmmt) cc_final: 0.9003 (tmtt) REVERT: I 200 ARG cc_start: 0.7776 (mtm180) cc_final: 0.7377 (mtm180) REVERT: I 230 PHE cc_start: 0.6319 (OUTLIER) cc_final: 0.5688 (t80) REVERT: I 319 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8300 (mm) REVERT: I 337 PHE cc_start: 0.8315 (t80) cc_final: 0.7751 (t80) REVERT: I 340 ASP cc_start: 0.8845 (m-30) cc_final: 0.8584 (p0) REVERT: I 488 MET cc_start: 0.8736 (mmp) cc_final: 0.8511 (tpt) REVERT: I 542 ARG cc_start: 0.7010 (ttt180) cc_final: 0.6167 (ttt180) REVERT: I 1304 MET cc_start: 0.9459 (OUTLIER) cc_final: 0.8367 (tpt) REVERT: J 134 ASP cc_start: 0.9527 (m-30) cc_final: 0.9252 (p0) REVERT: J 156 ARG cc_start: 0.9246 (tpp80) cc_final: 0.8951 (tpp80) REVERT: J 204 GLU cc_start: 0.9110 (OUTLIER) cc_final: 0.8811 (mm-30) REVERT: J 289 ASP cc_start: 0.8686 (m-30) cc_final: 0.8275 (p0) REVERT: J 802 ASP cc_start: 0.8759 (t70) cc_final: 0.8444 (t0) REVERT: J 990 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8696 (pmm-80) REVERT: J 1189 MET cc_start: 0.4642 (tpp) cc_final: 0.4368 (mmm) REVERT: J 1343 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7660 (mm-30) REVERT: K 42 GLU cc_start: 0.8431 (mm-30) cc_final: 0.7873 (mp0) REVERT: K 55 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8107 (mm-30) REVERT: K 56 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7693 (mp0) REVERT: K 67 ARG cc_start: 0.8757 (mmp80) cc_final: 0.8514 (mmm160) REVERT: C 68 TRP cc_start: 0.9048 (p-90) cc_final: 0.8554 (p90) REVERT: C 151 ASP cc_start: 0.9256 (t70) cc_final: 0.8563 (m-30) REVERT: C 159 PHE cc_start: 0.9230 (m-80) cc_final: 0.8881 (m-80) REVERT: C 187 PHE cc_start: 0.9065 (m-80) cc_final: 0.8732 (m-80) outliers start: 50 outliers final: 30 residues processed: 277 average time/residue: 0.7375 time to fit residues: 236.0132 Evaluate side-chains 267 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 229 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 158 ARG Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 230 PHE Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 1042 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1304 MET Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 204 GLU Chi-restraints excluded: chain J residue 394 ILE Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 990 ARG Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 58 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 279 optimal weight: 40.0000 chunk 78 optimal weight: 0.0870 chunk 174 optimal weight: 4.9990 chunk 217 optimal weight: 4.9990 chunk 212 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 284 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 68 optimal weight: 0.7980 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 489 ASN ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.126922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.075957 restraints weight = 56870.470| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.90 r_work: 0.2894 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.5713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27861 Z= 0.127 Angle : 0.675 19.006 37869 Z= 0.337 Chirality : 0.043 0.272 4327 Planarity : 0.004 0.060 4761 Dihedral : 11.097 84.054 4309 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.46 % Favored : 96.51 % Rotamer: Outliers : 1.48 % Allowed : 21.96 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.14), residues: 3325 helix: 1.40 (0.16), residues: 1162 sheet: 0.40 (0.26), residues: 423 loop : -1.23 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG K 69 TYR 0.014 0.001 TYR C 58 PHE 0.011 0.001 PHE I 514 TRP 0.019 0.001 TRP I 997 HIS 0.006 0.001 HIS C 177 Details of bonding type rmsd covalent geometry : bond 0.00302 (27855) covalent geometry : angle 0.67431 (37863) hydrogen bonds : bond 0.03663 ( 1068) hydrogen bonds : angle 4.31140 ( 3002) metal coordination : bond 0.00391 ( 6) metal coordination : angle 1.60161 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 231 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 137 ASN cc_start: 0.9447 (p0) cc_final: 0.9181 (p0) REVERT: H 158 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7710 (mpp80) REVERT: H 228 LEU cc_start: 0.9673 (OUTLIER) cc_final: 0.9365 (pp) REVERT: I 59 ILE cc_start: 0.9090 (pp) cc_final: 0.8822 (pp) REVERT: I 191 LYS cc_start: 0.9586 (mmmt) cc_final: 0.9040 (tmtt) REVERT: I 200 ARG cc_start: 0.7811 (mtm180) cc_final: 0.7399 (mtm180) REVERT: I 319 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8278 (OUTLIER) REVERT: I 337 PHE cc_start: 0.8328 (t80) cc_final: 0.7833 (t80) REVERT: I 340 ASP cc_start: 0.8843 (m-30) cc_final: 0.8608 (p0) REVERT: I 368 ARG cc_start: 0.9177 (ppp80) cc_final: 0.8872 (tmt-80) REVERT: I 407 ARG cc_start: 0.8855 (ttm-80) cc_final: 0.8604 (mtm110) REVERT: I 542 ARG cc_start: 0.7079 (ttt180) cc_final: 0.6253 (ttt180) REVERT: I 856 ASN cc_start: 0.8651 (m-40) cc_final: 0.8034 (t0) REVERT: I 1304 MET cc_start: 0.9469 (OUTLIER) cc_final: 0.8396 (tpt) REVERT: J 134 ASP cc_start: 0.9514 (m-30) cc_final: 0.9280 (p0) REVERT: J 156 ARG cc_start: 0.9236 (tpp80) cc_final: 0.8957 (tpp80) REVERT: J 204 GLU cc_start: 0.9118 (OUTLIER) cc_final: 0.8780 (mm-30) REVERT: J 289 ASP cc_start: 0.8630 (m-30) cc_final: 0.8247 (p0) REVERT: J 802 ASP cc_start: 0.8733 (t70) cc_final: 0.8425 (t0) REVERT: J 1189 MET cc_start: 0.4603 (tpp) cc_final: 0.4279 (mmm) REVERT: J 1343 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7656 (mm-30) REVERT: K 42 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8158 (mp0) REVERT: K 55 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8122 (mm-30) REVERT: K 56 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7696 (mp0) REVERT: K 67 ARG cc_start: 0.8755 (mmp80) cc_final: 0.8384 (mmm160) REVERT: K 71 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8454 (mm-30) REVERT: C 68 TRP cc_start: 0.9056 (p-90) cc_final: 0.8580 (p90) REVERT: C 187 PHE cc_start: 0.9087 (m-80) cc_final: 0.8738 (m-80) outliers start: 42 outliers final: 35 residues processed: 265 average time/residue: 0.7274 time to fit residues: 223.6237 Evaluate side-chains 264 residues out of total 2841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 224 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 158 ARG Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain I residue 1304 MET Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 204 GLU Chi-restraints excluded: chain J residue 394 ILE Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 990 ARG Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 58 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 130 optimal weight: 0.0980 chunk 312 optimal weight: 6.9990 chunk 216 optimal weight: 0.5980 chunk 99 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 174 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 126 optimal weight: 0.4980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 120 GLN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 465 GLN J 489 ASN ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.125136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.073644 restraints weight = 56371.921| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.88 r_work: 0.2849 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.5917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 27861 Z= 0.158 Angle : 0.688 17.098 37869 Z= 0.347 Chirality : 0.044 0.271 4327 Planarity : 0.005 0.066 4761 Dihedral : 11.146 86.679 4309 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.67 % Favored : 96.30 % Rotamer: Outliers : 1.48 % Allowed : 22.00 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.14), residues: 3325 helix: 1.34 (0.16), residues: 1169 sheet: 0.38 (0.26), residues: 418 loop : -1.25 (0.14), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I1034 TYR 0.013 0.001 TYR C 58 PHE 0.025 0.001 PHE J 35 TRP 0.014 0.001 TRP I 997 HIS 0.006 0.001 HIS C 182 Details of bonding type rmsd covalent geometry : bond 0.00380 (27855) covalent geometry : angle 0.68821 (37863) hydrogen bonds : bond 0.04258 ( 1068) hydrogen bonds : angle 4.36504 ( 3002) metal coordination : bond 0.00568 ( 6) metal coordination : angle 1.57184 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11418.52 seconds wall clock time: 194 minutes 32.08 seconds (11672.08 seconds total)