Starting phenix.real_space_refine on Sun Jul 5 13:28:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pid_17681/07_2026/8pid_17681.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pid_17681/07_2026/8pid_17681.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8pid_17681/07_2026/8pid_17681.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pid_17681/07_2026/8pid_17681.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pid_17681/07_2026/8pid_17681.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pid_17681/07_2026/8pid_17681.map" } resolution = 3.0 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= 0.007 sd= 0.047 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 89 5.49 5 Mg 1 5.21 5 S 112 5.16 5 C 17460 2.51 5 N 5013 2.21 5 O 5620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28297 Number of models: 1 Model: "" Number of chains: 10 Chain: "P" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1294 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 150} Chain: "I" Number of atoms: 10450 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1321, 10423 Classifications: {'peptide': 1321} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1265} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 1321, 10423 Classifications: {'peptide': 1321} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1265} Chain breaks: 1 bond proxies already assigned to first conformer: 10558 Chain: "J" Number of atoms: 10450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1343, 10450 Classifications: {'peptide': 1343} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1287} Chain breaks: 2 Chain: "K" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 655 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "G" Number of atoms: 1807 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 232, 1799 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 222} Conformer: "B" Number of residues, atoms: 232, 1799 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 222} bond proxies already assigned to first conformer: 1812 Chain: "H" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1780 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Chain: "A" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 771 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "B" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 784 Classifications: {'DNA': 38} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 37} Chain: "R" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 303 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 7, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 12} 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 12193 SG CYS J 70 24.334 70.291 85.576 1.00 90.31 S ATOM 12207 SG CYS J 72 23.326 66.614 85.192 1.00 91.52 S ATOM 12315 SG CYS J 85 21.696 68.777 87.827 1.00 90.44 S ATOM 12339 SG CYS J 88 25.403 67.813 88.170 1.00 87.37 S ATOM 18027 SG CYS J 814 56.468 126.456 93.755 1.00 74.29 S ATOM 18592 SG CYS J 888 58.541 123.452 93.071 1.00 72.59 S ATOM 18643 SG CYS J 895 57.575 126.019 90.253 1.00 67.71 S ATOM 18664 SG CYS J 898 60.271 126.753 92.762 1.00 68.41 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE I 156 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE I 156 " occ=0.50 Time building chain proxies: 7.63, per 1000 atoms: 0.27 Number of scatterers: 28297 At special positions: 0 Unit cell: (139.776, 169.728, 158.912, 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 89 15.00 Mg 1 11.99 O 5620 8.00 N 5013 7.00 C 17460 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: 2.57 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1501 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 72 " pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 898 " Number of angles added : 12 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6244 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 50 sheets defined 38.9% alpha, 18.1% beta 40 base pairs and 69 stacking pairs defined. Time for finding SS restraints: 3.46 Creating SS restraints... Processing helix chain 'P' and resid 13 through 24 Processing helix chain 'P' and resid 65 through 71 Processing helix chain 'P' and resid 89 through 100 removed outlier: 3.552A pdb=" N ILE P 93 " --> pdb=" O PRO P 89 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL P 98 " --> pdb=" O HIS P 94 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LYS P 100 " --> pdb=" O LEU P 96 " (cutoff:3.500A) Processing helix chain 'P' and resid 120 through 124 removed outlier: 3.704A pdb=" N PHE P 123 " --> pdb=" O GLU P 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 9 removed outlier: 3.639A pdb=" N LYS I 9 " --> pdb=" O TYR I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.990A pdb=" N LEU I 32 " --> pdb=" O LEU I 28 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 57 removed outlier: 3.708A pdb=" N ALA I 51 " --> pdb=" O TYR I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 163 through 167 removed outlier: 3.983A pdb=" N SER I 166 " --> pdb=" O LYS I 163 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER I 167 " --> pdb=" O THR I 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 163 through 167' Processing helix chain 'I' and resid 206 through 213 Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 Processing helix chain 'I' and resid 270 through 281 removed outlier: 3.775A pdb=" N ILE I 274 " --> pdb=" O THR I 270 " (cutoff:3.500A) Processing helix chain 'I' and resid 290 through 295 removed outlier: 3.738A pdb=" N GLY I 294 " --> pdb=" O TYR I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 328 Processing helix chain 'I' and resid 345 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 3.950A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 447 through 449 No H-bonds generated for 'chain 'I' and resid 447 through 449' Processing helix chain 'I' and resid 455 through 482 removed outlier: 3.552A pdb=" N MET I 459 " --> pdb=" O SER I 455 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER I 480 " --> pdb=" O LYS I 476 " (cutoff:3.500A) Processing helix chain 'I' and resid 488 through 493 removed outlier: 3.782A pdb=" N ILE I 493 " --> pdb=" O PRO I 489 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 508 Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 551 through 555 Processing helix chain 'I' and resid 608 through 612 removed outlier: 4.020A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 612' Processing helix chain 'I' and resid 624 through 628 removed outlier: 3.849A pdb=" N HIS I 628 " --> pdb=" O GLU I 625 " (cutoff:3.500A) Processing helix chain 'I' and resid 664 through 668 removed outlier: 3.514A pdb=" N LEU I 667 " --> pdb=" O GLY I 664 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE I 668 " --> pdb=" O ALA I 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 664 through 668' Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 687 removed outlier: 4.133A pdb=" N ARG I 687 " --> pdb=" O ALA I 683 " (cutoff:3.500A) Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 942 through 983 Processing helix chain 'I' and resid 985 through 991 Processing helix chain 'I' and resid 993 through 998 removed outlier: 3.534A pdb=" N TRP I 997 " --> pdb=" O ARG I 994 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU I 998 " --> pdb=" O ASP I 995 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1038 removed outlier: 3.582A 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 1107 removed outlier: 4.322A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG I1106 " --> pdb=" O GLY I1102 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.566A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 4.117A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1177 removed outlier: 3.591A pdb=" N ARG I1171 " --> pdb=" O GLU I1167 " (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 1282 Processing helix chain 'I' and resid 1283 through 1292 Processing helix chain 'I' and resid 1297 through 1310 Processing helix chain 'I' and resid 1320 through 1333 removed outlier: 3.747A 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 94 through 100 removed outlier: 3.570A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 removed outlier: 3.661A pdb=" N SER J 119 " --> pdb=" O TRP J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 181 through 191 removed outlier: 3.702A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 208 Processing helix chain 'J' and resid 210 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 256 through 258 No H-bonds generated for 'chain 'J' and resid 256 through 258' Processing helix chain 'J' and resid 263 through 285 Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 336 through 342 removed outlier: 3.556A pdb=" N LEU J 342 " --> pdb=" O PHE J 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 405 through 416 removed outlier: 3.502A pdb=" N ILE J 416 " --> pdb=" O LEU J 412 " (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 450 through 452 No H-bonds generated for 'chain 'J' and resid 450 through 452' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 485 through 489 Processing helix chain 'J' and resid 504 through 514 removed outlier: 3.722A pdb=" N LEU J 508 " --> pdb=" O GLN J 504 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.955A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 592 removed outlier: 3.936A pdb=" N ILE J 591 " --> pdb=" O PRO J 588 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 612 Processing helix chain 'J' and resid 614 through 636 removed outlier: 4.041A pdb=" N ILE J 619 " --> pdb=" O LYS J 615 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 703 removed outlier: 3.936A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 Processing helix chain 'J' and resid 768 through 804 removed outlier: 4.066A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA J 779 " --> pdb=" O SER J 775 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 removed outlier: 3.653A 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 896 through 900 Processing helix chain 'J' and resid 915 through 925 Processing helix chain 'J' and resid 926 through 930 Processing helix chain 'J' and resid 1137 through 1147 Processing helix chain 'J' and resid 1216 through 1225 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 3.537A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.347A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1296 Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1318 through 1326 removed outlier: 3.730A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN J1326 " --> pdb=" O ALA J1322 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1354 removed outlier: 3.730A pdb=" N ASN J1350 " --> pdb=" O GLY J1346 " (cutoff:3.500A) Processing helix chain 'J' and resid 1360 through 1375 removed outlier: 4.169A pdb=" N ALA J1364 " --> pdb=" O GLY J1360 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA J1375 " --> pdb=" O ARG J1371 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 17 through 32 removed outlier: 3.557A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 removed outlier: 3.609A pdb=" N GLU K 56 " --> pdb=" O ARG K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 84 Processing helix chain 'G' and resid 34 through 48 removed outlier: 4.136A pdb=" N ALA G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.566A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 154 through 159 Processing helix chain 'G' and resid 212 through 234 removed outlier: 4.169A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.576A 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 154 through 160 removed outlier: 3.609A pdb=" N ARG H 158 " --> pdb=" O PRO H 154 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N HIS H 160 " --> pdb=" O SER H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 166 removed outlier: 3.767A pdb=" N ASP H 164 " --> pdb=" O SER H 161 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG H 166 " --> pdb=" O GLU H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 227 Processing helix chain 'H' and resid 228 through 232 Processing sheet with id=AA1, first strand: chain 'P' and resid 27 through 29 Processing sheet with id=AA2, first strand: chain 'P' and resid 32 through 33 Processing sheet with id=AA3, first strand: chain 'P' and resid 149 through 155 removed outlier: 3.543A pdb=" N SER P 139 " --> pdb=" O VAL P 154 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N MET P 140 " --> pdb=" O THR P 131 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR P 131 " --> pdb=" O MET P 140 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE P 129 " --> pdb=" O LEU P 142 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ASN P 144 " --> pdb=" O GLN P 127 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N GLN P 127 " --> pdb=" O ASN P 144 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE P 126 " --> pdb=" O ILE P 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.608A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 59 through 60 removed outlier: 5.805A pdb=" N SER I 66 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N TYR I 105 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 136 through 138 Processing sheet with id=AA7, first strand: chain 'I' and resid 451 through 454 removed outlier: 6.307A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 154 through 159 removed outlier: 4.951A pdb=" N TYR I 172 " --> pdb=" O PHE I 188 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 227 through 231 Processing sheet with id=AB1, first strand: chain 'I' and resid 239 through 240 Processing sheet with id=AB2, first strand: chain 'I' and resid 255 through 257 removed outlier: 7.020A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 301 through 302 removed outlier: 3.559A pdb=" N CYS I 311 " --> pdb=" O TYR I 301 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.811A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N THR I 595 " --> pdb=" O THR I 600 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N THR I 600 " --> pdb=" O THR I 595 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AB6, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.671A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.239A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 755 through 758 Processing sheet with id=AB9, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC1, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.371A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 8.871A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 830 through 841 removed outlier: 4.024A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 849 through 850 removed outlier: 3.589A pdb=" N GLU I 849 " --> pdb=" O VAL I 887 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 882 through 884 removed outlier: 7.224A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AC6, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AC7, first strand: chain 'I' and resid 1335 through 1340 Processing sheet with id=AC8, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.713A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 10.261A pdb=" N SER J 109 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 10.110A pdb=" N ILE J 238 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 159 through 160 removed outlier: 6.807A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 253 through 254 Processing sheet with id=AD2, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AD3, first strand: chain 'J' and resid 706 through 708 Processing sheet with id=AD4, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AD5, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AD6, first strand: chain 'J' and resid 825 through 827 removed outlier: 7.261A pdb=" N VAL J 825 " --> pdb=" O LYS J 832 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP J 830 " --> pdb=" O GLU J 827 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 842 through 843 removed outlier: 4.009A pdb=" N ARG J 842 " --> pdb=" O LEU J 864 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 848 through 849 removed outlier: 6.528A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 949 through 951 removed outlier: 4.851A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 957 through 961 removed outlier: 4.362A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 1024 through 1028 removed outlier: 6.262A pdb=" N MET J1025 " --> pdb=" O ARG J1123 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG J1123 " --> pdb=" O MET J1025 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL J1027 " --> pdb=" O LEU J1121 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 1098 through 1100 Processing sheet with id=AE4, first strand: chain 'J' and resid 1046 through 1050 Processing sheet with id=AE5, first strand: chain 'J' and resid 1188 through 1191 removed outlier: 6.946A pdb=" N LYS J1172 " --> pdb=" O GLU J1168 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N GLU J1168 " --> pdb=" O LYS J1172 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ARG J1174 " --> pdb=" O GLY J1166 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.673A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 12 through 17 removed outlier: 6.781A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N HIS G 23 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N THR G 207 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.585A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLY G 149 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N CYS G 54 " --> pdb=" O GLY G 149 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 90 through 91 Processing sheet with id=AF1, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.948A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 152 through 153 Processing sheet with id=AF3, first strand: chain 'H' and resid 15 through 20 removed outlier: 6.662A pdb=" N HIS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU H 206 " --> pdb=" O ARG H 182 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ARG H 182 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 98 through 105 removed outlier: 3.899A pdb=" N GLU H 58 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 108 through 111 removed outlier: 6.605A pdb=" N GLY H 108 " --> pdb=" O HIS H 132 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N HIS H 132 " --> pdb=" O GLY H 108 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL H 110 " --> pdb=" O ILE H 130 " (cutoff:3.500A) 1141 hydrogen bonds defined for protein. 3188 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 104 hydrogen bonds 204 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 69 stacking parallelities Total time for adding SS restraints: 7.70 Time building geometry restraints manager: 3.25 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: 9135 1.34 - 1.46: 4057 1.46 - 1.58: 15362 1.58 - 1.70: 176 1.70 - 1.81: 194 Bond restraints: 28924 Sorted by residual: bond pdb=" C3' DC A 39 " pdb=" C2' DC A 39 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.19e+01 bond pdb=" C3' DA B 10 " pdb=" C2' DA B 10 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C3' DA A 34 " pdb=" C2' DA A 34 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.30e+00 bond pdb=" C3' DT A 18 " pdb=" C2' DT A 18 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.57e+00 bond pdb=" C3' DT A 27 " pdb=" C2' DT A 27 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.77e+00 ... (remaining 28919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 38885 1.73 - 3.46: 525 3.46 - 5.20: 44 5.20 - 6.93: 17 6.93 - 8.66: 6 Bond angle restraints: 39477 Sorted by residual: angle pdb=" N3 DT A 38 " pdb=" C4 DT A 38 " pdb=" O4 DT A 38 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT A 30 " pdb=" C4 DT A 30 " pdb=" O4 DT A 30 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.80e+01 angle pdb=" N3 DT A 28 " pdb=" C4 DT A 28 " pdb=" O4 DT A 28 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT A 26 " pdb=" C4 DT A 26 " pdb=" O4 DT A 26 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT B 36 " pdb=" C4 DT B 36 " pdb=" O4 DT B 36 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 ... (remaining 39472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.09: 16733 35.09 - 70.17: 829 70.17 - 105.26: 39 105.26 - 140.35: 0 140.35 - 175.43: 2 Dihedral angle restraints: 17603 sinusoidal: 7899 harmonic: 9704 Sorted by residual: dihedral pdb=" C4' DC B 28 " pdb=" C3' DC B 28 " pdb=" O3' DC B 28 " pdb=" P DC B 29 " ideal model delta sinusoidal sigma weight residual 220.00 44.57 175.43 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DC A 39 " pdb=" C3' DC A 39 " pdb=" O3' DC A 39 " pdb=" P DC A 40 " ideal model delta sinusoidal sigma weight residual 220.00 74.24 145.76 1 3.50e+01 8.16e-04 1.43e+01 dihedral pdb=" CA ASN I 314 " pdb=" C ASN I 314 " pdb=" N MET I 315 " pdb=" CA MET I 315 " ideal model delta harmonic sigma weight residual 180.00 161.33 18.67 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 17600 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 2798 0.027 - 0.055: 1009 0.055 - 0.082: 385 0.082 - 0.109: 247 0.109 - 0.137: 69 Chirality restraints: 4508 Sorted by residual: chirality pdb=" CA LYS I 236 " pdb=" N LYS I 236 " pdb=" C LYS I 236 " pdb=" CB LYS I 236 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CA ILE J1190 " pdb=" N ILE J1190 " pdb=" C ILE J1190 " pdb=" CB ILE J1190 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 chirality pdb=" CA ILE J1090 " pdb=" N ILE J1090 " pdb=" C ILE J1090 " pdb=" CB ILE J1090 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 ... (remaining 4505 not shown) Planarity restraints: 4852 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP I 189 " -0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO I 190 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO I 190 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO I 190 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET I 488 " 0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO I 489 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO I 489 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO I 489 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 153 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.15e+00 pdb=" N PRO G 154 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO G 154 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO G 154 " 0.020 5.00e-02 4.00e+02 ... (remaining 4849 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 200 2.53 - 3.12: 20579 3.12 - 3.71: 45657 3.71 - 4.31: 61162 4.31 - 4.90: 103643 Nonbonded interactions: 231241 Sorted by model distance: nonbonded pdb=" OD2 ASP J 460 " pdb=" OP1 U R 17 " model vdw 1.935 3.040 nonbonded pdb=" P U R 17 " pdb="MG MG J1503 " model vdw 2.054 2.530 nonbonded pdb=" OP1 U R 17 " pdb="MG MG J1503 " model vdw 2.067 2.170 nonbonded pdb=" OD2 ASP J 462 " pdb="MG MG J1503 " model vdw 2.081 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1503 " model vdw 2.086 2.170 ... (remaining 231236 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 4 through 218 or resid 220 through 233)) selection = (chain 'H' and (resid 4 through 218 or resid 220 through 233)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 4.040 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: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 33.780 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:6.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28932 Z= 0.187 Angle : 0.489 8.659 39489 Z= 0.315 Chirality : 0.040 0.137 4508 Planarity : 0.003 0.045 4852 Dihedral : 18.104 175.432 11359 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.39 % Favored : 97.58 % Rotamer: Outliers : 0.28 % Allowed : 18.47 % Favored : 81.25 % 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: 1.18 (0.15), residues: 3359 helix: 2.38 (0.16), residues: 1138 sheet: 0.38 (0.24), residues: 510 loop : -0.16 (0.15), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 69 TYR 0.009 0.001 TYR J 631 PHE 0.005 0.001 PHE I1025 TRP 0.009 0.001 TRP I 997 HIS 0.003 0.000 HIS P 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.19 (28924) covalent geometry : angle 0.48567 / 0.32 (39477) hydrogen bonds : bond 0.13424 / 8.88 ( 1243) hydrogen bonds : angle 5.15562 / 3.61 ( 3392) metal coordination : bond 0.00333 / 0.18 ( 8) metal coordination : angle 3.26912 / 1.56 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 184 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 1 MET cc_start: 0.6867 (tmm) cc_final: 0.6463 (tmm) REVERT: I 741 MET cc_start: 0.8463 (mmt) cc_final: 0.8141 (mmt) REVERT: J 1034 PHE cc_start: 0.8380 (m-80) cc_final: 0.7999 (m-80) REVERT: J 1040 MET cc_start: 0.6087 (ptt) cc_final: 0.5314 (pmt) REVERT: G 93 GLN cc_start: 0.8244 (pp30) cc_final: 0.7921 (pp30) outliers start: 5 outliers final: 2 residues processed: 187 average time/residue: 0.6889 time to fit residues: 150.8773 Evaluate side-chains 170 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 168 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 432 LEU Chi-restraints excluded: chain G residue 90 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1116 HIS ** J 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 ASN G 117 HIS ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.075937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.050972 restraints weight = 150051.449| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 4.34 r_work: 0.2683 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2684 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2684 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9003 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 28932 Z= 0.281 Angle : 0.622 10.710 39489 Z= 0.325 Chirality : 0.044 0.191 4508 Planarity : 0.005 0.079 4852 Dihedral : 15.872 178.291 4749 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.92 % Favored : 97.05 % Rotamer: Outliers : 2.99 % Allowed : 17.85 % Favored : 79.17 % 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: 0.88 (0.15), residues: 3359 helix: 1.99 (0.16), residues: 1169 sheet: 0.20 (0.23), residues: 508 loop : -0.26 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 996 TYR 0.022 0.002 TYR J 631 PHE 0.019 0.002 PHE I 812 TRP 0.007 0.001 TRP J 33 HIS 0.010 0.001 HIS G 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00635 / 0.28 (28924) covalent geometry : angle 0.61413 / 0.32 (39477) hydrogen bonds : bond 0.04544 / 3.07 ( 1243) hydrogen bonds : angle 4.32463 / 3.01 ( 3392) metal coordination : bond 0.01945 / 1.08 ( 8) metal coordination : angle 5.67161 / 3.00 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 171 time to evaluate : 1.133 Fit side-chains revert: symmetry clash REVERT: I 562 GLU cc_start: 0.9097 (OUTLIER) cc_final: 0.8305 (tm-30) REVERT: I 741 MET cc_start: 0.8852 (mmt) cc_final: 0.8446 (mmt) REVERT: J 136 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8427 (mp0) REVERT: J 895 CYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7839 (p) REVERT: J 902 ASP cc_start: 0.8629 (t0) cc_final: 0.8329 (t0) REVERT: J 913 GLU cc_start: 0.8289 (pp20) cc_final: 0.7968 (pp20) REVERT: J 1040 MET cc_start: 0.7154 (ptt) cc_final: 0.6179 (pmt) REVERT: G 93 GLN cc_start: 0.8705 (pp30) cc_final: 0.8181 (pp30) outliers start: 83 outliers final: 24 residues processed: 231 average time/residue: 0.6512 time to fit residues: 178.6297 Evaluate side-chains 183 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 562 GLU Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 38 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 286 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 225 optimal weight: 4.9990 chunk 299 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 249 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 97 optimal weight: 0.6980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1350 ASN K 15 ASN G 117 HIS ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.076592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.051937 restraints weight = 122129.144| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 3.95 r_work: 0.2720 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 28932 Z= 0.162 Angle : 0.527 9.473 39489 Z= 0.278 Chirality : 0.041 0.165 4508 Planarity : 0.004 0.052 4852 Dihedral : 15.860 178.919 4747 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.62 % Favored : 97.35 % Rotamer: Outliers : 1.91 % Allowed : 19.06 % Favored : 79.03 % 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: 0.93 (0.15), residues: 3359 helix: 2.10 (0.16), residues: 1169 sheet: 0.18 (0.23), residues: 519 loop : -0.28 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 996 TYR 0.016 0.001 TYR J 631 PHE 0.013 0.001 PHE I1323 TRP 0.005 0.001 TRP I 997 HIS 0.011 0.001 HIS G 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (28924) covalent geometry : angle 0.51838 / 0.28 (39477) hydrogen bonds : bond 0.03901 / 2.65 ( 1243) hydrogen bonds : angle 4.15013 / 2.89 ( 3392) metal coordination : bond 0.01048 / 0.58 ( 8) metal coordination : angle 5.61534 / 3.01 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 161 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 1 MET cc_start: 0.7717 (tmm) cc_final: 0.7494 (tmm) REVERT: I 562 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8753 (tp30) REVERT: I 741 MET cc_start: 0.8848 (mmt) cc_final: 0.8403 (mmt) REVERT: J 136 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8377 (mp0) REVERT: J 322 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8099 (mtm-85) REVERT: J 902 ASP cc_start: 0.8559 (t0) cc_final: 0.8260 (t0) REVERT: J 913 GLU cc_start: 0.8200 (pp20) cc_final: 0.7891 (pp20) REVERT: J 1040 MET cc_start: 0.7163 (ptt) cc_final: 0.6252 (pmt) REVERT: J 1101 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7644 (mp) REVERT: G 93 GLN cc_start: 0.8683 (pp30) cc_final: 0.8099 (pp30) REVERT: H 66 HIS cc_start: 0.9158 (OUTLIER) cc_final: 0.8837 (m-70) REVERT: H 93 GLN cc_start: 0.8682 (pp30) cc_final: 0.8467 (pp30) outliers start: 52 outliers final: 26 residues processed: 200 average time/residue: 0.6271 time to fit residues: 148.1622 Evaluate side-chains 187 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 145 LEU Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 485 ASP Chi-restraints excluded: chain I residue 562 GLU Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 322 ARG Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 432 LEU Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 196 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 127 optimal weight: 4.9990 chunk 3 optimal weight: 0.2980 chunk 23 optimal weight: 0.1980 chunk 141 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 250 optimal weight: 20.0000 chunk 207 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 198 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 910 ASN ** J 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 ASN G 117 HIS ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.076037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.050930 restraints weight = 153298.845| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 4.50 r_work: 0.2675 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9005 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 28932 Z= 0.188 Angle : 0.542 8.691 39489 Z= 0.284 Chirality : 0.042 0.194 4508 Planarity : 0.004 0.081 4852 Dihedral : 15.874 178.915 4747 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.95 % Favored : 96.99 % Rotamer: Outliers : 2.95 % Allowed : 18.82 % Favored : 78.23 % 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: 0.87 (0.15), residues: 3359 helix: 2.06 (0.16), residues: 1169 sheet: 0.12 (0.23), residues: 518 loop : -0.30 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG I 996 TYR 0.016 0.001 TYR J 631 PHE 0.012 0.001 PHE I1323 TRP 0.005 0.001 TRP I 997 HIS 0.012 0.001 HIS G 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 (28924) covalent geometry : angle 0.53238 / 0.28 (39477) hydrogen bonds : bond 0.03853 / 2.63 ( 1243) hydrogen bonds : angle 4.10561 / 2.85 ( 3392) metal coordination : bond 0.01206 / 0.68 ( 8) metal coordination : angle 5.71276 / 3.04 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 161 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 562 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8813 (tp30) REVERT: I 1219 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8532 (pm20) REVERT: J 136 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8444 (mp0) REVERT: J 322 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8105 (mtm-85) REVERT: J 541 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.9320 (mp) REVERT: J 875 ASN cc_start: 0.8295 (OUTLIER) cc_final: 0.7983 (t0) REVERT: J 902 ASP cc_start: 0.8600 (t0) cc_final: 0.8325 (t0) REVERT: J 913 GLU cc_start: 0.8349 (pp20) cc_final: 0.8032 (pp20) REVERT: J 1040 MET cc_start: 0.7275 (ptt) cc_final: 0.6348 (pmt) REVERT: J 1101 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7585 (mp) REVERT: G 93 GLN cc_start: 0.8696 (pp30) cc_final: 0.8067 (pp30) REVERT: H 66 HIS cc_start: 0.9197 (OUTLIER) cc_final: 0.8872 (m-70) REVERT: H 93 GLN cc_start: 0.8711 (pp30) cc_final: 0.8460 (pp30) outliers start: 82 outliers final: 37 residues processed: 229 average time/residue: 0.6417 time to fit residues: 174.7986 Evaluate side-chains 201 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 156 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 145 LEU Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 562 GLU Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 322 ARG Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 432 LEU Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 541 LEU Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 1047 THR Chi-restraints excluded: chain J residue 1101 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 196 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 22 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 330 optimal weight: 9.9990 chunk 262 optimal weight: 2.9990 chunk 66 optimal weight: 0.0870 chunk 260 optimal weight: 0.0060 chunk 82 optimal weight: 0.0000 chunk 56 optimal weight: 3.9990 chunk 73 optimal weight: 0.0030 chunk 119 optimal weight: 1.9990 overall best weight: 0.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.077786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.052812 restraints weight = 140299.733| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 4.25 r_work: 0.2738 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 28932 Z= 0.102 Angle : 0.513 10.132 39489 Z= 0.270 Chirality : 0.041 0.177 4508 Planarity : 0.003 0.048 4852 Dihedral : 15.822 179.611 4747 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.42 % Favored : 97.55 % Rotamer: Outliers : 1.91 % Allowed : 19.86 % Favored : 78.23 % 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: 0.98 (0.15), residues: 3359 helix: 2.17 (0.16), residues: 1165 sheet: 0.17 (0.23), residues: 498 loop : -0.25 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG I 996 TYR 0.012 0.001 TYR J 631 PHE 0.011 0.001 PHE I 405 TRP 0.007 0.001 TRP I 997 HIS 0.011 0.001 HIS G 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (28924) covalent geometry : angle 0.50458 / 0.27 (39477) hydrogen bonds : bond 0.03309 / 2.27 ( 1243) hydrogen bonds : angle 3.96366 / 2.75 ( 3392) metal coordination : bond 0.00406 / 0.22 ( 8) metal coordination : angle 5.34550 / 2.81 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 171 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 562 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8774 (tp30) REVERT: J 902 ASP cc_start: 0.8548 (t0) cc_final: 0.8278 (t0) REVERT: J 913 GLU cc_start: 0.8205 (pp20) cc_final: 0.7933 (pp20) REVERT: J 1040 MET cc_start: 0.7355 (ptt) cc_final: 0.6441 (pmt) REVERT: J 1095 MET cc_start: 0.8136 (tmt) cc_final: 0.7874 (tmm) REVERT: G 93 GLN cc_start: 0.8677 (pp30) cc_final: 0.8063 (pp30) REVERT: H 66 HIS cc_start: 0.9170 (OUTLIER) cc_final: 0.8850 (m-70) REVERT: H 93 GLN cc_start: 0.8733 (pp30) cc_final: 0.8471 (pp30) REVERT: H 147 GLN cc_start: 0.8967 (mt0) cc_final: 0.8755 (mt0) outliers start: 52 outliers final: 22 residues processed: 214 average time/residue: 0.6547 time to fit residues: 166.2089 Evaluate side-chains 188 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 145 LEU Chi-restraints excluded: chain I residue 101 ARG Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 541 GLU Chi-restraints excluded: chain I residue 562 GLU Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 432 LEU Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 92 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 164 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 120 optimal weight: 0.0020 chunk 153 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 292 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 180 optimal weight: 0.9980 chunk 319 optimal weight: 0.4980 chunk 39 optimal weight: 10.0000 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 ASN G 117 HIS H 41 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.077667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.052486 restraints weight = 158430.490| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 4.60 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2915 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.098 28932 Z= 0.109 Angle : 0.514 11.442 39489 Z= 0.268 Chirality : 0.041 0.177 4508 Planarity : 0.004 0.077 4852 Dihedral : 15.802 179.567 4747 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.54 % Favored : 97.44 % Rotamer: Outliers : 2.22 % Allowed : 19.83 % Favored : 77.95 % 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: 1.01 (0.15), residues: 3359 helix: 2.20 (0.16), residues: 1166 sheet: 0.19 (0.23), residues: 489 loop : -0.22 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG I 996 TYR 0.012 0.001 TYR J 631 PHE 0.010 0.001 PHE I 405 TRP 0.007 0.001 TRP I 997 HIS 0.012 0.001 HIS G 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (28924) covalent geometry : angle 0.50622 / 0.27 (39477) hydrogen bonds : bond 0.03271 / 2.25 ( 1243) hydrogen bonds : angle 3.89977 / 2.70 ( 3392) metal coordination : bond 0.00576 / 0.33 ( 8) metal coordination : angle 5.15127 / 2.67 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 167 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: I 562 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8632 (tp30) REVERT: J 136 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7957 (mp0) REVERT: J 504 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.7892 (mt0) REVERT: J 875 ASN cc_start: 0.8215 (OUTLIER) cc_final: 0.7883 (t0) REVERT: J 902 ASP cc_start: 0.8362 (t0) cc_final: 0.8088 (t0) REVERT: J 913 GLU cc_start: 0.7977 (pp20) cc_final: 0.7711 (pp20) REVERT: J 1040 MET cc_start: 0.7244 (ptt) cc_final: 0.6379 (pmt) REVERT: G 93 GLN cc_start: 0.8413 (pp30) cc_final: 0.7748 (pp30) REVERT: H 66 HIS cc_start: 0.9082 (OUTLIER) cc_final: 0.8759 (m-70) REVERT: H 93 GLN cc_start: 0.8754 (pp30) cc_final: 0.8339 (pp30) outliers start: 61 outliers final: 28 residues processed: 214 average time/residue: 0.6331 time to fit residues: 160.9386 Evaluate side-chains 192 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 145 LEU Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 562 GLU Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 432 LEU Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 504 GLN Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 1047 THR Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 92 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 71 optimal weight: 4.9990 chunk 315 optimal weight: 10.0000 chunk 255 optimal weight: 0.7980 chunk 237 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 132 optimal weight: 0.3980 chunk 149 optimal weight: 0.3980 chunk 31 optimal weight: 2.9990 chunk 253 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 762 ASN G 117 HIS ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 GLN H 186 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.076350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.051683 restraints weight = 122843.260| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 3.93 r_work: 0.2714 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 28932 Z= 0.180 Angle : 0.562 12.939 39489 Z= 0.291 Chirality : 0.042 0.178 4508 Planarity : 0.004 0.062 4852 Dihedral : 15.842 179.361 4747 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.15 % Allowed : 20.21 % Favored : 77.64 % 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: 0.95 (0.15), residues: 3359 helix: 2.15 (0.16), residues: 1166 sheet: 0.08 (0.23), residues: 511 loop : -0.25 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG I 996 TYR 0.014 0.001 TYR J 631 PHE 0.014 0.001 PHE I1221 TRP 0.007 0.001 TRP I 997 HIS 0.011 0.001 HIS G 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (28924) covalent geometry : angle 0.55410 / 0.29 (39477) hydrogen bonds : bond 0.03593 / 2.45 ( 1243) hydrogen bonds : angle 3.95887 / 2.73 ( 3392) metal coordination : bond 0.01134 / 0.63 ( 8) metal coordination : angle 5.33212 / 2.74 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 160 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: I 562 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8782 (tp30) REVERT: J 136 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8418 (mp0) REVERT: J 504 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8299 (mt0) REVERT: J 875 ASN cc_start: 0.8321 (OUTLIER) cc_final: 0.7981 (t0) REVERT: J 902 ASP cc_start: 0.8527 (t0) cc_final: 0.8261 (t0) REVERT: J 913 GLU cc_start: 0.8316 (pp20) cc_final: 0.7962 (pp20) REVERT: J 1040 MET cc_start: 0.7390 (ptt) cc_final: 0.6477 (pmt) REVERT: J 1095 MET cc_start: 0.8050 (tmt) cc_final: 0.7801 (tmm) REVERT: G 93 GLN cc_start: 0.8660 (pp30) cc_final: 0.8010 (pp30) REVERT: H 66 HIS cc_start: 0.9184 (OUTLIER) cc_final: 0.8863 (m-70) REVERT: H 168 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8343 (tp) outliers start: 59 outliers final: 34 residues processed: 209 average time/residue: 0.6448 time to fit residues: 160.0736 Evaluate side-chains 194 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 154 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 145 LEU Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 562 GLU Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 504 GLN Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 1047 THR Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 159 ILE Chi-restraints excluded: chain H residue 168 ILE Chi-restraints excluded: chain H residue 195 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 110 optimal weight: 5.9990 chunk 269 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 215 optimal weight: 0.5980 chunk 263 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 238 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 279 optimal weight: 0.8980 chunk 182 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 HIS ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.076321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.051408 restraints weight = 137097.343| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 4.22 r_work: 0.2702 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 28932 Z= 0.161 Angle : 0.558 13.300 39489 Z= 0.289 Chirality : 0.041 0.183 4508 Planarity : 0.004 0.059 4852 Dihedral : 15.854 179.274 4747 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.12 % Allowed : 20.69 % Favored : 77.19 % 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: 0.91 (0.15), residues: 3359 helix: 2.14 (0.16), residues: 1165 sheet: 0.01 (0.23), residues: 510 loop : -0.26 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG I 996 TYR 0.013 0.001 TYR J 631 PHE 0.011 0.001 PHE I 405 TRP 0.008 0.001 TRP I 997 HIS 0.010 0.001 HIS G 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (28924) covalent geometry : angle 0.54973 / 0.29 (39477) hydrogen bonds : bond 0.03542 / 2.43 ( 1243) hydrogen bonds : angle 3.95737 / 2.73 ( 3392) metal coordination : bond 0.00993 / 0.56 ( 8) metal coordination : angle 5.45603 / 2.83 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 165 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 562 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8789 (tp30) REVERT: J 136 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8438 (mp0) REVERT: J 875 ASN cc_start: 0.8329 (OUTLIER) cc_final: 0.7975 (t0) REVERT: J 902 ASP cc_start: 0.8535 (t0) cc_final: 0.8306 (t0) REVERT: J 1040 MET cc_start: 0.7469 (ptt) cc_final: 0.6562 (pmt) REVERT: J 1095 MET cc_start: 0.8060 (tmt) cc_final: 0.7805 (tmm) REVERT: G 93 GLN cc_start: 0.8732 (pp30) cc_final: 0.8086 (pp30) REVERT: H 65 LEU cc_start: 0.9548 (mp) cc_final: 0.9210 (pt) REVERT: H 66 HIS cc_start: 0.9193 (OUTLIER) cc_final: 0.8666 (m-70) REVERT: H 214 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7978 (pp20) outliers start: 58 outliers final: 35 residues processed: 211 average time/residue: 0.6593 time to fit residues: 164.8150 Evaluate side-chains 198 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 145 LEU Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 562 GLU Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 432 LEU Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 1047 THR Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 214 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 319 optimal weight: 0.9980 chunk 271 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 202 optimal weight: 0.0030 chunk 192 optimal weight: 4.9990 chunk 41 optimal weight: 0.0870 chunk 266 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 119 optimal weight: 0.5980 chunk 86 optimal weight: 6.9990 chunk 285 optimal weight: 1.9990 overall best weight: 0.5370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 HIS ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.077258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.051975 restraints weight = 169019.324| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 4.65 r_work: 0.2702 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2705 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2705 r_free = 0.2705 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2705 r_free = 0.2705 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2705 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 28932 Z= 0.111 Angle : 0.555 13.612 39489 Z= 0.287 Chirality : 0.041 0.184 4508 Planarity : 0.004 0.085 4852 Dihedral : 15.834 179.970 4747 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.56 % Allowed : 21.32 % Favored : 77.12 % 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: 0.94 (0.15), residues: 3359 helix: 2.16 (0.16), residues: 1166 sheet: 0.06 (0.23), residues: 502 loop : -0.26 (0.15), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG I 996 TYR 0.016 0.001 TYR I1053 PHE 0.011 0.001 PHE I 405 TRP 0.019 0.001 TRP I 997 HIS 0.028 0.001 HIS G 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (28924) covalent geometry : angle 0.54755 / 0.29 (39477) hydrogen bonds : bond 0.03302 / 2.26 ( 1243) hydrogen bonds : angle 3.90322 / 2.69 ( 3392) metal coordination : bond 0.00576 / 0.33 ( 8) metal coordination : angle 5.32437 / 2.76 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 161 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: I 562 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8793 (tp30) REVERT: I 1080 ASN cc_start: 0.9383 (t0) cc_final: 0.9159 (t0) REVERT: J 136 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8466 (mp0) REVERT: J 603 LYS cc_start: 0.8913 (tmmt) cc_final: 0.8615 (tppp) REVERT: J 875 ASN cc_start: 0.8308 (OUTLIER) cc_final: 0.7980 (t0) REVERT: J 902 ASP cc_start: 0.8557 (t0) cc_final: 0.8300 (t0) REVERT: J 964 LYS cc_start: 0.9420 (mmmt) cc_final: 0.8946 (mtmt) REVERT: J 1040 MET cc_start: 0.7567 (ptt) cc_final: 0.6692 (pmt) REVERT: J 1095 MET cc_start: 0.8152 (tmt) cc_final: 0.7912 (tmm) REVERT: K 69 ARG cc_start: 0.8273 (ttp80) cc_final: 0.8040 (ttp80) REVERT: G 93 GLN cc_start: 0.8739 (pp30) cc_final: 0.8102 (pp30) REVERT: G 156 SER cc_start: 0.9419 (m) cc_final: 0.9101 (t) REVERT: H 66 HIS cc_start: 0.9204 (OUTLIER) cc_final: 0.8872 (m-70) outliers start: 42 outliers final: 26 residues processed: 194 average time/residue: 0.6355 time to fit residues: 146.1550 Evaluate side-chains 190 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 160 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 145 LEU Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 562 GLU Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 1047 THR Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 159 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 337 optimal weight: 10.0000 chunk 133 optimal weight: 0.6980 chunk 304 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 175 optimal weight: 0.0170 chunk 260 optimal weight: 0.8980 chunk 238 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 151 optimal weight: 0.8980 chunk 154 optimal weight: 0.0270 chunk 179 optimal weight: 0.7980 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 465 GLN G 117 HIS ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.077615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.052638 restraints weight = 147643.404| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 4.36 r_work: 0.2731 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2732 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 28932 Z= 0.109 Angle : 0.563 14.269 39489 Z= 0.288 Chirality : 0.041 0.184 4508 Planarity : 0.004 0.074 4852 Dihedral : 15.813 179.392 4747 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.35 % Allowed : 21.63 % Favored : 77.01 % 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: 0.99 (0.15), residues: 3359 helix: 2.19 (0.16), residues: 1166 sheet: 0.15 (0.24), residues: 483 loop : -0.24 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG I 996 TYR 0.014 0.001 TYR I1053 PHE 0.011 0.001 PHE I 405 TRP 0.010 0.001 TRP I 997 HIS 0.014 0.001 HIS G 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (28924) covalent geometry : angle 0.55532 / 0.29 (39477) hydrogen bonds : bond 0.03197 / 2.19 ( 1243) hydrogen bonds : angle 3.86411 / 2.66 ( 3392) metal coordination : bond 0.00522 / 0.30 ( 8) metal coordination : angle 5.17733 / 2.65 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 164 time to evaluate : 0.944 Fit side-chains revert: symmetry clash REVERT: I 562 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8764 (tp30) REVERT: I 1080 ASN cc_start: 0.9355 (t0) cc_final: 0.9131 (t0) REVERT: J 603 LYS cc_start: 0.8887 (tmmt) cc_final: 0.8584 (tppp) REVERT: J 875 ASN cc_start: 0.8286 (OUTLIER) cc_final: 0.7953 (t0) REVERT: J 902 ASP cc_start: 0.8515 (t0) cc_final: 0.8224 (t0) REVERT: J 964 LYS cc_start: 0.9451 (mmmt) cc_final: 0.8935 (mttp) REVERT: J 1040 MET cc_start: 0.7451 (ptt) cc_final: 0.6540 (pmt) REVERT: J 1095 MET cc_start: 0.8146 (tmt) cc_final: 0.7905 (tmm) REVERT: G 93 GLN cc_start: 0.8723 (pp30) cc_final: 0.8080 (pp30) outliers start: 36 outliers final: 24 residues processed: 193 average time/residue: 0.6277 time to fit residues: 143.4734 Evaluate side-chains 187 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 145 LEU Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 239 MET Chi-restraints excluded: chain I residue 562 GLU Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 814 CYS Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 1047 THR Chi-restraints excluded: chain J residue 1280 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 92 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 35 optimal weight: 0.8980 chunk 296 optimal weight: 0.9980 chunk 72 optimal weight: 0.0470 chunk 116 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 302 optimal weight: 0.4980 chunk 19 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 279 optimal weight: 2.9990 chunk 320 optimal weight: 2.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1366 HIS ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.077565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.052707 restraints weight = 131204.839| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 4.20 r_work: 0.2741 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2745 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2745 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28932 Z= 0.113 Angle : 0.560 14.291 39489 Z= 0.287 Chirality : 0.041 0.184 4508 Planarity : 0.004 0.069 4852 Dihedral : 15.808 179.346 4747 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.22 % Allowed : 21.81 % Favored : 76.98 % 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: 0.98 (0.15), residues: 3359 helix: 2.20 (0.16), residues: 1165 sheet: 0.09 (0.23), residues: 493 loop : -0.23 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG I 996 TYR 0.014 0.001 TYR I1053 PHE 0.011 0.001 PHE I 405 TRP 0.012 0.001 TRP I 997 HIS 0.005 0.001 HIS I 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (28924) covalent geometry : angle 0.55275 / 0.29 (39477) hydrogen bonds : bond 0.03172 / 2.17 ( 1243) hydrogen bonds : angle 3.83685 / 2.64 ( 3392) metal coordination : bond 0.00578 / 0.33 ( 8) metal coordination : angle 5.07243 / 2.59 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9933.15 seconds wall clock time: 170 minutes 10.59 seconds (10210.59 seconds total)