Starting phenix.real_space_refine on Sun Jul 5 22:58:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gdp_51274/07_2026/9gdp_51274.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gdp_51274/07_2026/9gdp_51274.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gdp_51274/07_2026/9gdp_51274.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gdp_51274/07_2026/9gdp_51274.map" model { file = "/net/cci-nas-00/data/ceres_data/9gdp_51274/07_2026/9gdp_51274.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gdp_51274/07_2026/9gdp_51274.cif" } resolution = 2.6 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= 0.002 sd= 0.034 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 114 5.49 5 Mg 1 5.21 5 S 115 5.16 5 C 18589 2.51 5 N 5338 2.21 5 O 6027 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 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: 30186 Number of models: 1 Model: "" Number of chains: 11 Chain: "C" Number of atoms: 10027 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1280, 10016 Classifications: {'peptide': 1280} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1224} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 1280, 10016 Classifications: {'peptide': 1280} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1224} Chain breaks: 3 bond proxies already assigned to first conformer: 10163 Chain: "D" Number of atoms: 9408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1202, 9408 Classifications: {'peptide': 1202} Link IDs: {'PCIS': 2, 'PTRANS': 46, 'TRANS': 1153} Chain breaks: 4 Chain: "E" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 545 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "A" Number of atoms: 1786 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 231, 1776 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 221} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 231, 1776 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 221} Chain breaks: 1 bond proxies already assigned to first conformer: 1786 Chain: "B" Number of atoms: 1697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1697 Classifications: {'peptide': 222} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 213} Chain breaks: 1 Chain: "F" Number of atoms: 3810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3810 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 16, 'TRANS': 451} Chain breaks: 2 Chain: "H" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 106 Classifications: {'RNA': 5} Modifications used: {'5*END': 1, 'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna3p': 4} Chain: "G" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 557 Classifications: {'peptide': 71} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 67} Chain: "T" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 1131 Classifications: {'DNA': 55} Link IDs: {'rna3p': 54} Chain: "L" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 1116 Classifications: {'DNA': 55} Link IDs: {'rna3p': 54} Chain: "D" 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 10475 SG CYS D 70 80.663 116.640 121.594 1.00 77.81 S ATOM 10489 SG CYS D 72 78.949 116.544 125.190 1.00 94.11 S ATOM 10597 SG CYS D 85 82.682 116.933 124.933 1.00 74.96 S ATOM 10621 SG CYS D 88 80.972 113.760 124.033 1.00 86.55 S ATOM 16331 SG CYS D 814 105.948 65.510 85.981 1.00 64.57 S ATOM 16891 SG CYS D 888 102.453 66.616 86.840 1.00 56.19 S ATOM 16940 SG CYS D 895 104.331 68.132 83.857 1.00 55.98 S ATOM 16960 SG CYS D 898 103.071 64.632 83.608 1.00 55.91 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG C 97 " occ=0.62 ... (20 atoms not shown) pdb=" NH2BARG C 97 " occ=0.38 residue: pdb=" N AHIS A 37 " occ=0.45 ... (18 atoms not shown) pdb=" NE2BHIS A 37 " occ=0.55 Time building chain proxies: 8.52, per 1000 atoms: 0.28 Number of scatterers: 30186 At special positions: 0 Unit cell: (129.387, 184.212, 198.101, 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 115 16.00 P 114 15.00 Mg 1 11.99 O 6027 8.00 N 5338 7.00 C 18589 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: 2.81 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " Number of angles added : 12 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6582 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 44 sheets defined 46.2% alpha, 15.8% beta 43 base pairs and 93 stacking pairs defined. Time for finding SS restraints: 3.54 Creating SS restraints... Processing helix chain 'C' and resid 4 through 10 removed outlier: 3.977A pdb=" N ARG C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.972A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 212 removed outlier: 3.823A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 247 removed outlier: 3.949A pdb=" N LEU C 246 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG C 247 " --> pdb=" O PRO C 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 242 through 247' Processing helix chain 'C' and resid 257 through 261 removed outlier: 3.928A pdb=" N VAL C 261 " --> pdb=" O ASP C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 279 Processing helix chain 'C' and resid 289 through 294 removed outlier: 3.980A pdb=" N GLY C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 345 through 353 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 3.907A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 410 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 455 through 480 removed outlier: 3.952A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 495 through 509 removed outlier: 3.650A pdb=" N SER C 509 " --> pdb=" O PHE C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 544 through 549 removed outlier: 3.730A pdb=" N ARG C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.624A pdb=" N TYR C 555 " --> pdb=" O VAL C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 614 removed outlier: 3.630A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N PHE C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 608 through 614' Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 662 through 667 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 686 removed outlier: 3.627A pdb=" N MET C 681 " --> pdb=" O ASN C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 689 No H-bonds generated for 'chain 'C' and resid 687 through 689' Processing helix chain 'C' and resid 704 through 713 removed outlier: 4.119A pdb=" N GLY C 713 " --> pdb=" O ALA C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 741 removed outlier: 4.252A pdb=" N LEU C 741 " --> pdb=" O GLU C 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 738 through 741' Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 896 through 906 Processing helix chain 'C' and resid 942 through 972 Processing helix chain 'C' and resid 1022 through 1038 Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1099 through 1103 removed outlier: 3.569A pdb=" N GLY C1102 " --> pdb=" O ASN C1099 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL C1103 " --> pdb=" O PRO C1100 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1099 through 1103' Processing helix chain 'C' and resid 1109 through 1134 Processing helix chain 'C' and resid 1137 through 1150 Processing helix chain 'C' and resid 1159 through 1163 Processing helix chain 'C' and resid 1164 through 1175 Processing helix chain 'C' and resid 1190 through 1201 Processing helix chain 'C' and resid 1270 through 1281 Processing helix chain 'C' and resid 1282 through 1291 Processing helix chain 'C' and resid 1296 through 1309 removed outlier: 3.582A pdb=" N THR C1301 " --> pdb=" O VAL C1297 " (cutoff:3.500A) Processing helix chain 'C' and resid 1319 through 1332 removed outlier: 3.583A pdb=" N ASN C1323 " --> pdb=" O PRO C1319 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 77 through 81 Processing helix chain 'D' and resid 95 through 100 Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 173 Processing helix chain 'D' and resid 181 through 191 Processing helix chain 'D' and resid 193 through 207 Processing helix chain 'D' and resid 210 through 231 removed outlier: 3.503A pdb=" N GLY D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 286 removed outlier: 4.073A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 417 Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 504 through 514 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 574 through 581 Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.577A pdb=" N LEU D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.856A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 644 removed outlier: 3.625A pdb=" N MET D 644 " --> pdb=" O ILE D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 670 removed outlier: 4.316A pdb=" N THR D 652 " --> pdb=" O ALA D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 702 Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 805 removed outlier: 3.751A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS D 781 " --> pdb=" O HIS D 777 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.502A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 928 No H-bonds generated for 'chain 'D' and resid 926 through 928' Processing helix chain 'D' and resid 1137 through 1146 Processing helix chain 'D' and resid 1215 through 1223 Processing helix chain 'D' and resid 1224 through 1243 removed outlier: 3.811A pdb=" N GLN D1243 " --> pdb=" O VAL D1239 " (cutoff:3.500A) Processing helix chain 'D' and resid 1248 through 1260 removed outlier: 4.181A pdb=" N ILE D1252 " --> pdb=" O ASN D1248 " (cutoff:3.500A) Processing helix chain 'D' and resid 1281 through 1294 Processing helix chain 'D' and resid 1307 through 1314 Processing helix chain 'D' and resid 1317 through 1325 removed outlier: 3.547A pdb=" N ALA D1321 " --> pdb=" O SER D1317 " (cutoff:3.500A) Processing helix chain 'D' and resid 1326 through 1338 Processing helix chain 'D' and resid 1345 through 1352 removed outlier: 3.741A pdb=" N ASN D1349 " --> pdb=" O GLY D1345 " (cutoff:3.500A) Processing helix chain 'D' and resid 1358 through 1360 No H-bonds generated for 'chain 'D' and resid 1358 through 1360' Processing helix chain 'D' and resid 1361 through 1374 Processing helix chain 'E' and resid 7 through 14 Processing helix chain 'E' and resid 15 through 32 Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 74 Processing helix chain 'A' and resid 34 through 48 Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 213 through 234 removed outlier: 4.388A pdb=" N ALA A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N PHE A 232 " --> pdb=" O GLN A 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.694A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 160 Processing helix chain 'B' and resid 213 through 228 Processing helix chain 'F' and resid 98 through 109 removed outlier: 3.735A pdb=" N THR F 109 " --> pdb=" O ARG F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 138 Processing helix chain 'F' and resid 141 through 155 removed outlier: 3.659A pdb=" N TYR F 145 " --> pdb=" O GLY F 141 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA F 155 " --> pdb=" O ASP F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 163 removed outlier: 3.736A pdb=" N LEU F 163 " --> pdb=" O ARG F 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 159 through 163' Processing helix chain 'F' and resid 224 through 243 Processing helix chain 'F' and resid 250 through 266 removed outlier: 3.620A pdb=" N SER F 254 " --> pdb=" O SER F 250 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER F 257 " --> pdb=" O ALA F 253 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU F 266 " --> pdb=" O ASP F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 300 removed outlier: 3.576A pdb=" N THR F 280 " --> pdb=" O HIS F 276 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU F 281 " --> pdb=" O LEU F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 318 removed outlier: 4.615A pdb=" N THR F 315 " --> pdb=" O ILE F 311 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N GLY F 316 " --> pdb=" O ALA F 312 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU F 318 " --> pdb=" O PHE F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 330 removed outlier: 3.963A pdb=" N LEU F 324 " --> pdb=" O ASN F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 360 removed outlier: 4.151A pdb=" N GLU F 343 " --> pdb=" O ARG F 339 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLU F 344 " --> pdb=" O GLU F 340 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET F 354 " --> pdb=" O GLN F 350 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE F 355 " --> pdb=" O LYS F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 400 removed outlier: 5.157A pdb=" N ARG F 393 " --> pdb=" O GLU F 389 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LEU F 394 " --> pdb=" O ALA F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 403 No H-bonds generated for 'chain 'F' and resid 401 through 403' Processing helix chain 'F' and resid 408 through 426 removed outlier: 3.518A pdb=" N LYS F 426 " --> pdb=" O LYS F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 432 removed outlier: 6.724A pdb=" N ARG F 430 " --> pdb=" O PHE F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 455 removed outlier: 3.767A pdb=" N TYR F 438 " --> pdb=" O LYS F 434 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N TRP F 441 " --> pdb=" O THR F 437 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TRP F 442 " --> pdb=" O TYR F 438 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 483 Processing helix chain 'F' and resid 487 through 496 Processing helix chain 'F' and resid 498 through 508 Processing helix chain 'F' and resid 526 through 531 removed outlier: 3.707A pdb=" N ILE F 531 " --> pdb=" O GLY F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 558 removed outlier: 3.524A pdb=" N GLY F 558 " --> pdb=" O ASP F 554 " (cutoff:3.500A) Processing helix chain 'F' and resid 560 through 572 Processing helix chain 'F' and resid 580 through 586 Processing helix chain 'F' and resid 591 through 607 Processing helix chain 'F' and resid 608 through 611 Processing helix chain 'F' and resid 612 through 617 removed outlier: 3.794A pdb=" N SER F 617 " --> pdb=" O GLU F 613 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 262 removed outlier: 4.190A pdb=" N GLU G 262 " --> pdb=" O ASP G 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 274 Processing helix chain 'G' and resid 278 through 283 Processing helix chain 'G' and resid 285 through 291 removed outlier: 3.638A pdb=" N GLU G 289 " --> pdb=" O ARG G 285 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU G 290 " --> pdb=" O THR G 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 312 removed outlier: 3.804A pdb=" N LEU G 301 " --> pdb=" O GLY G 297 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR G 302 " --> pdb=" O LYS G 298 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.493A pdb=" N LYS C 13 " --> pdb=" O ALA C1182 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.119A pdb=" N SER C 66 " --> pdb=" O PHE C 105 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N PHE C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N LYS C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLU C 126 " --> pdb=" O LYS C 94 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AA4, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.480A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 154 through 159 removed outlier: 4.968A pdb=" N TYR C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 236 through 239 Processing sheet with id=AA7, first strand: chain 'C' and resid 301 through 302 removed outlier: 3.653A pdb=" N ILE C 311 " --> pdb=" O TYR C 301 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.612A pdb=" N GLU C 602 " --> pdb=" O ARG C 593 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N THR C 600 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AB1, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.452A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.643A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AB4, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AB5, first strand: chain 'C' and resid 1208 through 1209 removed outlier: 7.104A pdb=" N ILE C 816 " --> pdb=" O LYS C1078 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ASN C1080 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL C 818 " --> pdb=" O ASN C1080 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N THR C1225 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.747A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AB8, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.890A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 1243 through 1245 removed outlier: 6.242A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 1268 through 1269 Processing sheet with id=AC2, first strand: chain 'C' and resid 1334 through 1339 Processing sheet with id=AC3, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.531A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 9.894A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.616A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 159 through 160 removed outlier: 6.730A pdb=" N THR D 177 " --> pdb=" O THR D 147 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 253 through 254 removed outlier: 6.356A pdb=" N PHE D 260 " --> pdb=" O ILE F 513 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AC7, first strand: chain 'D' and resid 703 through 707 Processing sheet with id=AC8, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AC9, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AD1, first strand: chain 'D' and resid 825 through 826 removed outlier: 6.909A pdb=" N HIS D 825 " --> pdb=" O LYS D 832 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 848 through 849 removed outlier: 3.516A pdb=" N ILE D 858 " --> pdb=" O ILE D 848 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 991 through 995 Processing sheet with id=AD4, first strand: chain 'D' and resid 1155 through 1156 removed outlier: 6.535A pdb=" N ILE D1155 " --> pdb=" O ILE D1209 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 1184 through 1189 Processing sheet with id=AD6, first strand: chain 'D' and resid 1278 through 1280 removed outlier: 4.336A pdb=" N LYS D1262 " --> pdb=" O GLU D1304 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ARG D1300 " --> pdb=" O THR D1266 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 12 through 20 removed outlier: 5.000A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N HIS A 23 " --> pdb=" O ILE A 19 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N HIS A 23 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N THR A 208 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N LYS A 25 " --> pdb=" O MET A 206 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N MET A 206 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N THR A 27 " --> pdb=" O ILE A 204 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ILE A 204 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N GLU A 29 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LEU A 202 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 116 through 117 removed outlier: 3.599A pdb=" N GLU A 58 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N GLU A 148 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N VAL A 56 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLY A 150 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N CYS A 54 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AE1, first strand: chain 'A' and resid 109 through 112 Processing sheet with id=AE2, first strand: chain 'A' and resid 153 through 154 Processing sheet with id=AE3, first strand: chain 'B' and resid 13 through 18 removed outlier: 6.296A pdb=" N ASP B 200 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N THR B 197 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL B 193 " --> pdb=" O THR B 197 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 116 through 117 removed outlier: 3.530A pdb=" N THR B 102 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU B 58 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLU B 148 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N VAL B 56 " --> pdb=" O GLU B 148 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLY B 150 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N CYS B 54 " --> pdb=" O GLY B 150 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AE6, first strand: chain 'B' and resid 109 through 112 Processing sheet with id=AE7, first strand: chain 'B' and resid 153 through 154 Processing sheet with id=AE8, first strand: chain 'F' and resid 164 through 166 removed outlier: 6.724A pdb=" N ARG F 268 " --> pdb=" O SER F 165 " (cutoff:3.500A) 1342 hydrogen bonds defined for protein. 3809 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 105 hydrogen bonds 210 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 93 stacking parallelities Total time for adding SS restraints: 9.07 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8878 1.33 - 1.45: 4702 1.45 - 1.57: 16861 1.57 - 1.69: 226 1.69 - 1.81: 205 Bond restraints: 30872 Sorted by residual: bond pdb=" C3' DA T 6 " pdb=" C2' DA T 6 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.27e+01 bond pdb=" C3' DC T 1 " pdb=" C2' DC T 1 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.19e+01 bond pdb=" C3' DT L 42 " pdb=" C2' DT L 42 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C5' DC L -10 " pdb=" C4' DC L -10 " ideal model delta sigma weight residual 1.512 1.534 -0.022 7.00e-03 2.04e+04 9.96e+00 bond pdb=" C3' DT T -19 " pdb=" C2' DT T -19 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.55e+00 ... (remaining 30867 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 41210 1.77 - 3.54: 841 3.54 - 5.31: 88 5.31 - 7.08: 12 7.08 - 8.85: 4 Bond angle restraints: 42155 Sorted by residual: angle pdb=" N3 DT L 27 " pdb=" C4 DT L 27 " pdb=" O4 DT L 27 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.03e+01 angle pdb=" N3 DT L 13 " pdb=" C4 DT L 13 " pdb=" O4 DT L 13 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 angle pdb=" N3 DT L 29 " pdb=" C4 DT L 29 " pdb=" O4 DT L 29 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT L -8 " pdb=" C4 DT L -8 " pdb=" O4 DT L -8 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 angle pdb=" N3 DT T -40 " pdb=" C4 DT T -40 " pdb=" O4 DT T -40 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.83e+01 ... (remaining 42150 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.45: 16944 25.45 - 50.91: 1519 50.91 - 76.36: 244 76.36 - 101.81: 21 101.81 - 127.27: 1 Dihedral angle restraints: 18729 sinusoidal: 8536 harmonic: 10193 Sorted by residual: dihedral pdb=" CA MET C 238 " pdb=" C MET C 238 " pdb=" N MET C 239 " pdb=" CA MET C 239 " ideal model delta harmonic sigma weight residual 180.00 161.90 18.10 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CG ARG C 18 " pdb=" CD ARG C 18 " pdb=" NE ARG C 18 " pdb=" CZ ARG C 18 " ideal model delta sinusoidal sigma weight residual -90.00 -38.75 -51.25 2 1.50e+01 4.44e-03 1.30e+01 dihedral pdb=" C4' DA T 6 " pdb=" C3' DA T 6 " pdb=" O3' DA T 6 " pdb=" P DA T 7 " ideal model delta sinusoidal sigma weight residual 220.00 92.73 127.27 1 3.50e+01 8.16e-04 1.26e+01 ... (remaining 18726 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 3148 0.037 - 0.074: 1186 0.074 - 0.110: 401 0.110 - 0.147: 79 0.147 - 0.184: 4 Chirality restraints: 4818 Sorted by residual: chirality pdb=" CB ILE F 508 " pdb=" CA ILE F 508 " pdb=" CG1 ILE F 508 " pdb=" CG2 ILE F 508 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.44e-01 chirality pdb=" CA LYS F 507 " pdb=" N LYS F 507 " pdb=" C LYS F 507 " pdb=" CB LYS F 507 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.11e-01 chirality pdb=" CA ILE C 742 " pdb=" N ILE C 742 " pdb=" C ILE C 742 " pdb=" CB ILE C 742 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.08e-01 ... (remaining 4815 not shown) Planarity restraints: 5099 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN D1196 " -0.010 2.00e-02 2.50e+03 2.05e-02 4.22e+00 pdb=" C ASN D1196 " 0.036 2.00e-02 2.50e+03 pdb=" O ASN D1196 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL D1197 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D1152 " -0.033 5.00e-02 4.00e+02 5.05e-02 4.09e+00 pdb=" N PRO D1153 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO D1153 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D1153 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 242 " -0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO C 243 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 243 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 243 " -0.026 5.00e-02 4.00e+02 ... (remaining 5096 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 139 2.56 - 3.15: 22649 3.15 - 3.73: 46525 3.73 - 4.32: 66803 4.32 - 4.90: 110434 Nonbonded interactions: 246550 Sorted by model distance: nonbonded pdb=" O3' G H -1 " pdb="MG MG D1503 " model vdw 1.977 2.170 nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1503 " model vdw 2.003 2.170 nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1503 " model vdw 2.081 2.170 nonbonded pdb=" OG1 THR D1264 " pdb=" OE2 GLU D1304 " model vdw 2.166 3.040 nonbonded pdb=" N GLU C 244 " pdb=" OE1 GLU C 244 " model vdw 2.185 3.120 ... (remaining 246545 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 36 or resid 38 through 160 or resid 169 through \ 233)) selection = (chain 'B' and (resid 4 through 36 or resid 38 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=0.38 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: 6.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.820 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 39.100 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 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:6.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 30880 Z= 0.275 Angle : 0.584 8.847 42167 Z= 0.376 Chirality : 0.044 0.184 4818 Planarity : 0.004 0.051 5099 Dihedral : 18.070 127.269 12147 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.73 % Allowed : 15.83 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 1.09 (0.14), residues: 3513 helix: 1.55 (0.14), residues: 1479 sheet: 0.71 (0.25), residues: 417 loop : 0.04 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 18 TYR 0.019 0.001 TYR D 631 PHE 0.021 0.001 PHE C 514 TRP 0.014 0.001 TRP F 442 HIS 0.005 0.001 HIS C 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.27 (30872) covalent geometry : angle 0.58096 / 0.38 (42155) hydrogen bonds : bond 0.11473 / 7.51 ( 1445) hydrogen bonds : angle 5.37042 / 3.77 ( 4019) metal coordination : bond 0.00722 / 0.39 ( 8) metal coordination : angle 3.72422 / 2.11 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 699 time to evaluate : 1.124 Fit side-chains REVERT: C 1297 VAL cc_start: 0.8446 (t) cc_final: 0.8133 (m) REVERT: D 314 ARG cc_start: 0.7147 (ttp80) cc_final: 0.6916 (ttp80) REVERT: D 607 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7903 (mp0) REVERT: D 664 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7686 (tt) outliers start: 22 outliers final: 16 residues processed: 709 average time/residue: 0.8116 time to fit residues: 656.5832 Evaluate side-chains 711 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 694 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 1161 SER Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 1249 ASP Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain F residue 482 MET Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 596 ARG Chi-restraints excluded: chain F residue 597 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 197 optimal weight: 0.0010 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.0870 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.0030 chunk 298 optimal weight: 2.9990 overall best weight: 0.8178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 20 GLN C 494 ASN C1038 GLN D 603 ASN D 700 ASN D 861 ASN D 910 ASN D 951 GLN B 84 ASN F 454 GLN F 469 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.139017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.106770 restraints weight = 60233.653| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.98 r_work: 0.3220 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.0508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30880 Z= 0.148 Angle : 0.538 9.141 42167 Z= 0.293 Chirality : 0.042 0.221 4818 Planarity : 0.004 0.041 5099 Dihedral : 16.714 125.616 5181 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.92 % Allowed : 14.58 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 1.30 (0.14), residues: 3513 helix: 1.77 (0.14), residues: 1493 sheet: 0.64 (0.25), residues: 425 loop : 0.15 (0.15), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 18 TYR 0.019 0.001 TYR D 631 PHE 0.019 0.001 PHE C 514 TRP 0.007 0.001 TRP F 442 HIS 0.004 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (30872) covalent geometry : angle 0.53425 / 0.29 (42155) hydrogen bonds : bond 0.04679 / 3.17 ( 1445) hydrogen bonds : angle 4.49185 / 3.13 ( 4019) metal coordination : bond 0.00623 / 0.33 ( 8) metal coordination : angle 3.83547 / 2.17 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 702 time to evaluate : 1.185 Fit side-chains REVERT: C 1297 VAL cc_start: 0.8377 (t) cc_final: 0.8118 (m) REVERT: D 314 ARG cc_start: 0.8154 (ttp80) cc_final: 0.7886 (ttp80) REVERT: D 399 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8230 (mttp) REVERT: D 607 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8215 (mp0) REVERT: F 356 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.6314 (pm20) REVERT: F 603 LEU cc_start: 0.7746 (mm) cc_final: 0.7513 (mt) outliers start: 58 outliers final: 25 residues processed: 722 average time/residue: 0.7785 time to fit residues: 641.1471 Evaluate side-chains 718 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 691 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 1033 ARG Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 399 LYS Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 712 GLU Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 854 ASP Chi-restraints excluded: chain D residue 878 ASP Chi-restraints excluded: chain D residue 1192 HIS Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 535 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 24 optimal weight: 0.0030 chunk 250 optimal weight: 0.0980 chunk 7 optimal weight: 0.6980 chunk 145 optimal weight: 2.9990 chunk 309 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 239 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 353 optimal weight: 20.0000 chunk 112 optimal weight: 0.5980 chunk 157 optimal weight: 2.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1038 GLN D 158 GLN D 603 ASN D 680 ASN D 700 ASN D 861 ASN D 875 ASN D 910 ASN D 929 GLN B 84 ASN F 154 GLN F 469 ASN F 597 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.139907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.106874 restraints weight = 70943.495| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.23 r_work: 0.3213 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.0752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 30880 Z= 0.113 Angle : 0.496 10.430 42167 Z= 0.272 Chirality : 0.040 0.221 4818 Planarity : 0.004 0.044 5099 Dihedral : 16.620 125.610 5151 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.98 % Allowed : 14.94 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 1.47 (0.14), residues: 3513 helix: 1.95 (0.14), residues: 1494 sheet: 0.67 (0.24), residues: 429 loop : 0.21 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 18 TYR 0.018 0.001 TYR D 631 PHE 0.018 0.001 PHE C 385 TRP 0.006 0.001 TRP F 442 HIS 0.004 0.000 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (30872) covalent geometry : angle 0.49289 / 0.27 (42155) hydrogen bonds : bond 0.04131 / 2.80 ( 1445) hydrogen bonds : angle 4.28171 / 2.99 ( 4019) metal coordination : bond 0.00551 / 0.29 ( 8) metal coordination : angle 3.45277 / 1.95 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 713 time to evaluate : 1.054 Fit side-chains REVERT: C 349 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7916 (mp0) REVERT: C 1162 GLU cc_start: 0.8035 (mp0) cc_final: 0.7802 (mp0) REVERT: C 1297 VAL cc_start: 0.8302 (t) cc_final: 0.8033 (m) REVERT: D 314 ARG cc_start: 0.8192 (ttp80) cc_final: 0.7931 (ttp80) REVERT: D 399 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8256 (mttp) REVERT: D 607 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8253 (mp0) REVERT: D 1174 ARG cc_start: 0.7409 (mtm-85) cc_final: 0.6989 (mtm-85) REVERT: B 149 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.8225 (ttp-170) REVERT: F 104 MET cc_start: 0.8796 (mmt) cc_final: 0.8592 (mmt) REVERT: F 356 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6156 (pm20) REVERT: F 603 LEU cc_start: 0.7728 (mm) cc_final: 0.7488 (mt) REVERT: G 254 LEU cc_start: 0.8239 (mt) cc_final: 0.7992 (mt) outliers start: 60 outliers final: 30 residues processed: 729 average time/residue: 0.8222 time to fit residues: 685.8605 Evaluate side-chains 735 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 702 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 1033 ARG Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 399 LYS Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 712 GLU Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 1192 HIS Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 149 ARG Chi-restraints excluded: chain F residue 296 MET Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 510 LYS Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 591 THR Chi-restraints excluded: chain F residue 597 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 148 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 310 optimal weight: 10.0000 chunk 174 optimal weight: 2.9990 chunk 254 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1038 GLN D 603 ASN D 680 ASN D 700 ASN D 861 ASN D 875 ASN D 910 ASN D 929 GLN D1349 ASN A 104 ASN B 84 ASN F 454 GLN F 469 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.137263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.104799 restraints weight = 61866.123| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.01 r_work: 0.3188 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.0801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 30880 Z= 0.242 Angle : 0.568 9.306 42167 Z= 0.304 Chirality : 0.044 0.227 4818 Planarity : 0.004 0.045 5099 Dihedral : 16.697 122.512 5151 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.38 % Allowed : 15.27 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 1.26 (0.14), residues: 3513 helix: 1.76 (0.13), residues: 1498 sheet: 0.63 (0.25), residues: 427 loop : 0.08 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 18 TYR 0.022 0.002 TYR D 631 PHE 0.025 0.002 PHE C 514 TRP 0.007 0.001 TRP D 580 HIS 0.007 0.001 HIS F 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.24 (30872) covalent geometry : angle 0.56379 / 0.30 (42155) hydrogen bonds : bond 0.05098 / 3.46 ( 1445) hydrogen bonds : angle 4.37825 / 3.07 ( 4019) metal coordination : bond 0.00813 / 0.43 ( 8) metal coordination : angle 3.92691 / 2.27 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 697 time to evaluate : 1.181 Fit side-chains revert: symmetry clash REVERT: C 349 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7918 (mp0) REVERT: C 1162 GLU cc_start: 0.7977 (mp0) cc_final: 0.7724 (mp0) REVERT: D 95 THR cc_start: 0.8290 (OUTLIER) cc_final: 0.7970 (p) REVERT: D 399 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8242 (mttp) REVERT: D 607 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8232 (mp0) REVERT: D 680 ASN cc_start: 0.8403 (m110) cc_final: 0.8068 (m-40) REVERT: D 684 ASP cc_start: 0.7815 (m-30) cc_final: 0.7585 (m-30) REVERT: D 1174 ARG cc_start: 0.7338 (mtm-85) cc_final: 0.6942 (mtm-85) REVERT: B 21 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8627 (t) REVERT: B 94 GLU cc_start: 0.7805 (tp30) cc_final: 0.7577 (tp30) REVERT: F 101 ARG cc_start: 0.8343 (ttm110) cc_final: 0.8100 (tpp80) REVERT: F 353 GLN cc_start: 0.4429 (OUTLIER) cc_final: 0.3771 (tp40) REVERT: F 426 LYS cc_start: 0.8903 (ptpt) cc_final: 0.8660 (ptpp) REVERT: F 603 LEU cc_start: 0.7730 (mm) cc_final: 0.7473 (mt) outliers start: 72 outliers final: 42 residues processed: 715 average time/residue: 0.8607 time to fit residues: 703.0251 Evaluate side-chains 737 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 691 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 820 GLU Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 1033 ARG Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 399 LYS Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 712 GLU Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 837 GLU Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 1188 MET Chi-restraints excluded: chain D residue 1192 HIS Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain F residue 296 MET Chi-restraints excluded: chain F residue 353 GLN Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 510 LYS Chi-restraints excluded: chain F residue 511 GLU Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 591 THR Chi-restraints excluded: chain F residue 596 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 333 optimal weight: 0.4980 chunk 211 optimal weight: 1.9990 chunk 84 optimal weight: 0.0570 chunk 181 optimal weight: 3.9990 chunk 183 optimal weight: 0.6980 chunk 216 optimal weight: 0.2980 chunk 85 optimal weight: 0.7980 chunk 118 optimal weight: 0.8980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1038 GLN D 603 ASN D 700 ASN D 861 ASN D 875 ASN D 910 ASN D1196 ASN A 104 ASN B 84 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.139296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.106395 restraints weight = 72522.403| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.21 r_work: 0.3205 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 30880 Z= 0.116 Angle : 0.495 7.319 42167 Z= 0.271 Chirality : 0.040 0.226 4818 Planarity : 0.004 0.042 5099 Dihedral : 16.666 124.582 5151 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.85 % Allowed : 16.03 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 1.41 (0.14), residues: 3513 helix: 1.93 (0.14), residues: 1492 sheet: 0.67 (0.25), residues: 431 loop : 0.14 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 18 TYR 0.020 0.001 TYR D 631 PHE 0.024 0.001 PHE C 545 TRP 0.005 0.001 TRP D 580 HIS 0.003 0.000 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (30872) covalent geometry : angle 0.49153 / 0.27 (42155) hydrogen bonds : bond 0.04137 / 2.81 ( 1445) hydrogen bonds : angle 4.21309 / 2.94 ( 4019) metal coordination : bond 0.00522 / 0.28 ( 8) metal coordination : angle 3.50551 / 1.98 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 704 time to evaluate : 1.257 Fit side-chains revert: symmetry clash REVERT: C 349 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7977 (mp0) REVERT: C 1297 VAL cc_start: 0.8372 (t) cc_final: 0.8093 (m) REVERT: D 95 THR cc_start: 0.8290 (m) cc_final: 0.7965 (p) REVERT: D 399 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8230 (mttp) REVERT: D 680 ASN cc_start: 0.8292 (m110) cc_final: 0.7907 (m-40) REVERT: D 684 ASP cc_start: 0.7812 (m-30) cc_final: 0.7565 (m-30) REVERT: D 1174 ARG cc_start: 0.7356 (mtm-85) cc_final: 0.6953 (mtm-85) REVERT: F 101 ARG cc_start: 0.8363 (ttm110) cc_final: 0.8102 (tpp80) REVERT: F 353 GLN cc_start: 0.4351 (OUTLIER) cc_final: 0.3792 (tp40) REVERT: F 603 LEU cc_start: 0.7724 (mm) cc_final: 0.7473 (mt) REVERT: G 254 LEU cc_start: 0.8209 (mt) cc_final: 0.7973 (mt) outliers start: 56 outliers final: 32 residues processed: 721 average time/residue: 0.8541 time to fit residues: 704.5461 Evaluate side-chains 725 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 691 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 957 LYS Chi-restraints excluded: chain C residue 1033 ARG Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 399 LYS Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 712 GLU Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 1192 HIS Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain F residue 296 MET Chi-restraints excluded: chain F residue 353 GLN Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 510 LYS Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 591 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 164 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 299 optimal weight: 0.0030 chunk 95 optimal weight: 3.9990 chunk 144 optimal weight: 0.5980 chunk 312 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 168 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 494 ASN D 603 ASN D 700 ASN D 861 ASN D 875 ASN D 910 ASN D 929 GLN B 84 ASN F 454 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.137632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.104902 restraints weight = 65227.404| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.25 r_work: 0.3182 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 30880 Z= 0.210 Angle : 0.546 9.663 42167 Z= 0.293 Chirality : 0.043 0.228 4818 Planarity : 0.004 0.044 5099 Dihedral : 16.687 122.701 5151 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.79 % Allowed : 16.96 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 1.31 (0.14), residues: 3513 helix: 1.82 (0.13), residues: 1497 sheet: 0.68 (0.25), residues: 427 loop : 0.07 (0.15), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 18 TYR 0.022 0.001 TYR D 631 PHE 0.022 0.002 PHE C 545 TRP 0.006 0.001 TRP D 868 HIS 0.006 0.001 HIS F 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.21 (30872) covalent geometry : angle 0.54280 / 0.29 (42155) hydrogen bonds : bond 0.04785 / 3.25 ( 1445) hydrogen bonds : angle 4.28653 / 3.00 ( 4019) metal coordination : bond 0.00730 / 0.39 ( 8) metal coordination : angle 3.69175 / 2.14 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 699 time to evaluate : 1.154 Fit side-chains revert: symmetry clash REVERT: C 349 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7972 (mp0) REVERT: D 95 THR cc_start: 0.8275 (m) cc_final: 0.7995 (p) REVERT: D 399 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8266 (mttp) REVERT: D 607 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7649 (mp0) REVERT: D 680 ASN cc_start: 0.8381 (m110) cc_final: 0.8014 (m-40) REVERT: D 684 ASP cc_start: 0.7859 (m-30) cc_final: 0.7620 (m-30) REVERT: D 1174 ARG cc_start: 0.7350 (mtm-85) cc_final: 0.6967 (mtm-85) REVERT: A 117 THR cc_start: 0.8876 (OUTLIER) cc_final: 0.8568 (p) REVERT: B 94 GLU cc_start: 0.7852 (tp30) cc_final: 0.7615 (tp30) REVERT: B 220 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8391 (mtm-85) REVERT: F 101 ARG cc_start: 0.8401 (ttm110) cc_final: 0.8154 (tpp80) REVERT: F 353 GLN cc_start: 0.4413 (OUTLIER) cc_final: 0.3878 (tp40) REVERT: F 411 ASP cc_start: 0.8382 (m-30) cc_final: 0.7987 (m-30) REVERT: F 507 LYS cc_start: 0.8003 (ptpp) cc_final: 0.7715 (ptpp) REVERT: F 575 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8388 (mtt) REVERT: F 603 LEU cc_start: 0.7704 (mm) cc_final: 0.7454 (mt) REVERT: G 254 LEU cc_start: 0.8208 (mt) cc_final: 0.7972 (mt) outliers start: 54 outliers final: 34 residues processed: 714 average time/residue: 0.7847 time to fit residues: 639.6757 Evaluate side-chains 732 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 692 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 1033 ARG Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 222 LYS Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 399 LYS Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 607 GLU Chi-restraints excluded: chain D residue 712 GLU Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 1188 MET Chi-restraints excluded: chain D residue 1192 HIS Chi-restraints excluded: chain D residue 1221 ARG Chi-restraints excluded: chain D residue 1249 ASP Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain F residue 296 MET Chi-restraints excluded: chain F residue 353 GLN Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 510 LYS Chi-restraints excluded: chain F residue 511 GLU Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 575 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 159 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 59 optimal weight: 0.0170 chunk 301 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 317 optimal weight: 5.9990 chunk 236 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 519 ASN D 700 ASN D 713 GLN D 861 ASN D 875 ASN D 910 ASN B 84 ASN F 454 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.139156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.107307 restraints weight = 57700.124| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.89 r_work: 0.3232 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30880 Z= 0.127 Angle : 0.507 9.411 42167 Z= 0.275 Chirality : 0.041 0.226 4818 Planarity : 0.004 0.043 5099 Dihedral : 16.660 123.903 5151 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.65 % Allowed : 16.96 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 1.41 (0.14), residues: 3513 helix: 1.95 (0.14), residues: 1491 sheet: 0.68 (0.25), residues: 431 loop : 0.11 (0.15), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 18 TYR 0.021 0.001 TYR C 73 PHE 0.021 0.001 PHE C 545 TRP 0.006 0.001 TRP D 580 HIS 0.004 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (30872) covalent geometry : angle 0.50420 / 0.27 (42155) hydrogen bonds : bond 0.04197 / 2.86 ( 1445) hydrogen bonds : angle 4.20115 / 2.94 ( 4019) metal coordination : bond 0.00550 / 0.30 ( 8) metal coordination : angle 3.41631 / 1.94 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 701 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 349 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7948 (mp0) REVERT: C 1038 GLN cc_start: 0.8536 (pt0) cc_final: 0.8328 (pt0) REVERT: C 1297 VAL cc_start: 0.8345 (t) cc_final: 0.8076 (m) REVERT: D 95 THR cc_start: 0.8277 (m) cc_final: 0.7996 (p) REVERT: D 200 GLN cc_start: 0.8034 (tm-30) cc_final: 0.7528 (tm-30) REVERT: D 201 MET cc_start: 0.8519 (mtm) cc_final: 0.8296 (mtm) REVERT: D 399 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8169 (mttp) REVERT: D 603 ASN cc_start: 0.8403 (t0) cc_final: 0.7896 (t0) REVERT: D 607 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7550 (mp0) REVERT: D 680 ASN cc_start: 0.8230 (m110) cc_final: 0.7787 (m-40) REVERT: D 684 ASP cc_start: 0.7766 (m-30) cc_final: 0.7491 (m-30) REVERT: D 1174 ARG cc_start: 0.7327 (mtm-85) cc_final: 0.6930 (mtm-85) REVERT: B 94 GLU cc_start: 0.7808 (tp30) cc_final: 0.7587 (tp30) REVERT: B 149 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8151 (ttp-170) REVERT: F 101 ARG cc_start: 0.8339 (ttm110) cc_final: 0.8067 (tpp80) REVERT: F 235 LYS cc_start: 0.5987 (OUTLIER) cc_final: 0.5636 (tmtt) REVERT: F 353 GLN cc_start: 0.4435 (OUTLIER) cc_final: 0.3983 (tp40) REVERT: F 411 ASP cc_start: 0.8280 (m-30) cc_final: 0.7878 (m-30) REVERT: F 603 LEU cc_start: 0.7654 (mm) cc_final: 0.7410 (mt) REVERT: G 254 LEU cc_start: 0.8170 (mt) cc_final: 0.7930 (mt) outliers start: 50 outliers final: 36 residues processed: 719 average time/residue: 0.7900 time to fit residues: 648.3323 Evaluate side-chains 732 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 691 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 726 SER Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 1033 ARG Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 399 LYS Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 607 GLU Chi-restraints excluded: chain D residue 712 GLU Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 1192 HIS Chi-restraints excluded: chain D residue 1221 ARG Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 149 ARG Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain F residue 235 LYS Chi-restraints excluded: chain F residue 296 MET Chi-restraints excluded: chain F residue 353 GLN Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 510 LYS Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 591 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 345 optimal weight: 0.1980 chunk 45 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 306 optimal weight: 0.0050 chunk 252 optimal weight: 0.7980 chunk 301 optimal weight: 3.9990 chunk 324 optimal weight: 0.0970 chunk 42 optimal weight: 2.9990 chunk 247 optimal weight: 0.9980 chunk 360 optimal weight: 9.9990 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 618 GLN D 700 ASN D 713 GLN D 861 ASN D 875 ASN D 910 ASN A 104 ASN B 84 ASN F 454 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.140276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.107745 restraints weight = 72228.634| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.17 r_work: 0.3227 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 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 : 0.002 0.041 30880 Z= 0.108 Angle : 0.494 9.797 42167 Z= 0.267 Chirality : 0.040 0.225 4818 Planarity : 0.004 0.046 5099 Dihedral : 16.599 123.483 5151 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.52 % Allowed : 17.39 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 1.52 (0.14), residues: 3513 helix: 2.05 (0.14), residues: 1493 sheet: 0.71 (0.24), residues: 435 loop : 0.16 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 18 TYR 0.018 0.001 TYR D 631 PHE 0.019 0.001 PHE C 545 TRP 0.005 0.001 TRP D 33 HIS 0.004 0.000 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (30872) covalent geometry : angle 0.49107 / 0.27 (42155) hydrogen bonds : bond 0.03811 / 2.59 ( 1445) hydrogen bonds : angle 4.09824 / 2.86 ( 4019) metal coordination : bond 0.00526 / 0.28 ( 8) metal coordination : angle 3.27156 / 1.86 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 708 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 349 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7987 (mp0) REVERT: C 1297 VAL cc_start: 0.8263 (t) cc_final: 0.7988 (m) REVERT: D 95 THR cc_start: 0.8272 (m) cc_final: 0.7983 (p) REVERT: D 200 GLN cc_start: 0.8092 (tm-30) cc_final: 0.7589 (tm-30) REVERT: D 201 MET cc_start: 0.8541 (mtm) cc_final: 0.8292 (mtm) REVERT: D 399 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8209 (mttp) REVERT: D 603 ASN cc_start: 0.8422 (t0) cc_final: 0.7920 (t0) REVERT: D 607 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7597 (mp0) REVERT: D 680 ASN cc_start: 0.8251 (m110) cc_final: 0.7759 (m-40) REVERT: D 684 ASP cc_start: 0.7730 (m-30) cc_final: 0.7466 (m-30) REVERT: D 1174 ARG cc_start: 0.7331 (mtm-85) cc_final: 0.7001 (mtm-85) REVERT: B 94 GLU cc_start: 0.7867 (tp30) cc_final: 0.7614 (tp30) REVERT: B 216 GLU cc_start: 0.8016 (tp30) cc_final: 0.7803 (tp30) REVERT: F 101 ARG cc_start: 0.8388 (ttm110) cc_final: 0.8004 (tpp80) REVERT: F 353 GLN cc_start: 0.4423 (OUTLIER) cc_final: 0.4029 (tp40) REVERT: F 411 ASP cc_start: 0.8309 (m-30) cc_final: 0.7920 (m-30) REVERT: F 495 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7844 (mmm) REVERT: F 596 ARG cc_start: 0.7599 (tpt90) cc_final: 0.7352 (tpt90) REVERT: F 603 LEU cc_start: 0.7662 (mm) cc_final: 0.7411 (mt) REVERT: G 254 LEU cc_start: 0.8189 (mt) cc_final: 0.7949 (mt) outliers start: 46 outliers final: 30 residues processed: 723 average time/residue: 0.7956 time to fit residues: 656.7336 Evaluate side-chains 727 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 693 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 399 LYS Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 607 GLU Chi-restraints excluded: chain D residue 712 GLU Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 854 ASP Chi-restraints excluded: chain D residue 1192 HIS Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain F residue 296 MET Chi-restraints excluded: chain F residue 353 GLN Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 495 MET Chi-restraints excluded: chain F residue 510 LYS Chi-restraints excluded: chain F residue 540 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 254 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 227 optimal weight: 10.0000 chunk 285 optimal weight: 0.8980 chunk 191 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 700 ASN D 713 GLN D 861 ASN D 875 ASN D 910 ASN D 929 GLN B 84 ASN F 454 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.137796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.106353 restraints weight = 52524.732| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.79 r_work: 0.3219 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 30880 Z= 0.219 Angle : 0.563 10.285 42167 Z= 0.300 Chirality : 0.044 0.226 4818 Planarity : 0.004 0.043 5099 Dihedral : 16.637 120.657 5149 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.55 % Allowed : 18.12 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 1.34 (0.14), residues: 3513 helix: 1.87 (0.13), residues: 1499 sheet: 0.78 (0.25), residues: 421 loop : 0.05 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 18 TYR 0.022 0.002 TYR C 73 PHE 0.022 0.002 PHE C 514 TRP 0.006 0.001 TRP D 868 HIS 0.006 0.001 HIS F 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.22 (30872) covalent geometry : angle 0.55864 / 0.30 (42155) hydrogen bonds : bond 0.04791 / 3.26 ( 1445) hydrogen bonds : angle 4.25652 / 2.98 ( 4019) metal coordination : bond 0.00740 / 0.40 ( 8) metal coordination : angle 4.00831 / 2.35 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 703 time to evaluate : 1.118 Fit side-chains revert: symmetry clash REVERT: C 349 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7935 (mp0) REVERT: C 1038 GLN cc_start: 0.8545 (pt0) cc_final: 0.8310 (pt0) REVERT: D 95 THR cc_start: 0.8222 (m) cc_final: 0.7961 (p) REVERT: D 200 GLN cc_start: 0.8052 (tm-30) cc_final: 0.7581 (tm-30) REVERT: D 201 MET cc_start: 0.8500 (mtm) cc_final: 0.8292 (mtm) REVERT: D 399 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8193 (mttp) REVERT: D 603 ASN cc_start: 0.8386 (t0) cc_final: 0.7850 (t0) REVERT: D 607 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7533 (mp0) REVERT: D 680 ASN cc_start: 0.8310 (m110) cc_final: 0.7838 (m-40) REVERT: D 684 ASP cc_start: 0.7747 (m-30) cc_final: 0.7491 (m-30) REVERT: D 1174 ARG cc_start: 0.7302 (mtm-85) cc_final: 0.6981 (mtm-85) REVERT: F 101 ARG cc_start: 0.8307 (ttm110) cc_final: 0.8091 (ttm-80) REVERT: F 353 GLN cc_start: 0.4403 (OUTLIER) cc_final: 0.3954 (tp40) REVERT: F 411 ASP cc_start: 0.8306 (m-30) cc_final: 0.7924 (m-30) REVERT: F 603 LEU cc_start: 0.7673 (mm) cc_final: 0.7433 (mt) REVERT: G 254 LEU cc_start: 0.8177 (mt) cc_final: 0.7943 (mt) outliers start: 47 outliers final: 36 residues processed: 718 average time/residue: 0.8206 time to fit residues: 673.3245 Evaluate side-chains 735 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 696 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1197 MET Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 222 LYS Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 399 LYS Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 607 GLU Chi-restraints excluded: chain D residue 837 GLU Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 1192 HIS Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain F residue 296 MET Chi-restraints excluded: chain F residue 353 GLN Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 510 LYS Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 591 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 183 optimal weight: 0.8980 chunk 322 optimal weight: 4.9990 chunk 271 optimal weight: 1.9990 chunk 358 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 199 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 chunk 287 optimal weight: 0.0370 chunk 212 optimal weight: 0.0870 chunk 218 optimal weight: 0.8980 chunk 257 optimal weight: 0.8980 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 519 ASN D 700 ASN D 713 GLN D 861 ASN D 875 ASN D 910 ASN B 84 ASN F 454 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.139447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.107578 restraints weight = 58504.887| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.06 r_work: 0.3229 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30880 Z= 0.119 Angle : 0.518 11.738 42167 Z= 0.278 Chirality : 0.040 0.224 4818 Planarity : 0.004 0.045 5099 Dihedral : 16.611 122.501 5149 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.22 % Allowed : 18.48 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 1.46 (0.14), residues: 3513 helix: 1.99 (0.14), residues: 1494 sheet: 0.70 (0.24), residues: 445 loop : 0.12 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 18 TYR 0.019 0.001 TYR D 631 PHE 0.019 0.001 PHE C 545 TRP 0.006 0.001 TRP F 442 HIS 0.003 0.000 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (30872) covalent geometry : angle 0.51444 / 0.28 (42155) hydrogen bonds : bond 0.04067 / 2.78 ( 1445) hydrogen bonds : angle 4.16025 / 2.90 ( 4019) metal coordination : bond 0.00563 / 0.30 ( 8) metal coordination : angle 3.65951 / 2.10 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 700 time to evaluate : 1.140 Fit side-chains REVERT: C 349 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7946 (mp0) REVERT: C 1297 VAL cc_start: 0.8345 (t) cc_final: 0.8073 (m) REVERT: D 95 THR cc_start: 0.8241 (m) cc_final: 0.7965 (p) REVERT: D 200 GLN cc_start: 0.8062 (tm-30) cc_final: 0.7559 (tm-30) REVERT: D 201 MET cc_start: 0.8519 (mtm) cc_final: 0.8304 (mtm) REVERT: D 399 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8205 (mttp) REVERT: D 680 ASN cc_start: 0.8208 (m110) cc_final: 0.7681 (m-40) REVERT: D 684 ASP cc_start: 0.7727 (m-30) cc_final: 0.7467 (m-30) REVERT: D 1174 ARG cc_start: 0.7303 (mtm-85) cc_final: 0.6958 (mtm-85) REVERT: F 101 ARG cc_start: 0.8353 (ttm110) cc_final: 0.8121 (ttm-80) REVERT: F 353 GLN cc_start: 0.4364 (OUTLIER) cc_final: 0.3530 (tp40) REVERT: F 356 GLU cc_start: 0.6533 (OUTLIER) cc_final: 0.5978 (pm20) REVERT: F 411 ASP cc_start: 0.8304 (m-30) cc_final: 0.7905 (m-30) REVERT: F 603 LEU cc_start: 0.7662 (mm) cc_final: 0.7406 (mt) REVERT: G 254 LEU cc_start: 0.8169 (mt) cc_final: 0.7927 (mt) outliers start: 37 outliers final: 31 residues processed: 713 average time/residue: 0.8032 time to fit residues: 653.3482 Evaluate side-chains 729 residues out of total 3021 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 695 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 399 LYS Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 1192 HIS Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 149 ARG Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain F residue 296 MET Chi-restraints excluded: chain F residue 353 GLN Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 510 LYS Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 591 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 183 optimal weight: 2.9990 chunk 341 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 222 optimal weight: 0.0050 chunk 253 optimal weight: 3.9990 chunk 229 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 304 optimal weight: 6.9990 chunk 295 optimal weight: 4.9990 chunk 197 optimal weight: 0.0770 chunk 358 optimal weight: 5.9990 overall best weight: 0.8954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 677 ASN C1038 GLN D 603 ASN D 700 ASN D 713 GLN D 861 ASN D 875 ASN D 910 ASN D 929 GLN B 84 ASN F 454 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.138800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.106287 restraints weight = 62307.274| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.20 r_work: 0.3207 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3041 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30880 Z= 0.149 Angle : 0.527 11.568 42167 Z= 0.282 Chirality : 0.041 0.225 4818 Planarity : 0.004 0.042 5099 Dihedral : 16.597 121.701 5149 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.22 % Allowed : 18.48 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 1.42 (0.14), residues: 3513 helix: 1.97 (0.14), residues: 1493 sheet: 0.72 (0.25), residues: 428 loop : 0.09 (0.15), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 18 TYR 0.021 0.001 TYR C 73 PHE 0.019 0.001 PHE C 545 TRP 0.005 0.001 TRP D 868 HIS 0.004 0.001 HIS F 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (30872) covalent geometry : angle 0.52361 / 0.28 (42155) hydrogen bonds : bond 0.04236 / 2.89 ( 1445) hydrogen bonds : angle 4.16524 / 2.91 ( 4019) metal coordination : bond 0.00580 / 0.31 ( 8) metal coordination : angle 3.71192 / 2.16 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18297.92 seconds wall clock time: 309 minutes 51.24 seconds (18591.24 seconds total)