Starting phenix.real_space_refine on Sun Jul 5 05:34:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ypb_33998/07_2026/7ypb_33998.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ypb_33998/07_2026/7ypb_33998.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7ypb_33998/07_2026/7ypb_33998.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ypb_33998/07_2026/7ypb_33998.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ypb_33998/07_2026/7ypb_33998.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ypb_33998/07_2026/7ypb_33998.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ypb_33998/07_2026/7ypb_33998.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ypb_33998/07_2026/7ypb_33998.map" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 55 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 15895 2.51 5 N 4529 2.21 5 O 5038 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 136 residue(s): 0.02s 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: 25626 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1692 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1699 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 212} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 10195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1292, 10195 Classifications: {'peptide': 1292} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 1237} Chain breaks: 2 Chain: "D" Number of atoms: 10273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1321, 10273 Classifications: {'peptide': 1321} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1265} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 631 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "F" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 502 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "G" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 417 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 106 Classifications: {'RNA': 5} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 3} Link IDs: {'rna3p': 4} Chain: "I" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 108 Classifications: {'RNA': 5} Modifications used: {'rna3p_pur': 3, 'rna3p_pyr': 2} Link IDs: {'rna3p': 4} 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 14031 SG CYS D 70 61.205 23.424 49.526 1.00 60.53 S ATOM 14153 SG CYS D 85 65.074 20.630 48.803 1.00 57.91 S ATOM 20430 SG CYS D 888 84.694 44.497 108.295 1.00 26.18 S ATOM 20481 SG CYS D 895 81.226 44.496 110.729 1.00 21.09 S ATOM 20502 SG CYS D 898 83.980 46.903 111.006 1.00 22.31 S Time building chain proxies: 4.64, per 1000 atoms: 0.18 Number of scatterers: 25626 At special positions: 0 Unit cell: (160.6, 134.2, 165, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 106 16.00 P 55 15.00 Mg 1 11.99 O 5038 8.00 N 4529 7.00 C 15895 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: 2.18 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5784 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 41 sheets defined 34.5% alpha, 15.1% beta 22 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 2.58 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.969A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.803A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.706A pdb=" N ASP A 114 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE A 115 " --> pdb=" O ALA A 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 111 through 115' Processing helix chain 'A' and resid 212 through 228 Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'B' and resid 34 through 50 removed outlier: 4.366A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA B 42 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER B 49 " --> pdb=" O ARG B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 111 through 115 removed outlier: 3.645A pdb=" N ASP B 114 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE B 115 " --> pdb=" O ALA B 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 111 through 115' Processing helix chain 'B' and resid 212 through 227 Processing helix chain 'C' and resid 28 through 40 removed outlier: 4.588A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 55 removed outlier: 3.695A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.699A pdb=" N CYS C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN C 86 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE C 87 " --> pdb=" O GLN C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 217 through 225 removed outlier: 3.728A pdb=" N LEU C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASP C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N LEU C 223 " --> pdb=" O GLN C 219 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 288 through 292 removed outlier: 3.835A pdb=" N TYR C 291 " --> pdb=" O PRO C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 removed outlier: 3.700A pdb=" N GLY C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 351 removed outlier: 3.507A pdb=" N GLU C 349 " --> pdb=" O PRO C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 378 through 390 removed outlier: 4.355A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 408 Processing helix chain 'C' and resid 421 through 438 removed outlier: 4.400A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE C 426 " --> pdb=" O LYS C 422 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP C 434 " --> pdb=" O LYS C 430 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE C 435 " --> pdb=" O LYS C 431 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG C 436 " --> pdb=" O LEU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 480 removed outlier: 3.586A pdb=" N GLU C 461 " --> pdb=" O GLY C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 506 Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 544 through 549 removed outlier: 3.839A pdb=" N ARG C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 removed outlier: 3.586A pdb=" N HIS C 673 " --> pdb=" O PHE C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 687 removed outlier: 3.575A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 removed outlier: 3.603A pdb=" N SER C 712 " --> pdb=" O VAL C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 825 removed outlier: 4.164A pdb=" N VAL C 823 " --> pdb=" O SER C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 860 through 865 removed outlier: 3.949A pdb=" N LYS C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 865 " --> pdb=" O ALA C 861 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 860 through 865' Processing helix chain 'C' and resid 944 through 979 removed outlier: 3.645A pdb=" N ILE C 948 " --> pdb=" O ARG C 944 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE C 966 " --> pdb=" O GLU C 962 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LEU C 967 " --> pdb=" O GLU C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 1006 through 1037 Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 3.874A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1130 removed outlier: 3.625A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1149 Processing helix chain 'C' and resid 1160 through 1164 removed outlier: 3.828A pdb=" N THR C1163 " --> pdb=" O ASP C1160 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1176 removed outlier: 4.024A pdb=" N MET C1170 " --> pdb=" O ASP C1166 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG C1171 " --> pdb=" O GLU C1167 " (cutoff:3.500A) Processing helix chain 'C' and resid 1191 through 1202 removed outlier: 3.535A pdb=" N ILE C1195 " --> pdb=" O LYS C1191 " (cutoff:3.500A) Processing helix chain 'C' and resid 1238 through 1242 Processing helix chain 'C' and resid 1271 through 1281 removed outlier: 3.609A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1292 removed outlier: 3.768A pdb=" N LEU C1291 " --> pdb=" O LEU C1287 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR C1292 " --> pdb=" O GLN C1288 " (cutoff:3.500A) Processing helix chain 'C' and resid 1299 through 1311 removed outlier: 3.837A pdb=" N LYS C1303 " --> pdb=" O ASN C1299 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1331 removed outlier: 3.583A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 removed outlier: 3.557A pdb=" N SER D 34 " --> pdb=" O ILE D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 81 removed outlier: 3.550A pdb=" N ARG D 81 " --> pdb=" O LEU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 100 removed outlier: 3.618A pdb=" N GLU D 100 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.551A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 172 removed outlier: 4.497A pdb=" N ASP D 167 " --> pdb=" O GLU D 163 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE D 172 " --> pdb=" O ALA D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 192 removed outlier: 3.932A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 204 Processing helix chain 'D' and resid 205 through 207 No H-bonds generated for 'chain 'D' and resid 205 through 207' Processing helix chain 'D' and resid 210 through 230 Processing helix chain 'D' and resid 233 through 238 removed outlier: 3.743A pdb=" N MET D 237 " --> pdb=" O PRO D 234 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE D 238 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 284 removed outlier: 3.682A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 370 through 376 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 402 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 removed outlier: 3.512A pdb=" N LEU D 508 " --> pdb=" O GLN D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 540 Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.970A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 removed outlier: 4.019A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 removed outlier: 4.180A pdb=" N ILE D 601 " --> pdb=" O GLY D 597 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER D 602 " --> pdb=" O LYS D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.552A pdb=" N VAL D 618 " --> pdb=" O LEU D 614 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE D 619 " --> pdb=" O LYS D 615 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP D 622 " --> pdb=" O VAL D 618 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA D 633 " --> pdb=" O PHE D 629 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG D 634 " --> pdb=" O ALA D 630 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 671 removed outlier: 3.510A pdb=" N ILE D 653 " --> pdb=" O LYS D 649 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY D 671 " --> pdb=" O GLN D 667 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 removed outlier: 4.105A pdb=" N ASN D 680 " --> pdb=" O GLY D 676 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 741 removed outlier: 3.719A pdb=" N ILE D 737 " --> pdb=" O SER D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 772 through 802 removed outlier: 3.668A pdb=" N THR D 776 " --> pdb=" O TYR D 772 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASP D 802 " --> pdb=" O ARG D 798 " (cutoff:3.500A) Processing helix chain 'D' and resid 867 through 876 removed outlier: 3.741A pdb=" N LEU D 871 " --> pdb=" O GLN D 867 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.913A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1147 Processing helix chain 'D' and resid 1216 through 1224 removed outlier: 3.825A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU D1221 " --> pdb=" O PRO D1217 " (cutoff:3.500A) Processing helix chain 'D' and resid 1228 through 1245 removed outlier: 3.967A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1261 removed outlier: 3.882A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1294 removed outlier: 3.673A pdb=" N ARG D1290 " --> pdb=" O LYS D1286 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLU D1291 " --> pdb=" O ILE D1287 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU D1292 " --> pdb=" O ALA D1288 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA D1294 " --> pdb=" O ARG D1290 " (cutoff:3.500A) Processing helix chain 'D' and resid 1310 through 1315 Processing helix chain 'D' and resid 1328 through 1339 Processing helix chain 'D' and resid 1347 through 1354 removed outlier: 3.706A pdb=" N VAL D1351 " --> pdb=" O LEU D1347 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE D1352 " --> pdb=" O LYS D1348 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL D1353 " --> pdb=" O GLU D1349 " (cutoff:3.500A) Processing helix chain 'D' and resid 1359 through 1373 Processing helix chain 'E' and resid 7 through 13 Processing helix chain 'E' and resid 17 through 30 removed outlier: 3.631A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN E 29 " --> pdb=" O ARG E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 removed outlier: 3.532A pdb=" N GLU E 55 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY E 57 " --> pdb=" O GLU E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 81 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 17 removed outlier: 5.370A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ARG A 182 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 105 removed outlier: 3.689A pdb=" N MET A 142 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LYS A 104 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE A 140 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 110 removed outlier: 3.860A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 153 removed outlier: 3.896A pdb=" N VAL A 153 " --> pdb=" O ALA A 175 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA A 175 " --> pdb=" O VAL A 153 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 23 through 31 removed outlier: 6.636A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 104 removed outlier: 4.005A pdb=" N GLU B 58 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 91 removed outlier: 3.807A pdb=" N ARG B 91 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU B 122 " --> pdb=" O ARG B 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.628A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 59 through 60 removed outlier: 4.094A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU C 68 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET C 124 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU C 100 " --> pdb=" O GLN C 120 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN C 120 " --> pdb=" O LEU C 100 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 136 through 137 removed outlier: 3.818A pdb=" N GLN C 513 " --> pdb=" O VAL C 144 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 451 through 454 removed outlier: 3.613A pdb=" N SER C 531 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 154 through 160 removed outlier: 3.684A pdb=" N LEU C 171 " --> pdb=" O ASP C 160 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TYR C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 228 through 230 Processing sheet with id=AB6, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.995A pdb=" N ALA C 257 " --> pdb=" O VAL C 261 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N VAL C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 580 through 581 removed outlier: 6.892A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS C 593 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AB9, first strand: chain 'C' and resid 616 through 617 Processing sheet with id=AC1, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.628A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 749 through 752 removed outlier: 5.985A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC4, first strand: chain 'C' and resid 817 through 818 removed outlier: 8.701A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET C 800 " --> pdb=" O MET C1230 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 817 through 818 removed outlier: 8.701A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET C 800 " --> pdb=" O MET C1230 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE C1210 " --> pdb=" O VAL C1225 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.602A pdb=" N SER C 840 " --> pdb=" O LYS C1048 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 882 through 884 removed outlier: 3.671A pdb=" N VAL C 884 " --> pdb=" O LEU C 918 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 887 through 888 removed outlier: 3.673A pdb=" N LYS C 914 " --> pdb=" O THR C 888 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 6.869A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1269 through 1270 Processing sheet with id=AD2, first strand: chain 'C' and resid 1335 through 1340 Processing sheet with id=AD3, first strand: chain 'D' and resid 104 through 111 removed outlier: 6.671A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 144 through 145 removed outlier: 3.784A pdb=" N LEU D 160 " --> pdb=" O TYR D 144 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 547 through 556 removed outlier: 3.807A pdb=" N VAL D 550 " --> pdb=" O LYS D 570 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS D 570 " --> pdb=" O VAL D 550 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 706 through 708 Processing sheet with id=AD7, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AD8, first strand: chain 'D' and resid 949 through 951 removed outlier: 6.591A pdb=" N ILE D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN D1019 " --> pdb=" O VAL D1002 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL D1002 " --> pdb=" O ASN D1019 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 957 through 961 removed outlier: 3.527A pdb=" N SER D 961 " --> pdb=" O GLU D 981 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 966 through 967 Processing sheet with id=AE2, first strand: chain 'D' and resid 1077 through 1081 removed outlier: 3.942A pdb=" N GLY D1033 " --> pdb=" O ILE D1115 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1046 through 1049 removed outlier: 4.131A pdb=" N GLN D1049 " --> pdb=" O SER D1058 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N SER D1058 " --> pdb=" O GLN D1049 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA D1105 " --> pdb=" O VAL D1061 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1162 through 1165 removed outlier: 3.835A pdb=" N LEU D1175 " --> pdb=" O GLU D1188 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU D1188 " --> pdb=" O LEU D1175 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 6.717A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) 874 hydrogen bonds defined for protein. 2469 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 59 hydrogen bonds 118 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 6.01 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7988 1.34 - 1.46: 3735 1.46 - 1.57: 14100 1.57 - 1.69: 105 1.69 - 1.81: 184 Bond restraints: 26112 Sorted by residual: bond pdb=" C3' DC G -7 " pdb=" O3' DC G -7 " ideal model delta sigma weight residual 1.435 1.487 -0.052 1.30e-02 5.92e+03 1.58e+01 bond pdb=" C3' DC F 3 " pdb=" C2' DC F 3 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.50e+00 bond pdb=" C3' DC F 13 " pdb=" C2' DC F 13 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.13e+00 bond pdb=" C3' DC G -7 " pdb=" C2' DC G -7 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.75e+00 bond pdb=" C1' DT F -3 " pdb=" N1 DT F -3 " ideal model delta sigma weight residual 1.468 1.504 -0.036 1.40e-02 5.10e+03 6.43e+00 ... (remaining 26107 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 35195 2.57 - 5.14: 262 5.14 - 7.72: 25 7.72 - 10.29: 9 10.29 - 12.86: 1 Bond angle restraints: 35492 Sorted by residual: angle pdb=" N3 DT G -2 " pdb=" C4 DT G -2 " pdb=" O4 DT G -2 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT F 10 " pdb=" C4 DT F 10 " pdb=" O4 DT F 10 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT F -3 " pdb=" C4 DT F -3 " pdb=" O4 DT F -3 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT F 0 " pdb=" C4 DT F 0 " pdb=" O4 DT F 0 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 angle pdb=" N3 DT F -6 " pdb=" C4 DT F -6 " pdb=" O4 DT F -6 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 ... (remaining 35487 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 15548 36.00 - 71.99: 345 71.99 - 107.99: 22 107.99 - 143.99: 0 143.99 - 179.98: 1 Dihedral angle restraints: 15916 sinusoidal: 6927 harmonic: 8989 Sorted by residual: dihedral pdb=" C4' DC G -7 " pdb=" C3' DC G -7 " pdb=" O3' DC G -7 " pdb=" P DG G -6 " ideal model delta sinusoidal sigma weight residual 220.00 40.02 179.98 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA LEU C 237 " pdb=" C LEU C 237 " pdb=" N GLN C 238 " pdb=" CA GLN C 238 " ideal model delta harmonic sigma weight residual 180.00 -161.84 -18.16 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA ALA D 426 " pdb=" C ALA D 426 " pdb=" N PRO D 427 " pdb=" CA PRO D 427 " ideal model delta harmonic sigma weight residual 180.00 163.12 16.88 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 15913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 3168 0.049 - 0.098: 671 0.098 - 0.147: 198 0.147 - 0.196: 23 0.196 - 0.245: 4 Chirality restraints: 4064 Sorted by residual: chirality pdb=" CB ILE C1076 " pdb=" CA ILE C1076 " pdb=" CG1 ILE C1076 " pdb=" CG2 ILE C1076 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CB VAL D1027 " pdb=" CA VAL D1027 " pdb=" CG1 VAL D1027 " pdb=" CG2 VAL D1027 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CB ILE C 850 " pdb=" CA ILE C 850 " pdb=" CG1 ILE C 850 " pdb=" CG2 ILE C 850 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 4061 not shown) Planarity restraints: 4454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP C 485 " 0.011 2.00e-02 2.50e+03 2.34e-02 5.50e+00 pdb=" CG ASP C 485 " -0.041 2.00e-02 2.50e+03 pdb=" OD1 ASP C 485 " 0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP C 485 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS C 551 " 0.036 5.00e-02 4.00e+02 5.49e-02 4.82e+00 pdb=" N PRO C 552 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 552 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 552 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D1138 " -0.034 5.00e-02 4.00e+02 5.10e-02 4.17e+00 pdb=" N PRO D1139 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO D1139 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D1139 " -0.029 5.00e-02 4.00e+02 ... (remaining 4451 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1161 2.73 - 3.27: 22084 3.27 - 3.81: 39391 3.81 - 4.36: 46723 4.36 - 4.90: 80617 Nonbonded interactions: 189976 Sorted by model distance: nonbonded pdb=" OD1 ASP D 464 " pdb="MG MG D1503 " model vdw 2.184 2.170 nonbonded pdb=" OD2 ASP D 464 " pdb="MG MG D1503 " model vdw 2.241 2.170 nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1503 " model vdw 2.278 2.170 nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1503 " model vdw 2.324 2.170 nonbonded pdb=" O GLY D 613 " pdb=" OG1 THR D 617 " model vdw 2.326 3.040 ... (remaining 189971 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 7 through 158 or resid 168 through 205 or (resid 206 and ( \ name N or name CA or name C or name O or name CB )) or resid 207 through 233)) selection = (chain 'B' and (resid 7 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 26.660 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 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 0.402 26117 Z= 0.236 Angle : 0.586 12.862 35492 Z= 0.360 Chirality : 0.045 0.245 4064 Planarity : 0.005 0.055 4454 Dihedral : 14.015 179.982 10132 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.04 % Allowed : 5.25 % Favored : 94.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % 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: -4.01 (0.11), residues: 3107 helix: -3.01 (0.10), residues: 991 sheet: -1.19 (0.26), residues: 373 loop : -2.86 (0.11), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 3 TYR 0.010 0.001 TYR C 62 PHE 0.032 0.001 PHE C1025 TRP 0.008 0.001 TRP D1193 HIS 0.003 0.000 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.19 (26112) covalent geometry : angle 0.58608 / 0.36 (35492) hydrogen bonds : bond 0.18926 / 12.97 ( 923) hydrogen bonds : angle 6.97293 / 4.79 ( 2587) metal coordination : bond 0.30672 / 16.62 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 533 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 129 VAL cc_start: 0.7292 (m) cc_final: 0.7069 (p) REVERT: C 46 GLN cc_start: 0.5720 (tt0) cc_final: 0.5511 (tm-30) REVERT: C 1053 TYR cc_start: 0.8606 (m-80) cc_final: 0.8323 (m-80) REVERT: C 1140 LYS cc_start: 0.7203 (ttpt) cc_final: 0.6815 (ptmt) REVERT: C 1231 TYR cc_start: 0.9047 (t80) cc_final: 0.8743 (t80) REVERT: C 1290 MET cc_start: 0.8437 (tpp) cc_final: 0.8196 (mmt) REVERT: C 1292 THR cc_start: 0.8519 (p) cc_final: 0.8095 (p) REVERT: D 460 ASP cc_start: 0.8337 (p0) cc_final: 0.8105 (p0) REVERT: D 484 MET cc_start: 0.9340 (mtp) cc_final: 0.9049 (mtm) REVERT: D 716 GLN cc_start: 0.8018 (pt0) cc_final: 0.7748 (pt0) outliers start: 1 outliers final: 1 residues processed: 534 average time/residue: 0.2110 time to fit residues: 166.3438 Evaluate side-chains 312 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 311 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.0470 chunk 298 optimal weight: 6.9990 overall best weight: 1.2882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN A 75 GLN A 147 GLN B 23 HIS C 31 GLN C 36 GLN C 133 ASN C 219 GLN C 258 ASN C 330 HIS C 463 GLN C 519 ASN C 620 ASN C 808 ASN ** C 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1008 GLN D 164 GLN D 232 ASN D 266 ASN D 277 ASN D 294 ASN D 335 GLN D 419 HIS D 489 ASN D 560 ASN D 669 GLN D 861 ASN D 865 HIS D 875 ASN D1084 GLN D1235 ASN D1279 GLN E 29 GLN E 73 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.206057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.173441 restraints weight = 32648.848| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.66 r_work: 0.3529 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26117 Z= 0.145 Angle : 0.517 9.946 35492 Z= 0.271 Chirality : 0.042 0.195 4064 Planarity : 0.004 0.064 4454 Dihedral : 12.222 177.151 4017 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.35 % Allowed : 10.62 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % 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: -2.40 (0.13), residues: 3107 helix: -0.62 (0.15), residues: 994 sheet: -0.66 (0.26), residues: 362 loop : -2.49 (0.12), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 542 TYR 0.012 0.001 TYR D 795 PHE 0.011 0.001 PHE D 338 TRP 0.006 0.001 TRP C 183 HIS 0.010 0.001 HIS D 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (26112) covalent geometry : angle 0.51699 / 0.27 (35492) hydrogen bonds : bond 0.03664 / 2.48 ( 923) hydrogen bonds : angle 4.74655 / 3.22 ( 2587) metal coordination : bond 0.01285 / 0.71 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 337 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: A 23 HIS cc_start: 0.7441 (p-80) cc_final: 0.7120 (p-80) REVERT: A 51 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7797 (mmt) REVERT: A 97 GLU cc_start: 0.7301 (mm-30) cc_final: 0.7014 (mm-30) REVERT: A 205 MET cc_start: 0.8314 (ptm) cc_final: 0.7990 (ptm) REVERT: B 129 VAL cc_start: 0.7464 (m) cc_final: 0.7243 (p) REVERT: C 546 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7127 (mp0) REVERT: C 1231 TYR cc_start: 0.8945 (t80) cc_final: 0.8741 (t80) REVERT: C 1290 MET cc_start: 0.8882 (tpp) cc_final: 0.8393 (mmt) REVERT: D 148 GLU cc_start: 0.5026 (tm-30) cc_final: 0.4127 (mm-30) REVERT: D 322 ARG cc_start: 0.7078 (ptp90) cc_final: 0.6696 (ptt180) REVERT: D 348 ASP cc_start: 0.8778 (m-30) cc_final: 0.8422 (m-30) REVERT: D 484 MET cc_start: 0.9365 (mtp) cc_final: 0.8992 (mtm) REVERT: D 992 LYS cc_start: 0.4378 (mttt) cc_final: 0.3947 (mmmm) outliers start: 36 outliers final: 22 residues processed: 357 average time/residue: 0.1743 time to fit residues: 99.4114 Evaluate side-chains 311 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 288 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 573 ASN Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 1064 ASP Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 1209 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 32 optimal weight: 0.0570 chunk 122 optimal weight: 5.9990 chunk 309 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 161 optimal weight: 0.5980 chunk 106 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 273 optimal weight: 8.9990 chunk 116 optimal weight: 1.9990 chunk 210 optimal weight: 5.9990 overall best weight: 0.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 186 ASN C 620 ASN ** C 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN D 777 HIS E 29 GLN E 31 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.204434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.171894 restraints weight = 32673.837| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.82 r_work: 0.3482 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 26117 Z= 0.103 Angle : 0.458 9.680 35492 Z= 0.240 Chirality : 0.040 0.229 4064 Planarity : 0.003 0.055 4454 Dihedral : 12.213 176.372 4017 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.50 % Allowed : 12.19 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % 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: -1.60 (0.14), residues: 3107 helix: 0.38 (0.16), residues: 1004 sheet: -0.46 (0.26), residues: 377 loop : -2.18 (0.13), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D1341 TYR 0.012 0.001 TYR D 795 PHE 0.013 0.001 PHE C 385 TRP 0.004 0.001 TRP D 236 HIS 0.005 0.001 HIS B 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (26112) covalent geometry : angle 0.45838 / 0.24 (35492) hydrogen bonds : bond 0.03227 / 2.16 ( 923) hydrogen bonds : angle 4.23170 / 2.88 ( 2587) metal coordination : bond 0.00471 / 0.24 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 318 time to evaluate : 0.875 Fit side-chains REVERT: A 23 HIS cc_start: 0.7646 (p-80) cc_final: 0.7233 (p-80) REVERT: A 97 GLU cc_start: 0.7195 (mm-30) cc_final: 0.6956 (mm-30) REVERT: A 123 ILE cc_start: 0.8326 (mm) cc_final: 0.8113 (mm) REVERT: A 205 MET cc_start: 0.8334 (ptm) cc_final: 0.8049 (ptm) REVERT: B 120 ASP cc_start: 0.6915 (p0) cc_final: 0.6701 (p0) REVERT: C 3 TYR cc_start: 0.7427 (m-80) cc_final: 0.7177 (m-80) REVERT: C 546 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7208 (mp0) REVERT: C 550 VAL cc_start: 0.5794 (OUTLIER) cc_final: 0.5543 (p) REVERT: C 1231 TYR cc_start: 0.8885 (t80) cc_final: 0.8645 (t80) REVERT: C 1299 ASN cc_start: 0.7414 (p0) cc_final: 0.7195 (p0) REVERT: D 140 TYR cc_start: 0.5970 (m-10) cc_final: 0.4596 (m-80) REVERT: D 148 GLU cc_start: 0.5205 (tm-30) cc_final: 0.4214 (mm-30) REVERT: D 301 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7309 (mm-30) REVERT: D 322 ARG cc_start: 0.7062 (ptp90) cc_final: 0.6718 (ptt180) REVERT: D 340 GLN cc_start: 0.8401 (tt0) cc_final: 0.8142 (mm-40) REVERT: D 348 ASP cc_start: 0.8957 (m-30) cc_final: 0.8692 (m-30) REVERT: D 861 ASN cc_start: 0.6901 (m-40) cc_final: 0.5425 (p0) REVERT: D 992 LYS cc_start: 0.4699 (mttt) cc_final: 0.4231 (mmmm) outliers start: 40 outliers final: 26 residues processed: 340 average time/residue: 0.1687 time to fit residues: 92.6070 Evaluate side-chains 307 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 280 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 1064 ASP Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 248 ASP Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 774 ILE Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 46 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 58 optimal weight: 2.9990 chunk 11 optimal weight: 0.0970 chunk 197 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 292 optimal weight: 3.9990 chunk 271 optimal weight: 9.9990 chunk 280 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 83 GLN C 618 GLN C 620 ASN C 834 GLN C1256 GLN D 335 GLN D 489 ASN D1279 GLN E 31 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.196236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.163271 restraints weight = 32158.065| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.99 r_work: 0.3279 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 26117 Z= 0.151 Angle : 0.517 11.096 35492 Z= 0.271 Chirality : 0.042 0.221 4064 Planarity : 0.004 0.053 4454 Dihedral : 12.295 175.903 4017 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.10 % Allowed : 13.73 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % 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: -1.20 (0.14), residues: 3107 helix: 0.72 (0.17), residues: 1027 sheet: -0.23 (0.26), residues: 395 loop : -2.01 (0.13), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 838 TYR 0.014 0.001 TYR A 185 PHE 0.015 0.001 PHE D 620 TRP 0.009 0.001 TRP C 183 HIS 0.010 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (26112) covalent geometry : angle 0.51748 / 0.27 (35492) hydrogen bonds : bond 0.03565 / 2.40 ( 923) hydrogen bonds : angle 4.07009 / 2.77 ( 2587) metal coordination : bond 0.01001 / 0.50 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 297 time to evaluate : 0.943 Fit side-chains REVERT: A 51 MET cc_start: 0.8496 (mmt) cc_final: 0.8278 (mmp) REVERT: A 205 MET cc_start: 0.8399 (ptm) cc_final: 0.8107 (ptm) REVERT: B 60 GLU cc_start: 0.5957 (mp0) cc_final: 0.5689 (mp0) REVERT: B 129 VAL cc_start: 0.7571 (m) cc_final: 0.7364 (p) REVERT: C 546 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7309 (mp0) REVERT: C 964 LEU cc_start: 0.3654 (pp) cc_final: 0.2974 (mp) REVERT: C 1158 LYS cc_start: 0.8234 (mttp) cc_final: 0.7801 (mttt) REVERT: C 1297 ASP cc_start: 0.8164 (m-30) cc_final: 0.7929 (m-30) REVERT: C 1299 ASN cc_start: 0.7755 (p0) cc_final: 0.7548 (p0) REVERT: D 140 TYR cc_start: 0.6207 (m-10) cc_final: 0.4787 (m-80) REVERT: D 148 GLU cc_start: 0.5163 (tm-30) cc_final: 0.4835 (tm-30) REVERT: D 322 ARG cc_start: 0.7214 (ptp90) cc_final: 0.6898 (ptt180) REVERT: D 341 ASN cc_start: 0.8521 (m-40) cc_final: 0.8299 (m110) REVERT: D 992 LYS cc_start: 0.5043 (mttt) cc_final: 0.4496 (mmmm) outliers start: 56 outliers final: 38 residues processed: 335 average time/residue: 0.1506 time to fit residues: 83.2690 Evaluate side-chains 315 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 277 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 1064 ASP Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 46 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 222 optimal weight: 0.6980 chunk 65 optimal weight: 8.9990 chunk 23 optimal weight: 0.6980 chunk 305 optimal weight: 5.9990 chunk 256 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 134 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 299 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 295 optimal weight: 7.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 186 ASN C 69 GLN C 620 ASN D 94 GLN D 335 GLN D 777 HIS E 29 GLN E 31 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.191323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.157527 restraints weight = 32194.764| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 3.23 r_work: 0.3293 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26117 Z= 0.173 Angle : 0.535 11.857 35492 Z= 0.280 Chirality : 0.043 0.225 4064 Planarity : 0.004 0.051 4454 Dihedral : 12.344 174.663 4017 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.18 % Allowed : 15.00 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % 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: -1.06 (0.14), residues: 3107 helix: 0.79 (0.17), residues: 1023 sheet: -0.11 (0.26), residues: 370 loop : -1.87 (0.13), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 919 TYR 0.017 0.001 TYR C1281 PHE 0.014 0.002 PHE D 620 TRP 0.007 0.001 TRP D1020 HIS 0.008 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (26112) covalent geometry : angle 0.53508 / 0.28 (35492) hydrogen bonds : bond 0.03784 / 2.53 ( 923) hydrogen bonds : angle 4.09765 / 2.79 ( 2587) metal coordination : bond 0.00365 / 0.20 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 286 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: A 51 MET cc_start: 0.8682 (mmt) cc_final: 0.8472 (mmp) REVERT: A 97 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7759 (mm-30) REVERT: A 205 MET cc_start: 0.8377 (ptm) cc_final: 0.8080 (ptm) REVERT: B 60 GLU cc_start: 0.5932 (mp0) cc_final: 0.5669 (mp0) REVERT: B 129 VAL cc_start: 0.7644 (m) cc_final: 0.7444 (p) REVERT: C 546 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7243 (mp0) REVERT: C 1299 ASN cc_start: 0.8189 (p0) cc_final: 0.7935 (p0) REVERT: D 148 GLU cc_start: 0.5171 (tm-30) cc_final: 0.4598 (tm-30) REVERT: D 301 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7271 (mm-30) REVERT: D 322 ARG cc_start: 0.7447 (ptp90) cc_final: 0.7138 (ptt180) REVERT: D 341 ASN cc_start: 0.8764 (m-40) cc_final: 0.8551 (m110) REVERT: D 348 ASP cc_start: 0.9160 (m-30) cc_final: 0.8922 (m-30) REVERT: D 484 MET cc_start: 0.9407 (mtp) cc_final: 0.8964 (mtm) REVERT: D 837 ASP cc_start: 0.7304 (m-30) cc_final: 0.7081 (m-30) REVERT: D 839 VAL cc_start: 0.7425 (m) cc_final: 0.7223 (t) REVERT: D 867 GLN cc_start: 0.5462 (mp10) cc_final: 0.4596 (pp30) REVERT: D 992 LYS cc_start: 0.4835 (mttt) cc_final: 0.4298 (mmmm) outliers start: 58 outliers final: 40 residues processed: 328 average time/residue: 0.1509 time to fit residues: 80.9311 Evaluate side-chains 304 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 264 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 774 ILE Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 864 LEU Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1220 ILE Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 46 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 107 optimal weight: 1.9990 chunk 208 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 142 optimal weight: 0.8980 chunk 65 optimal weight: 0.4980 chunk 297 optimal weight: 8.9990 chunk 235 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 11 optimal weight: 0.0970 chunk 21 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN D 489 ASN D 777 HIS E 31 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.192551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.162864 restraints weight = 32266.231| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.22 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 26117 Z= 0.107 Angle : 0.466 10.754 35492 Z= 0.245 Chirality : 0.041 0.226 4064 Planarity : 0.003 0.050 4454 Dihedral : 12.304 175.015 4017 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.88 % Allowed : 16.24 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.15), residues: 3107 helix: 1.11 (0.17), residues: 1016 sheet: -0.08 (0.26), residues: 382 loop : -1.73 (0.14), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 88 TYR 0.014 0.001 TYR A 185 PHE 0.013 0.001 PHE C 337 TRP 0.009 0.001 TRP C 183 HIS 0.011 0.001 HIS A 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (26112) covalent geometry : angle 0.46605 / 0.25 (35492) hydrogen bonds : bond 0.03186 / 2.13 ( 923) hydrogen bonds : angle 3.96130 / 2.70 ( 2587) metal coordination : bond 0.00212 / 0.11 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 265 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.8387 (mmt) cc_final: 0.8163 (mmp) REVERT: A 205 MET cc_start: 0.8081 (ptm) cc_final: 0.7860 (ptm) REVERT: B 60 GLU cc_start: 0.6235 (mp0) cc_final: 0.6032 (mp0) REVERT: C 546 GLU cc_start: 0.6891 (mm-30) cc_final: 0.6690 (mp0) REVERT: C 964 LEU cc_start: 0.5147 (pp) cc_final: 0.4325 (mp) REVERT: C 1299 ASN cc_start: 0.7698 (p0) cc_final: 0.7430 (p0) REVERT: D 148 GLU cc_start: 0.5197 (tm-30) cc_final: 0.4978 (tm-30) REVERT: D 301 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6433 (mm-30) REVERT: D 341 ASN cc_start: 0.8002 (m-40) cc_final: 0.7754 (m110) REVERT: D 348 ASP cc_start: 0.8854 (m-30) cc_final: 0.8533 (m-30) REVERT: D 769 VAL cc_start: 0.9200 (OUTLIER) cc_final: 0.8898 (m) REVERT: D 867 GLN cc_start: 0.5185 (mp10) cc_final: 0.4746 (pp30) outliers start: 50 outliers final: 39 residues processed: 301 average time/residue: 0.1505 time to fit residues: 74.9640 Evaluate side-chains 294 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 254 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 864 LEU Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1059 LEU Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1298 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 62 optimal weight: 0.3980 chunk 34 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 244 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 287 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 240 optimal weight: 0.6980 chunk 85 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 150 HIS ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN D 777 HIS D 861 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.190084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.160204 restraints weight = 32113.458| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.23 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26117 Z= 0.143 Angle : 0.507 11.332 35492 Z= 0.264 Chirality : 0.042 0.228 4064 Planarity : 0.004 0.049 4454 Dihedral : 12.247 175.136 4017 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.33 % Allowed : 16.43 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.15), residues: 3107 helix: 1.08 (0.17), residues: 1025 sheet: -0.06 (0.26), residues: 388 loop : -1.64 (0.14), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 88 TYR 0.016 0.001 TYR A 185 PHE 0.016 0.001 PHE D 668 TRP 0.009 0.001 TRP C 183 HIS 0.011 0.001 HIS A 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (26112) covalent geometry : angle 0.50657 / 0.26 (35492) hydrogen bonds : bond 0.03497 / 2.34 ( 923) hydrogen bonds : angle 3.96644 / 2.70 ( 2587) metal coordination : bond 0.00290 / 0.15 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 270 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.8469 (mmt) cc_final: 0.8231 (mmp) REVERT: A 205 MET cc_start: 0.8029 (ptm) cc_final: 0.7763 (ptm) REVERT: C 1299 ASN cc_start: 0.7905 (p0) cc_final: 0.7641 (p0) REVERT: D 140 TYR cc_start: 0.6128 (m-10) cc_final: 0.5561 (m-80) REVERT: D 148 GLU cc_start: 0.5253 (tm-30) cc_final: 0.4986 (tm-30) REVERT: D 341 ASN cc_start: 0.8066 (m-40) cc_final: 0.7849 (m110) REVERT: D 348 ASP cc_start: 0.8879 (m-30) cc_final: 0.8525 (m-30) REVERT: D 769 VAL cc_start: 0.9252 (OUTLIER) cc_final: 0.9003 (m) REVERT: D 867 GLN cc_start: 0.5237 (mp10) cc_final: 0.4947 (pp30) outliers start: 62 outliers final: 46 residues processed: 316 average time/residue: 0.1469 time to fit residues: 76.3556 Evaluate side-chains 300 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 253 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 774 ILE Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 864 LEU Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1059 LEU Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1298 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 19 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 61 optimal weight: 4.9990 chunk 177 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 292 optimal weight: 4.9990 chunk 255 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 308 optimal weight: 1.9990 chunk 285 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 163 optimal weight: 0.9980 chunk 247 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN D 365 GLN D 777 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.190720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.157225 restraints weight = 32255.725| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.82 r_work: 0.3248 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26117 Z= 0.118 Angle : 0.482 10.985 35492 Z= 0.252 Chirality : 0.041 0.231 4064 Planarity : 0.003 0.054 4454 Dihedral : 12.196 174.498 4017 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.03 % Allowed : 17.10 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.15), residues: 3107 helix: 1.25 (0.17), residues: 1017 sheet: 0.04 (0.27), residues: 382 loop : -1.56 (0.14), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 88 TYR 0.026 0.001 TYR C 70 PHE 0.012 0.001 PHE D 668 TRP 0.011 0.001 TRP C 183 HIS 0.014 0.001 HIS A 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (26112) covalent geometry : angle 0.48176 / 0.25 (35492) hydrogen bonds : bond 0.03215 / 2.14 ( 923) hydrogen bonds : angle 3.90340 / 2.66 ( 2587) metal coordination : bond 0.00204 / 0.10 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 276 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.8719 (mmt) cc_final: 0.8491 (mmp) REVERT: A 205 MET cc_start: 0.8336 (ptm) cc_final: 0.8085 (ptm) REVERT: B 79 LEU cc_start: 0.7723 (mm) cc_final: 0.7506 (mt) REVERT: C 341 LEU cc_start: 0.6231 (OUTLIER) cc_final: 0.5877 (pt) REVERT: C 465 ARG cc_start: 0.8466 (tmt170) cc_final: 0.7466 (ttm170) REVERT: C 964 LEU cc_start: 0.4160 (pp) cc_final: 0.3252 (mp) REVERT: C 1016 GLU cc_start: 0.4547 (OUTLIER) cc_final: 0.4318 (pp20) REVERT: C 1299 ASN cc_start: 0.8369 (p0) cc_final: 0.8162 (p0) REVERT: C 1331 ARG cc_start: 0.8258 (mtp85) cc_final: 0.8020 (mtp85) REVERT: D 118 LYS cc_start: 0.7402 (mtpp) cc_final: 0.7034 (mtpp) REVERT: D 140 TYR cc_start: 0.6693 (m-10) cc_final: 0.5976 (m-80) REVERT: D 148 GLU cc_start: 0.5348 (tm-30) cc_final: 0.4712 (tm-30) REVERT: D 348 ASP cc_start: 0.9176 (m-30) cc_final: 0.8886 (m-30) REVERT: D 769 VAL cc_start: 0.9353 (OUTLIER) cc_final: 0.9128 (m) REVERT: D 867 GLN cc_start: 0.5738 (mp10) cc_final: 0.4844 (pp30) REVERT: D 881 LYS cc_start: 0.6487 (tttp) cc_final: 0.6222 (tptp) outliers start: 54 outliers final: 44 residues processed: 318 average time/residue: 0.1661 time to fit residues: 85.2140 Evaluate side-chains 308 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 261 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 1016 GLU Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 774 ILE Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1059 LEU Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1298 VAL Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 46 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 238 optimal weight: 9.9990 chunk 159 optimal weight: 0.7980 chunk 283 optimal weight: 9.9990 chunk 234 optimal weight: 0.7980 chunk 315 optimal weight: 30.0000 chunk 82 optimal weight: 4.9990 chunk 196 optimal weight: 0.0070 chunk 310 optimal weight: 0.0770 chunk 24 optimal weight: 6.9990 chunk 173 optimal weight: 6.9990 chunk 178 optimal weight: 9.9990 overall best weight: 1.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN D 365 GLN D 777 HIS D 861 ASN D 865 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.189136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.158720 restraints weight = 32218.028| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.27 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26117 Z= 0.138 Angle : 0.507 11.277 35492 Z= 0.264 Chirality : 0.041 0.231 4064 Planarity : 0.004 0.050 4454 Dihedral : 12.205 174.296 4017 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.33 % Allowed : 17.22 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.15), residues: 3107 helix: 1.21 (0.17), residues: 1018 sheet: 0.06 (0.26), residues: 392 loop : -1.54 (0.14), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 88 TYR 0.026 0.001 TYR C 70 PHE 0.013 0.001 PHE D 668 TRP 0.009 0.001 TRP C 183 HIS 0.014 0.001 HIS A 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (26112) covalent geometry : angle 0.50708 / 0.26 (35492) hydrogen bonds : bond 0.03412 / 2.28 ( 923) hydrogen bonds : angle 3.92625 / 2.68 ( 2587) metal coordination : bond 0.00230 / 0.12 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 259 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.8439 (mmt) cc_final: 0.8183 (mmp) REVERT: A 205 MET cc_start: 0.8069 (ptm) cc_final: 0.7823 (ptm) REVERT: C 341 LEU cc_start: 0.5259 (OUTLIER) cc_final: 0.4960 (pt) REVERT: C 465 ARG cc_start: 0.7931 (tmt170) cc_final: 0.7572 (ttm170) REVERT: C 964 LEU cc_start: 0.5456 (pp) cc_final: 0.4457 (mp) REVERT: C 1299 ASN cc_start: 0.8204 (p0) cc_final: 0.7981 (p0) REVERT: D 140 TYR cc_start: 0.6221 (m-10) cc_final: 0.5614 (m-80) REVERT: D 348 ASP cc_start: 0.8867 (m-30) cc_final: 0.8468 (m-30) REVERT: D 769 VAL cc_start: 0.9281 (OUTLIER) cc_final: 0.9040 (m) REVERT: D 867 GLN cc_start: 0.5696 (mp10) cc_final: 0.5203 (pp30) outliers start: 62 outliers final: 51 residues processed: 309 average time/residue: 0.1527 time to fit residues: 76.7701 Evaluate side-chains 308 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 255 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1287 LEU Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 774 ILE Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1059 LEU Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1298 VAL Chi-restraints excluded: chain E residue 46 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 201 optimal weight: 5.9990 chunk 72 optimal weight: 0.0010 chunk 169 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 56 optimal weight: 0.0470 chunk 222 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 130 optimal weight: 10.0000 chunk 58 optimal weight: 0.7980 chunk 133 optimal weight: 10.0000 chunk 140 optimal weight: 0.4980 overall best weight: 0.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN D 365 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.191845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.158746 restraints weight = 32090.097| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.40 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 26117 Z= 0.092 Angle : 0.461 10.277 35492 Z= 0.243 Chirality : 0.040 0.235 4064 Planarity : 0.003 0.057 4454 Dihedral : 12.141 173.792 4017 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.61 % Allowed : 18.08 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.15), residues: 3107 helix: 1.41 (0.17), residues: 1017 sheet: 0.13 (0.27), residues: 386 loop : -1.45 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 88 TYR 0.029 0.001 TYR C 70 PHE 0.012 0.001 PHE D 668 TRP 0.014 0.001 TRP C 183 HIS 0.013 0.001 HIS A 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.09 (26112) covalent geometry : angle 0.46126 / 0.24 (35492) hydrogen bonds : bond 0.02938 / 1.96 ( 923) hydrogen bonds : angle 3.83866 / 2.62 ( 2587) metal coordination : bond 0.00073 / 0.04 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6214 Ramachandran restraints generated. 3107 Oldfield, 0 Emsley, 3107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 266 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.8318 (mmt) cc_final: 0.8051 (mmp) REVERT: A 205 MET cc_start: 0.7979 (ptm) cc_final: 0.7756 (ptm) REVERT: C 341 LEU cc_start: 0.5389 (OUTLIER) cc_final: 0.5074 (pt) REVERT: C 964 LEU cc_start: 0.4854 (pp) cc_final: 0.4057 (mp) REVERT: C 1299 ASN cc_start: 0.7988 (p0) cc_final: 0.7788 (p0) REVERT: D 140 TYR cc_start: 0.6323 (m-10) cc_final: 0.5712 (m-80) REVERT: D 348 ASP cc_start: 0.8819 (m-30) cc_final: 0.8560 (m-30) REVERT: D 769 VAL cc_start: 0.9224 (OUTLIER) cc_final: 0.8991 (m) REVERT: D 867 GLN cc_start: 0.5600 (mp10) cc_final: 0.5177 (pp30) outliers start: 43 outliers final: 39 residues processed: 298 average time/residue: 0.1555 time to fit residues: 75.5133 Evaluate side-chains 300 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 259 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 774 ILE Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1059 LEU Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1298 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 21 optimal weight: 4.9990 chunk 225 optimal weight: 0.3980 chunk 4 optimal weight: 0.8980 chunk 291 optimal weight: 2.9990 chunk 277 optimal weight: 0.0000 chunk 106 optimal weight: 0.9980 chunk 187 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 312 optimal weight: 30.0000 chunk 43 optimal weight: 0.9980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 83 GLN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 GLN D 335 GLN ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.191522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.158571 restraints weight = 31872.903| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.89 r_work: 0.3326 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 26117 Z= 0.100 Angle : 0.466 10.232 35492 Z= 0.244 Chirality : 0.040 0.234 4064 Planarity : 0.003 0.057 4454 Dihedral : 12.121 174.108 4017 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.95 % Allowed : 17.82 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.15), residues: 3107 helix: 1.48 (0.17), residues: 1016 sheet: 0.26 (0.27), residues: 370 loop : -1.40 (0.14), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 88 TYR 0.029 0.001 TYR C 70 PHE 0.012 0.001 PHE D 668 TRP 0.013 0.001 TRP C 183 HIS 0.013 0.001 HIS A 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (26112) covalent geometry : angle 0.46585 / 0.24 (35492) hydrogen bonds : bond 0.02953 / 1.97 ( 923) hydrogen bonds : angle 3.80141 / 2.60 ( 2587) metal coordination : bond 0.00094 / 0.05 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4717.85 seconds wall clock time: 82 minutes 2.55 seconds (4922.55 seconds total)