Starting phenix.real_space_refine on Mon Sep 14 01:10:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6c6u_7351/09_2026/6c6u_7351_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6c6u_7351/09_2026/6c6u_7351.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6c6u_7351/09_2026/6c6u_7351_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6c6u_7351/09_2026/6c6u_7351_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6c6u_7351/09_2026/6c6u_7351.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6c6u_7351/09_2026/6c6u_7351.map" } resolution = 3.7 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 59 5.49 5 Mg 1 5.21 5 S 112 5.16 5 C 16653 2.51 5 N 4758 2.21 5 O 5281 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26866 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 453 Classifications: {'DNA': 22} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 21} Chain breaks: 1 Chain: "B" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 585 Classifications: {'DNA': 29} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 28} Chain: "R" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 218 Classifications: {'RNA': 10} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 7, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 8} Chain: "G" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1698 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1677 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 209} 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: "I" Number of atoms: 10388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1317, 10388 Classifications: {'peptide': 1317} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 54, 'TRANS': 1258} Chain breaks: 1 Chain: "J" Number of atoms: 10404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 10404 Classifications: {'peptide': 1337} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 54, 'TRANS': 1279} Chain breaks: 2 Chain: "K" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 650 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "N" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 790 Classifications: {'peptide': 98} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 91} Chain breaks: 1 Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15477 SG CYS J 70 55.449 118.908 61.662 1.00 54.45 S ATOM 15491 SG CYS J 72 56.064 122.416 62.090 1.00 61.90 S ATOM 15599 SG CYS J 85 54.353 121.380 59.073 1.00 61.46 S ATOM 21311 SG CYS J 814 52.943 52.213 50.188 1.00 44.90 S ATOM 21876 SG CYS J 888 55.566 55.602 50.931 1.00 40.12 S ATOM 21927 SG CYS J 895 53.284 54.291 53.446 1.00 35.12 S ATOM 21948 SG CYS J 898 55.585 51.651 52.757 1.00 35.99 S Time building chain proxies: 5.07, per 1000 atoms: 0.19 Number of scatterers: 26866 At special positions: 0 Unit cell: (154.08, 142.31, 149.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 112 16.00 P 59 15.00 Mg 1 11.99 O 5281 8.00 N 4758 7.00 C 16653 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: 2.33 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1501 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 72 " pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 895 " Number of angles added : 6 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6042 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 45 sheets defined 36.7% alpha, 14.9% beta 27 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 3.36 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.550A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 Processing helix chain 'G' and resid 212 through 228 Processing helix chain 'G' and resid 229 through 232 removed outlier: 3.840A pdb=" N VAL G 232 " --> pdb=" O GLU G 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 229 through 232' Processing helix chain 'H' and resid 34 through 50 removed outlier: 4.043A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 removed outlier: 3.562A pdb=" N GLY H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 212 through 227 Processing helix chain 'I' and resid 4 through 8 Processing helix chain 'I' and resid 28 through 39 Processing helix chain 'I' and resid 48 through 56 removed outlier: 4.131A pdb=" N ALA I 52 " --> pdb=" O GLY I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 163 through 167 removed outlier: 3.840A pdb=" N SER I 166 " --> pdb=" O LYS I 163 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER I 167 " --> pdb=" O THR I 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 163 through 167' Processing helix chain 'I' and resid 206 through 213 removed outlier: 4.055A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 removed outlier: 3.578A pdb=" N ARG I 247 " --> pdb=" O GLU I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 280 Processing helix chain 'I' and resid 318 through 327 removed outlier: 3.691A pdb=" N GLN I 327 " --> pdb=" O ALA I 323 " (cutoff:3.500A) Processing helix chain 'I' and resid 345 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 389 removed outlier: 4.130A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 408 Processing helix chain 'I' and resid 421 through 438 removed outlier: 3.758A pdb=" N ILE I 425 " --> pdb=" O SER I 421 " (cutoff:3.500A) Processing helix chain 'I' and resid 455 through 480 removed outlier: 4.514A pdb=" N SER I 480 " --> pdb=" O LYS I 476 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 508 Processing helix chain 'I' and resid 519 through 527 Processing helix chain 'I' and resid 609 through 614 removed outlier: 4.047A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR I 614 " --> pdb=" O GLU I 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 609 through 614' Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 688 Processing helix chain 'I' and resid 704 through 711 Processing helix chain 'I' and resid 738 through 741 removed outlier: 3.792A pdb=" N MET I 741 " --> pdb=" O GLU I 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 738 through 741' Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 858 through 863 Processing helix chain 'I' and resid 942 through 979 Processing helix chain 'I' and resid 987 through 991 removed outlier: 3.827A pdb=" N ASP I 990 " --> pdb=" O GLU I 987 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS I 991 " --> pdb=" O LYS I 988 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 987 through 991' Processing helix chain 'I' and resid 1005 through 1038 Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 4.550A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG I1106 " --> pdb=" O GLY I1102 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1101 through 1106' Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.694A pdb=" N LEU I1113 " --> pdb=" O ILE I1109 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN I1134 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.880A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU I1151 " --> pdb=" O ARG I1147 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 4.190A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1177 Processing helix chain 'I' and resid 1191 through 1202 removed outlier: 3.551A pdb=" N GLY I1202 " --> pdb=" O LEU I1198 " (cutoff:3.500A) Processing helix chain 'I' and resid 1271 through 1281 removed outlier: 3.624A pdb=" N TYR I1281 " --> pdb=" O ALA I1277 " (cutoff:3.500A) Processing helix chain 'I' and resid 1284 through 1292 Processing helix chain 'I' and resid 1297 through 1310 Processing helix chain 'I' and resid 1320 through 1332 removed outlier: 3.652A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 77 through 81 removed outlier: 3.555A pdb=" N ARG J 81 " --> pdb=" O LEU J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.507A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 181 through 191 Processing helix chain 'J' and resid 193 through 208 Processing helix chain 'J' and resid 210 through 229 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 removed outlier: 3.617A pdb=" N ARG J 250 " --> pdb=" O PRO J 247 " (cutoff:3.500A) Processing helix chain 'J' and resid 263 through 285 removed outlier: 3.712A pdb=" N ASP J 267 " --> pdb=" O SER J 263 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 removed outlier: 3.646A pdb=" N ASP J 308 " --> pdb=" O ASP J 304 " (cutoff:3.500A) Processing helix chain 'J' and resid 327 through 332 Processing helix chain 'J' and resid 370 through 377 removed outlier: 3.558A pdb=" N PHE J 377 " --> pdb=" O ALA J 373 " (cutoff:3.500A) Processing helix chain 'J' and resid 377 through 389 Processing helix chain 'J' and resid 393 through 404 removed outlier: 3.810A pdb=" N ALA J 397 " --> pdb=" O THR J 393 " (cutoff:3.500A) Processing helix chain 'J' and resid 407 through 417 removed outlier: 4.022A pdb=" N ARG J 417 " --> pdb=" O ASP J 413 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 451 through 456 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 504 through 514 Processing helix chain 'J' and resid 529 through 539 removed outlier: 3.723A pdb=" N SER J 539 " --> pdb=" O ARG J 535 " (cutoff:3.500A) Processing helix chain 'J' and resid 573 through 581 removed outlier: 3.656A pdb=" N ALA J 577 " --> pdb=" O THR J 573 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 592 removed outlier: 3.957A pdb=" N ILE J 591 " --> pdb=" O PRO J 588 " (cutoff:3.500A) Processing helix chain 'J' and resid 598 through 613 Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.604A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 669 Processing helix chain 'J' and resid 674 through 703 removed outlier: 3.600A pdb=" N ARG J 678 " --> pdb=" O THR J 674 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 removed outlier: 3.578A pdb=" N ILE J 737 " --> pdb=" O SER J 733 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 804 removed outlier: 4.057A pdb=" N TYR J 795 " --> pdb=" O ALA J 791 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 876 removed outlier: 3.718A pdb=" N ASN J 875 " --> pdb=" O LEU J 871 " (cutoff:3.500A) Processing helix chain 'J' and resid 884 through 888 Processing helix chain 'J' and resid 914 through 925 removed outlier: 3.811A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 928 No H-bonds generated for 'chain 'J' and resid 926 through 928' Processing helix chain 'J' and resid 1068 through 1073 removed outlier: 4.381A pdb=" N ASP J1073 " --> pdb=" O ALA J1069 " (cutoff:3.500A) Processing helix chain 'J' and resid 1137 through 1146 Processing helix chain 'J' and resid 1216 through 1224 Processing helix chain 'J' and resid 1226 through 1244 removed outlier: 4.085A pdb=" N VAL J1240 " --> pdb=" O GLU J1236 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.481A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1294 Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1318 through 1325 removed outlier: 3.587A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 removed outlier: 3.721A pdb=" N VAL J1331 " --> pdb=" O GLU J1327 " (cutoff:3.500A) Processing helix chain 'J' and resid 1346 through 1354 removed outlier: 4.033A pdb=" N ASN J1350 " --> pdb=" O GLY J1346 " (cutoff:3.500A) Processing helix chain 'J' and resid 1360 through 1372 removed outlier: 3.951A pdb=" N ALA J1364 " --> pdb=" O GLY J1360 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 12 Processing helix chain 'K' and resid 17 through 32 removed outlier: 3.523A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL K 32 " --> pdb=" O ARG K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 57 Processing helix chain 'K' and resid 60 through 84 removed outlier: 3.955A pdb=" N GLN K 75 " --> pdb=" O GLU K 71 " (cutoff:3.500A) Processing helix chain 'N' and resid 18 through 33 Processing helix chain 'N' and resid 35 through 37 No H-bonds generated for 'chain 'N' and resid 35 through 37' Processing helix chain 'N' and resid 76 through 86 Processing helix chain 'N' and resid 104 through 117 Processing sheet with id=AA1, first strand: chain 'G' and resid 12 through 13 removed outlier: 6.338A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL G 202 " --> pdb=" O ASN G 186 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 52 through 53 removed outlier: 3.520A pdb=" N GLY G 53 " --> pdb=" O GLY G 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 115 through 116 removed outlier: 4.248A pdb=" N THR G 101 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N SER G 141 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ILE G 61 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 90 through 91 Processing sheet with id=AA5, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.837A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 23 through 31 removed outlier: 7.013A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG H 182 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 53 through 61 removed outlier: 4.075A pdb=" N ALA H 55 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AA9, first strand: chain 'H' and resid 108 through 111 removed outlier: 4.051A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 152 through 153 removed outlier: 3.625A pdb=" N VAL H 153 " --> pdb=" O ALA H 175 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.571A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 59 through 60 removed outlier: 6.927A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB5, first strand: chain 'I' and resid 451 through 454 removed outlier: 6.321A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 154 through 158 removed outlier: 3.580A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 228 through 231 Processing sheet with id=AB8, first strand: chain 'I' and resid 239 through 240 Processing sheet with id=AB9, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.575A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 301 through 302 removed outlier: 7.195A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 580 through 581 removed outlier: 3.689A pdb=" N GLU I 588 " --> pdb=" O GLN I 580 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS I 593 " --> pdb=" O GLU I 602 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 580 through 581 removed outlier: 3.689A pdb=" N GLU I 588 " --> pdb=" O GLN I 580 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.634A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 757 through 758 removed outlier: 3.992A pdb=" N THR I 757 " --> pdb=" O ILE I 765 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 768 through 769 Processing sheet with id=AC7, first strand: chain 'I' and resid 789 through 790 removed outlier: 3.592A pdb=" N ASP I 790 " --> pdb=" O GLU I 793 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 1066 through 1067 removed outlier: 4.451A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 1066 through 1067 Processing sheet with id=AD1, first strand: chain 'I' and resid 846 through 847 removed outlier: 3.863A pdb=" N GLY I 846 " --> pdb=" O THR I 843 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N THR I 843 " --> pdb=" O GLY I 846 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N THR I 830 " --> pdb=" O LYS I1057 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N LYS I1057 " --> pdb=" O THR I 830 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N HIS I 832 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ALA I1055 " --> pdb=" O HIS I 832 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLN I 834 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N TYR I1053 " --> pdb=" O GLN I 834 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU I 836 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LYS I1051 " --> pdb=" O LEU I 836 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N CYS I 838 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ILE I1049 " --> pdb=" O CYS I 838 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N SER I 840 " --> pdb=" O LEU I1047 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY I 926 " --> pdb=" O VAL I 877 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 882 through 884 removed outlier: 3.869A pdb=" N VAL I 884 " --> pdb=" O LEU I 918 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 887 through 888 Processing sheet with id=AD4, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 3.519A pdb=" N CYS J 366 " --> pdb=" O GLU J 438 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 8.073A pdb=" N ILE J 447 " --> pdb=" O ARG J 352 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL J 354 " --> pdb=" O ILE J 447 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AD7, first strand: chain 'I' and resid 1335 through 1337 Processing sheet with id=AD8, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.581A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY J 103 " --> pdb=" O VAL J 244 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 10.358A pdb=" N SER J 109 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 10.182A pdb=" N ILE J 238 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 144 through 145 removed outlier: 3.836A pdb=" N TYR J 144 " --> pdb=" O LEU J 160 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 526 through 527 removed outlier: 3.534A pdb=" N ARG J 551 " --> pdb=" O LEU J 527 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 820 through 822 removed outlier: 3.829A pdb=" N MET J 822 " --> pdb=" O VAL J 880 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL J 880 " --> pdb=" O MET J 822 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 949 through 950 removed outlier: 3.747A pdb=" N ILE J 950 " --> pdb=" O ALA J1018 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 957 through 961 removed outlier: 3.945A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 1035 through 1038 removed outlier: 3.582A pdb=" N ARG J1036 " --> pdb=" O LYS J1079 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS J1079 " --> pdb=" O ARG J1036 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 1046 through 1049 removed outlier: 4.088A pdb=" N GLN J1049 " --> pdb=" O SER J1058 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER J1058 " --> pdb=" O GLN J1049 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU J1059 " --> pdb=" O VAL J1107 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N VAL J1107 " --> pdb=" O LEU J1059 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 1162 through 1165 removed outlier: 4.659A pdb=" N TYR J1186 " --> pdb=" O ILE J1177 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 3.744A pdb=" N VAL J1267 " --> pdb=" O THR J1301 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'N' and resid 39 through 43 removed outlier: 4.150A pdb=" N GLU N 41 " --> pdb=" O GLN N 72 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN N 72 " --> pdb=" O GLU N 41 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N VAL N 11 " --> pdb=" O PHE N 92 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N PHE N 92 " --> pdb=" O VAL N 11 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN N 13 " --> pdb=" O MET N 90 " (cutoff:3.500A) 1014 hydrogen bonds defined for protein. 2841 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 72 hydrogen bonds 144 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 6.78 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6829 1.33 - 1.45: 4977 1.45 - 1.57: 15276 1.57 - 1.69: 116 1.69 - 1.81: 196 Bond restraints: 27394 Sorted by residual: bond pdb=" C3' DT B 13 " pdb=" O3' DT B 13 " ideal model delta sigma weight residual 1.435 1.386 0.049 1.30e-02 5.92e+03 1.44e+01 bond pdb=" C4' DC B 17 " pdb=" C3' DC B 17 " ideal model delta sigma weight residual 1.529 1.494 0.035 1.00e-02 1.00e+04 1.23e+01 bond pdb=" C3' DT B 15 " pdb=" O3' DT B 15 " ideal model delta sigma weight residual 1.435 1.391 0.044 1.30e-02 5.92e+03 1.16e+01 bond pdb=" C3' DC B 27 " pdb=" C2' DC B 27 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C5' DG A 3 " pdb=" C4' DG A 3 " ideal model delta sigma weight residual 1.512 1.535 -0.023 7.00e-03 2.04e+04 1.04e+01 ... (remaining 27389 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 36022 2.55 - 5.11: 1066 5.11 - 7.66: 137 7.66 - 10.22: 31 10.22 - 12.77: 2 Bond angle restraints: 37258 Sorted by residual: angle pdb=" O4' DG B 12 " pdb=" C4' DG B 12 " pdb=" C3' DG B 12 " ideal model delta sigma weight residual 106.00 101.91 4.09 6.00e-01 2.78e+00 4.66e+01 angle pdb=" O4' DG A 2 " pdb=" C4' DG A 2 " pdb=" C3' DG A 2 " ideal model delta sigma weight residual 106.00 102.07 3.93 6.00e-01 2.78e+00 4.29e+01 angle pdb=" C THR J 853 " pdb=" N ALA J 854 " pdb=" CA ALA J 854 " ideal model delta sigma weight residual 122.74 130.94 -8.20 1.44e+00 4.82e-01 3.24e+01 angle pdb=" N ASP J1184 " pdb=" CA ASP J1184 " pdb=" C ASP J1184 " ideal model delta sigma weight residual 109.81 121.80 -11.99 2.21e+00 2.05e-01 2.94e+01 angle pdb=" C ARG J 709 " pdb=" N ASP J 710 " pdb=" CA ASP J 710 " ideal model delta sigma weight residual 126.45 135.40 -8.95 1.77e+00 3.19e-01 2.56e+01 ... (remaining 37253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.71: 16133 26.71 - 53.41: 467 53.41 - 80.12: 90 80.12 - 106.83: 5 106.83 - 133.53: 1 Dihedral angle restraints: 16696 sinusoidal: 7306 harmonic: 9390 Sorted by residual: dihedral pdb=" CA VAL G 192 " pdb=" C VAL G 192 " pdb=" N GLU G 193 " pdb=" CA GLU G 193 " ideal model delta harmonic sigma weight residual -180.00 -126.71 -53.29 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" CA GLN J1326 " pdb=" C GLN J1326 " pdb=" N GLU J1327 " pdb=" CA GLU J1327 " ideal model delta harmonic sigma weight residual 180.00 -132.61 -47.39 0 5.00e+00 4.00e-02 8.98e+01 dihedral pdb=" CA LEU J1344 " pdb=" C LEU J1344 " pdb=" N ARG J1345 " pdb=" CA ARG J1345 " ideal model delta harmonic sigma weight residual 180.00 134.91 45.09 0 5.00e+00 4.00e-02 8.13e+01 ... (remaining 16693 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 3883 0.107 - 0.214: 351 0.214 - 0.321: 16 0.321 - 0.428: 2 0.428 - 0.536: 1 Chirality restraints: 4253 Sorted by residual: chirality pdb=" CB ILE I1079 " pdb=" CA ILE I1079 " pdb=" CG1 ILE I1079 " pdb=" CG2 ILE I1079 " both_signs ideal model delta sigma weight residual False 2.64 2.11 0.54 2.00e-01 2.50e+01 7.17e+00 chirality pdb=" CB ILE I 765 " pdb=" CA ILE I 765 " pdb=" CG1 ILE I 765 " pdb=" CG2 ILE I 765 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" CB ILE I 11 " pdb=" CA ILE I 11 " pdb=" CG1 ILE I 11 " pdb=" CG2 ILE I 11 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 4250 not shown) Planarity restraints: 4665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL G 192 " 0.016 2.00e-02 2.50e+03 3.34e-02 1.12e+01 pdb=" C VAL G 192 " -0.058 2.00e-02 2.50e+03 pdb=" O VAL G 192 " 0.022 2.00e-02 2.50e+03 pdb=" N GLU G 193 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE I 127 " 0.053 5.00e-02 4.00e+02 8.08e-02 1.05e+01 pdb=" N PRO I 128 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO I 128 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO I 128 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE J 416 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.28e+00 pdb=" C ILE J 416 " 0.053 2.00e-02 2.50e+03 pdb=" O ILE J 416 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG J 417 " -0.018 2.00e-02 2.50e+03 ... (remaining 4662 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 305 2.64 - 3.20: 22391 3.20 - 3.77: 39354 3.77 - 4.33: 53343 4.33 - 4.90: 88687 Nonbonded interactions: 204080 Sorted by model distance: nonbonded pdb=" O3' A R 20 " pdb="MG MG R1501 " model vdw 2.073 2.170 nonbonded pdb=" OD1 ASP J 464 " pdb="MG MG R1501 " model vdw 2.115 2.170 nonbonded pdb=" OP2 DG A 3 " pdb=" OH TYR J 46 " model vdw 2.160 3.040 nonbonded pdb=" O ASP I 516 " pdb=" OD1 ASP I 516 " model vdw 2.226 3.040 nonbonded pdb=" OH TYR J 679 " pdb=" O ILE J 754 " model vdw 2.230 3.040 ... (remaining 204075 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'G' and (resid 7 through 135 or (resid 136 and (name N or name CA or name \ C or name O or name CB )) or resid 137 through 158 or resid 169 through 232)) selection = (chain 'H' and (resid 7 through 190 or (resid 191 through 192 and (name N or nam \ e CA or name C or name O or name CB )) or resid 193 or (resid 194 and (name N or \ name CA or name C or name O or name CB )) or resid 195 through 232)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 30.860 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 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 : 0.009 0.185 27401 Z= 0.405 Angle : 1.071 18.185 37264 Z= 0.615 Chirality : 0.063 0.536 4253 Planarity : 0.008 0.081 4665 Dihedral : 12.769 133.535 10654 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.85 % Favored : 92.03 % Rotamer: Outliers : 0.29 % Allowed : 2.55 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -4.18 (0.12), residues: 3249 helix: -2.73 (0.11), residues: 1103 sheet: -1.98 (0.25), residues: 376 loop : -3.06 (0.12), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG J 352 TYR 0.038 0.003 TYR I1229 PHE 0.038 0.003 PHE J 620 TRP 0.043 0.004 TRP I 183 HIS 0.016 0.002 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00839 / 0.40 (27394) covalent geometry : angle 1.05619 / 0.61 (37258) hydrogen bonds : bond 0.15505 / 17.77 ( 1079) hydrogen bonds : angle 6.62078 / 7.39 ( 2985) metal coordination : bond 0.13816 / 14.90 ( 7) metal coordination : angle 14.19233 / 25.88 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 605 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 170 ARG cc_start: 0.6968 (ttm170) cc_final: 0.6277 (ptp-170) REVERT: I 36 GLN cc_start: 0.7853 (tp40) cc_final: 0.7647 (tp40) REVERT: I 47 TYR cc_start: 0.4935 (m-80) cc_final: 0.4496 (m-80) REVERT: I 339 ASN cc_start: 0.7844 (t0) cc_final: 0.7436 (t0) REVERT: I 383 SER cc_start: 0.8402 (m) cc_final: 0.7981 (p) REVERT: I 496 LYS cc_start: 0.8756 (mmtt) cc_final: 0.8556 (tppt) REVERT: I 516 ASP cc_start: 0.6864 (p0) cc_final: 0.6525 (p0) REVERT: I 559 CYS cc_start: 0.9326 (t) cc_final: 0.8976 (t) REVERT: I 603 ILE cc_start: 0.8685 (pt) cc_final: 0.8385 (pt) REVERT: I 1290 MET cc_start: 0.8632 (tpp) cc_final: 0.8417 (tpp) REVERT: J 197 GLU cc_start: 0.6576 (mm-30) cc_final: 0.6361 (mt-10) REVERT: J 372 MET cc_start: 0.9020 (mtp) cc_final: 0.8797 (ttm) REVERT: J 521 LYS cc_start: 0.8740 (mttt) cc_final: 0.8460 (mtpp) REVERT: J 582 ILE cc_start: 0.8848 (mt) cc_final: 0.8582 (mt) REVERT: J 821 MET cc_start: 0.7697 (tpp) cc_final: 0.7366 (mtp) REVERT: J 1243 LEU cc_start: 0.8640 (tp) cc_final: 0.8368 (tp) REVERT: N 41 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7190 (mt-10) outliers start: 8 outliers final: 1 residues processed: 612 average time/residue: 0.1921 time to fit residues: 178.3275 Evaluate side-chains 315 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 314 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 514 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 137 ASN H 37 HIS H 103 ASN H 117 HIS H 127 GLN I 69 GLN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 150 HIS I 214 ASN I 314 ASN I 330 HIS I 513 GLN I 604 HIS I 834 GLN I1080 ASN ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1313 HIS J 157 GLN J 365 GLN J 805 GLN J 910 ASN J1108 GLN N 29 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.156175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.124139 restraints weight = 37930.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.123794 restraints weight = 38330.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.125007 restraints weight = 31027.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.124825 restraints weight = 23344.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.124940 restraints weight = 21331.817| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.122 27401 Z= 0.148 Angle : 0.677 9.442 37264 Z= 0.362 Chirality : 0.046 0.354 4253 Planarity : 0.006 0.059 4665 Dihedral : 14.271 128.304 4261 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.69 % Favored : 94.21 % Rotamer: Outliers : 1.97 % Allowed : 8.22 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.81 (0.13), residues: 3249 helix: -0.80 (0.14), residues: 1112 sheet: -1.63 (0.24), residues: 411 loop : -2.74 (0.13), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 84 TYR 0.019 0.001 TYR G 177 PHE 0.018 0.001 PHE I 514 TRP 0.011 0.001 TRP I 183 HIS 0.011 0.001 HIS G 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (27394) covalent geometry : angle 0.67522 / 0.36 (37258) hydrogen bonds : bond 0.05002 / 5.49 ( 1079) hydrogen bonds : angle 5.15877 / 5.58 ( 2985) metal coordination : bond 0.01440 / 1.33 ( 7) metal coordination : angle 3.58997 / 6.48 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 361 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 51 MET cc_start: 0.7987 (mmm) cc_final: 0.7701 (mtp) REVERT: H 170 ARG cc_start: 0.7006 (ttm170) cc_final: 0.6255 (ptp-170) REVERT: I 47 TYR cc_start: 0.4770 (m-80) cc_final: 0.4282 (m-80) REVERT: I 383 SER cc_start: 0.8650 (m) cc_final: 0.8323 (p) REVERT: I 496 LYS cc_start: 0.8855 (mmtt) cc_final: 0.8653 (tppt) REVERT: I 559 CYS cc_start: 0.9219 (t) cc_final: 0.8904 (t) REVERT: I 951 MET cc_start: 0.7566 (ttp) cc_final: 0.7208 (ttm) REVERT: I 1085 MET cc_start: 0.8889 (mmt) cc_final: 0.8664 (mmp) REVERT: J 200 GLN cc_start: 0.7801 (tp40) cc_final: 0.7319 (tt0) REVERT: J 505 ASP cc_start: 0.8721 (OUTLIER) cc_final: 0.7868 (t0) REVERT: J 582 ILE cc_start: 0.8861 (mt) cc_final: 0.8580 (mt) REVERT: J 821 MET cc_start: 0.7592 (tpp) cc_final: 0.7280 (mtp) REVERT: J 1188 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6907 (mt-10) REVERT: J 1281 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7169 (mt-10) REVERT: N 27 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.7151 (mmm-85) outliers start: 55 outliers final: 26 residues processed: 402 average time/residue: 0.1694 time to fit residues: 110.0370 Evaluate side-chains 316 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 286 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 851 THR Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain J residue 1188 GLU Chi-restraints excluded: chain J residue 1281 GLU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain N residue 27 ARG Chi-restraints excluded: chain N residue 90 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 321 optimal weight: 10.0000 chunk 163 optimal weight: 2.9990 chunk 294 optimal weight: 10.0000 chunk 323 optimal weight: 0.9980 chunk 193 optimal weight: 6.9990 chunk 204 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 154 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 220 optimal weight: 0.7980 chunk 146 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 137 ASN H 103 ASN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 214 ASN I 580 GLN I1108 ASN I1268 GLN J 365 GLN J 450 HIS J 805 GLN J1010 GLN ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.155965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.123334 restraints weight = 38158.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.121774 restraints weight = 32600.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.122788 restraints weight = 30736.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.123947 restraints weight = 23547.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.123750 restraints weight = 20008.410| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.156 27401 Z= 0.137 Angle : 0.628 9.375 37264 Z= 0.334 Chirality : 0.045 0.369 4253 Planarity : 0.005 0.060 4665 Dihedral : 13.977 123.037 4260 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.63 % Favored : 94.28 % Rotamer: Outliers : 2.51 % Allowed : 10.20 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.14 (0.14), residues: 3249 helix: 0.04 (0.15), residues: 1111 sheet: -1.48 (0.24), residues: 422 loop : -2.49 (0.13), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 84 TYR 0.019 0.001 TYR G 185 PHE 0.015 0.001 PHE I 337 TRP 0.008 0.001 TRP N 9 HIS 0.009 0.001 HIS G 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (27394) covalent geometry : angle 0.62748 / 0.33 (37258) hydrogen bonds : bond 0.04510 / 4.93 ( 1079) hydrogen bonds : angle 4.84365 / 5.26 ( 2985) metal coordination : bond 0.00376 / 0.36 ( 7) metal coordination : angle 2.25953 / 4.10 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 321 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 51 MET cc_start: 0.8042 (mmm) cc_final: 0.7584 (mtp) REVERT: H 170 ARG cc_start: 0.7121 (ttm170) cc_final: 0.6281 (ptp-170) REVERT: H 226 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7423 (mm-30) REVERT: I 47 TYR cc_start: 0.4672 (m-80) cc_final: 0.4183 (m-80) REVERT: I 337 PHE cc_start: 0.7052 (t80) cc_final: 0.6788 (t80) REVERT: I 339 ASN cc_start: 0.7783 (t0) cc_final: 0.7372 (m-40) REVERT: I 383 SER cc_start: 0.8552 (m) cc_final: 0.8143 (p) REVERT: I 496 LYS cc_start: 0.8925 (mmtt) cc_final: 0.8695 (tppt) REVERT: I 516 ASP cc_start: 0.7600 (p0) cc_final: 0.6444 (p0) REVERT: I 559 CYS cc_start: 0.9312 (t) cc_final: 0.8979 (t) REVERT: I 1047 LEU cc_start: 0.8141 (mm) cc_final: 0.7834 (mt) REVERT: I 1322 SER cc_start: 0.8717 (p) cc_final: 0.8510 (m) REVERT: J 157 GLN cc_start: 0.7845 (mm110) cc_final: 0.7513 (mm110) REVERT: J 171 GLU cc_start: 0.7710 (mp0) cc_final: 0.7290 (mp0) REVERT: J 200 GLN cc_start: 0.7556 (tp40) cc_final: 0.7071 (tt0) REVERT: J 205 LEU cc_start: 0.6899 (OUTLIER) cc_final: 0.6522 (mm) REVERT: J 431 ARG cc_start: 0.9223 (OUTLIER) cc_final: 0.9017 (ptt90) REVERT: J 505 ASP cc_start: 0.8868 (OUTLIER) cc_final: 0.8186 (t0) REVERT: J 581 MET cc_start: 0.8771 (mtp) cc_final: 0.8455 (mtp) REVERT: J 582 ILE cc_start: 0.8897 (mt) cc_final: 0.8583 (mt) REVERT: J 666 GLU cc_start: 0.6524 (mt-10) cc_final: 0.6203 (tm-30) REVERT: J 821 MET cc_start: 0.7656 (tpp) cc_final: 0.7393 (mtp) REVERT: J 1188 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.7006 (mt-10) REVERT: N 27 ARG cc_start: 0.7387 (tpp80) cc_final: 0.7162 (mmm-85) outliers start: 70 outliers final: 34 residues processed: 369 average time/residue: 0.1719 time to fit residues: 103.0087 Evaluate side-chains 319 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 281 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 851 THR Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1154 ASP Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 431 ARG Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 749 LYS Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 793 SER Chi-restraints excluded: chain J residue 1188 GLU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain N residue 73 MET Chi-restraints excluded: chain N residue 90 MET Chi-restraints excluded: chain N residue 115 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 312 optimal weight: 2.9990 chunk 217 optimal weight: 6.9990 chunk 231 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 304 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 298 optimal weight: 0.5980 chunk 142 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 266 optimal weight: 0.3980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 127 GLN H 227 GLN I 513 GLN I1108 ASN I1244 HIS J 365 GLN ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.154446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.122100 restraints weight = 37804.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.122875 restraints weight = 35111.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.123854 restraints weight = 27802.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.123939 restraints weight = 20253.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.124062 restraints weight = 18799.792| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.120 27401 Z= 0.133 Angle : 0.603 10.763 37264 Z= 0.319 Chirality : 0.045 0.321 4253 Planarity : 0.004 0.063 4665 Dihedral : 13.751 117.655 4260 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.79 % Favored : 94.18 % Rotamer: Outliers : 2.62 % Allowed : 11.71 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.71 (0.14), residues: 3249 helix: 0.52 (0.15), residues: 1112 sheet: -1.27 (0.24), residues: 425 loop : -2.32 (0.14), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 84 TYR 0.017 0.001 TYR G 177 PHE 0.015 0.001 PHE J 620 TRP 0.009 0.001 TRP N 9 HIS 0.008 0.001 HIS G 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (27394) covalent geometry : angle 0.60229 / 0.32 (37258) hydrogen bonds : bond 0.04221 / 4.60 ( 1079) hydrogen bonds : angle 4.60952 / 5.06 ( 2985) metal coordination : bond 0.00510 / 0.49 ( 7) metal coordination : angle 1.69327 / 3.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 290 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 170 ARG cc_start: 0.7160 (ttm170) cc_final: 0.6333 (ptp-170) REVERT: I 47 TYR cc_start: 0.4775 (m-80) cc_final: 0.4251 (m-80) REVERT: I 383 SER cc_start: 0.8667 (m) cc_final: 0.8340 (p) REVERT: I 516 ASP cc_start: 0.7636 (p0) cc_final: 0.6434 (p0) REVERT: I 559 CYS cc_start: 0.9266 (t) cc_final: 0.8940 (t) REVERT: I 1127 LYS cc_start: 0.8551 (tptt) cc_final: 0.8272 (mmmm) REVERT: I 1131 MET cc_start: 0.7140 (mtt) cc_final: 0.6681 (mtt) REVERT: J 205 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6746 (mm) REVERT: J 431 ARG cc_start: 0.9186 (OUTLIER) cc_final: 0.8962 (ptt90) REVERT: J 505 ASP cc_start: 0.8789 (OUTLIER) cc_final: 0.8165 (t0) REVERT: J 581 MET cc_start: 0.8729 (mtp) cc_final: 0.8459 (mtp) REVERT: J 582 ILE cc_start: 0.8856 (mt) cc_final: 0.8541 (mt) REVERT: J 821 MET cc_start: 0.7500 (tpp) cc_final: 0.7209 (mtp) REVERT: J 1188 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.7065 (mt-10) REVERT: N 27 ARG cc_start: 0.7445 (tpp80) cc_final: 0.7237 (mmm-85) outliers start: 73 outliers final: 39 residues processed: 339 average time/residue: 0.1669 time to fit residues: 93.1210 Evaluate side-chains 321 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 278 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 851 THR Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1154 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 431 ARG Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 793 SER Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 1188 GLU Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain N residue 90 MET Chi-restraints excluded: chain N residue 115 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 108 optimal weight: 4.9990 chunk 250 optimal weight: 10.0000 chunk 73 optimal weight: 30.0000 chunk 10 optimal weight: 3.9990 chunk 240 optimal weight: 0.9990 chunk 159 optimal weight: 0.0980 chunk 121 optimal weight: 1.9990 chunk 255 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 247 optimal weight: 3.9990 chunk 275 optimal weight: 0.0970 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 103 ASN H 103 ASN H 127 GLN H 128 HIS I1108 ASN I1244 HIS J 365 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.154910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.122575 restraints weight = 37854.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.121809 restraints weight = 35633.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.122621 restraints weight = 35132.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.123146 restraints weight = 27096.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.123556 restraints weight = 22595.153| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.120 27401 Z= 0.122 Angle : 0.584 12.336 37264 Z= 0.308 Chirality : 0.043 0.293 4253 Planarity : 0.004 0.063 4665 Dihedral : 13.583 112.259 4260 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.54 % Favored : 94.43 % Rotamer: Outliers : 2.33 % Allowed : 12.60 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.39 (0.14), residues: 3249 helix: 0.86 (0.16), residues: 1115 sheet: -1.14 (0.24), residues: 436 loop : -2.18 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I1301 TYR 0.015 0.001 TYR G 177 PHE 0.014 0.001 PHE I 337 TRP 0.008 0.001 TRP N 9 HIS 0.007 0.001 HIS G 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (27394) covalent geometry : angle 0.58379 / 0.31 (37258) hydrogen bonds : bond 0.04002 / 4.37 ( 1079) hydrogen bonds : angle 4.44826 / 4.91 ( 2985) metal coordination : bond 0.00418 / 0.41 ( 7) metal coordination : angle 1.63257 / 2.96 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 300 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 133 LEU cc_start: 0.8255 (mt) cc_final: 0.7962 (mt) REVERT: H 170 ARG cc_start: 0.7219 (ttm170) cc_final: 0.6391 (ptp-170) REVERT: I 47 TYR cc_start: 0.4893 (m-80) cc_final: 0.4370 (m-80) REVERT: I 383 SER cc_start: 0.8587 (m) cc_final: 0.8227 (p) REVERT: I 559 CYS cc_start: 0.9310 (t) cc_final: 0.9010 (t) REVERT: I 1127 LYS cc_start: 0.8551 (tptt) cc_final: 0.8244 (mmmm) REVERT: J 114 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.9024 (mm) REVERT: J 171 GLU cc_start: 0.7681 (mp0) cc_final: 0.7359 (mp0) REVERT: J 180 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.7382 (ttm) REVERT: J 200 GLN cc_start: 0.7651 (tp40) cc_final: 0.7368 (tt0) REVERT: J 205 LEU cc_start: 0.7121 (OUTLIER) cc_final: 0.6733 (mm) REVERT: J 505 ASP cc_start: 0.8779 (OUTLIER) cc_final: 0.8089 (t0) REVERT: J 581 MET cc_start: 0.8712 (mtp) cc_final: 0.8431 (mtp) REVERT: J 582 ILE cc_start: 0.8866 (mt) cc_final: 0.8544 (mt) REVERT: J 821 MET cc_start: 0.7590 (tpp) cc_final: 0.7340 (mtp) REVERT: K 58 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7787 (pp) outliers start: 65 outliers final: 43 residues processed: 342 average time/residue: 0.1639 time to fit residues: 92.2424 Evaluate side-chains 325 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 277 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 127 GLN Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 819 SER Chi-restraints excluded: chain I residue 851 THR Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1154 ASP Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 793 SER Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain N residue 16 SER Chi-restraints excluded: chain N residue 73 MET Chi-restraints excluded: chain N residue 90 MET Chi-restraints excluded: chain N residue 115 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 163 optimal weight: 0.9980 chunk 233 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 268 optimal weight: 0.0020 chunk 247 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 199 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 152 optimal weight: 5.9990 overall best weight: 1.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1108 ASN I1244 HIS ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.152526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.119701 restraints weight = 37929.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.117887 restraints weight = 36129.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.118794 restraints weight = 35151.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.120181 restraints weight = 25473.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.120127 restraints weight = 20641.584| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 27401 Z= 0.172 Angle : 0.614 11.811 37264 Z= 0.322 Chirality : 0.045 0.266 4253 Planarity : 0.004 0.063 4665 Dihedral : 13.529 108.260 4260 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.19 % Favored : 93.78 % Rotamer: Outliers : 2.44 % Allowed : 13.29 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.14), residues: 3249 helix: 0.96 (0.16), residues: 1121 sheet: -1.05 (0.25), residues: 435 loop : -2.19 (0.14), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG J 312 TYR 0.019 0.001 TYR J 140 PHE 0.014 0.001 PHE J 620 TRP 0.008 0.001 TRP N 9 HIS 0.008 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (27394) covalent geometry : angle 0.61343 / 0.32 (37258) hydrogen bonds : bond 0.04213 / 4.59 ( 1079) hydrogen bonds : angle 4.42610 / 4.91 ( 2985) metal coordination : bond 0.00719 / 0.68 ( 7) metal coordination : angle 1.78486 / 3.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 289 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 LYS cc_start: 0.8969 (ptmt) cc_final: 0.8744 (ptmt) REVERT: H 127 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.7371 (tp-100) REVERT: H 133 LEU cc_start: 0.8342 (mt) cc_final: 0.8087 (mt) REVERT: H 170 ARG cc_start: 0.7268 (ttm170) cc_final: 0.6461 (ptp-170) REVERT: I 47 TYR cc_start: 0.4963 (m-80) cc_final: 0.4384 (m-80) REVERT: I 339 ASN cc_start: 0.8089 (t0) cc_final: 0.7670 (m-40) REVERT: I 383 SER cc_start: 0.8477 (m) cc_final: 0.8114 (p) REVERT: I 559 CYS cc_start: 0.9322 (t) cc_final: 0.8982 (t) REVERT: I 1108 ASN cc_start: 0.9056 (OUTLIER) cc_final: 0.8804 (p0) REVERT: J 136 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7383 (mt-10) REVERT: J 180 MET cc_start: 0.7684 (ttm) cc_final: 0.7483 (ttm) REVERT: J 200 GLN cc_start: 0.7615 (tp40) cc_final: 0.7247 (tt0) REVERT: J 205 LEU cc_start: 0.7082 (OUTLIER) cc_final: 0.6706 (mm) REVERT: J 505 ASP cc_start: 0.8919 (OUTLIER) cc_final: 0.8284 (t0) REVERT: J 581 MET cc_start: 0.8761 (mtp) cc_final: 0.8501 (mtp) REVERT: J 582 ILE cc_start: 0.8895 (mt) cc_final: 0.8601 (mt) REVERT: J 1040 MET cc_start: 0.0270 (tpt) cc_final: -0.0144 (mmm) REVERT: J 1144 LEU cc_start: 0.9225 (mt) cc_final: 0.8998 (tp) REVERT: J 1188 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7213 (mt-10) REVERT: K 58 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7877 (pp) REVERT: N 32 LEU cc_start: 0.8778 (tp) cc_final: 0.8364 (tt) outliers start: 68 outliers final: 48 residues processed: 337 average time/residue: 0.1623 time to fit residues: 90.3948 Evaluate side-chains 326 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 272 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 127 GLN Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 819 SER Chi-restraints excluded: chain I residue 851 THR Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1108 ASN Chi-restraints excluded: chain I residue 1154 ASP Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 733 SER Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 793 SER Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain J residue 1188 GLU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain N residue 73 MET Chi-restraints excluded: chain N residue 90 MET Chi-restraints excluded: chain N residue 115 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 199 optimal weight: 3.9990 chunk 309 optimal weight: 6.9990 chunk 326 optimal weight: 2.9990 chunk 248 optimal weight: 0.9990 chunk 308 optimal weight: 1.9990 chunk 76 optimal weight: 40.0000 chunk 250 optimal weight: 4.9990 chunk 212 optimal weight: 4.9990 chunk 298 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 240 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 132 HIS H 103 ASN H 127 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1108 ASN I1244 HIS J 792 ASN ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.151248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.119365 restraints weight = 37897.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.117835 restraints weight = 40409.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.119657 restraints weight = 38569.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.119659 restraints weight = 25915.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.120029 restraints weight = 23577.112| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 27401 Z= 0.184 Angle : 0.624 11.536 37264 Z= 0.327 Chirality : 0.045 0.259 4253 Planarity : 0.004 0.066 4665 Dihedral : 13.498 104.608 4260 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.19 % Favored : 93.75 % Rotamer: Outliers : 2.80 % Allowed : 13.39 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.27 (0.14), residues: 3249 helix: 1.00 (0.16), residues: 1124 sheet: -1.06 (0.25), residues: 432 loop : -2.17 (0.14), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I1106 TYR 0.017 0.001 TYR J 140 PHE 0.013 0.001 PHE J 620 TRP 0.009 0.001 TRP J 115 HIS 0.008 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 (27394) covalent geometry : angle 0.62327 / 0.33 (37258) hydrogen bonds : bond 0.04296 / 4.68 ( 1079) hydrogen bonds : angle 4.43560 / 4.93 ( 2985) metal coordination : bond 0.00780 / 0.74 ( 7) metal coordination : angle 1.95175 / 3.52 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 276 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 LYS cc_start: 0.8936 (ptmt) cc_final: 0.8697 (ptmt) REVERT: H 133 LEU cc_start: 0.8330 (mt) cc_final: 0.8045 (mt) REVERT: H 170 ARG cc_start: 0.7334 (ttm170) cc_final: 0.6535 (ptp-170) REVERT: I 47 TYR cc_start: 0.5144 (m-80) cc_final: 0.4473 (m-80) REVERT: I 87 ILE cc_start: 0.8654 (mm) cc_final: 0.8375 (tt) REVERT: I 383 SER cc_start: 0.8514 (m) cc_final: 0.8176 (p) REVERT: I 559 CYS cc_start: 0.9344 (t) cc_final: 0.9054 (t) REVERT: I 1056 VAL cc_start: 0.9076 (OUTLIER) cc_final: 0.8830 (m) REVERT: J 200 GLN cc_start: 0.7734 (tp40) cc_final: 0.7398 (tt0) REVERT: J 205 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6813 (mm) REVERT: J 505 ASP cc_start: 0.8938 (OUTLIER) cc_final: 0.8088 (t0) REVERT: J 581 MET cc_start: 0.8691 (mtp) cc_final: 0.8386 (mtp) REVERT: J 582 ILE cc_start: 0.8927 (mt) cc_final: 0.8632 (mt) REVERT: J 1188 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7164 (mt-10) REVERT: K 58 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7945 (pp) REVERT: N 32 LEU cc_start: 0.8803 (tp) cc_final: 0.8389 (tt) outliers start: 78 outliers final: 54 residues processed: 331 average time/residue: 0.1561 time to fit residues: 85.8359 Evaluate side-chains 322 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 263 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 819 SER Chi-restraints excluded: chain I residue 851 THR Chi-restraints excluded: chain I residue 873 ILE Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1154 ASP Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 733 SER Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 793 SER Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain J residue 1188 GLU Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain N residue 73 MET Chi-restraints excluded: chain N residue 86 VAL Chi-restraints excluded: chain N residue 90 MET Chi-restraints excluded: chain N residue 115 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 164 optimal weight: 0.0980 chunk 234 optimal weight: 8.9990 chunk 273 optimal weight: 2.9990 chunk 272 optimal weight: 8.9990 chunk 279 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 235 optimal weight: 0.6980 chunk 281 optimal weight: 0.8980 chunk 125 optimal weight: 0.3980 chunk 178 optimal weight: 3.9990 chunk 270 optimal weight: 0.0870 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1108 ASN I1244 HIS ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.155456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.123929 restraints weight = 37907.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.123029 restraints weight = 39302.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.124241 restraints weight = 36327.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.124747 restraints weight = 25081.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.124762 restraints weight = 22483.126| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 27401 Z= 0.115 Angle : 0.581 12.741 37264 Z= 0.305 Chirality : 0.043 0.329 4253 Planarity : 0.004 0.068 4665 Dihedral : 13.337 95.883 4260 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.29 % Favored : 94.68 % Rotamer: Outliers : 1.94 % Allowed : 14.04 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.15), residues: 3249 helix: 1.24 (0.16), residues: 1121 sheet: -0.89 (0.25), residues: 432 loop : -2.02 (0.14), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 12 TYR 0.015 0.001 TYR J 140 PHE 0.013 0.001 PHE I 514 TRP 0.019 0.001 TRP J 115 HIS 0.008 0.001 HIS J 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (27394) covalent geometry : angle 0.58121 / 0.31 (37258) hydrogen bonds : bond 0.03792 / 4.14 ( 1079) hydrogen bonds : angle 4.28130 / 4.79 ( 2985) metal coordination : bond 0.00265 / 0.27 ( 7) metal coordination : angle 1.27994 / 2.26 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 299 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 LYS cc_start: 0.8937 (ptmt) cc_final: 0.8699 (ptmt) REVERT: H 133 LEU cc_start: 0.8220 (mt) cc_final: 0.7926 (mt) REVERT: H 170 ARG cc_start: 0.7362 (ttm170) cc_final: 0.6477 (ptp-170) REVERT: I 47 TYR cc_start: 0.4998 (m-80) cc_final: 0.4515 (m-80) REVERT: I 383 SER cc_start: 0.8539 (m) cc_final: 0.8148 (p) REVERT: I 559 CYS cc_start: 0.9334 (t) cc_final: 0.9058 (t) REVERT: I 917 SER cc_start: 0.8690 (p) cc_final: 0.8314 (t) REVERT: I 1170 MET cc_start: 0.7023 (tpp) cc_final: 0.6544 (ttm) REVERT: J 130 MET cc_start: 0.8307 (tpp) cc_final: 0.8088 (mmt) REVERT: J 200 GLN cc_start: 0.7764 (tp40) cc_final: 0.7389 (tt0) REVERT: J 205 LEU cc_start: 0.6960 (OUTLIER) cc_final: 0.6640 (mm) REVERT: J 505 ASP cc_start: 0.8895 (OUTLIER) cc_final: 0.8234 (t0) REVERT: J 581 MET cc_start: 0.8523 (mtp) cc_final: 0.8235 (mtp) REVERT: J 582 ILE cc_start: 0.8910 (mt) cc_final: 0.8621 (mt) REVERT: K 58 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7859 (pp) REVERT: N 27 ARG cc_start: 0.7357 (tpp80) cc_final: 0.7105 (mtt-85) REVERT: N 32 LEU cc_start: 0.8822 (tp) cc_final: 0.8428 (tt) REVERT: N 36 GLU cc_start: 0.8324 (tp30) cc_final: 0.8116 (tp30) outliers start: 54 outliers final: 38 residues processed: 332 average time/residue: 0.1585 time to fit residues: 86.9753 Evaluate side-chains 311 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 270 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 819 SER Chi-restraints excluded: chain I residue 851 THR Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1108 ASN Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 285 LEU Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain N residue 73 MET Chi-restraints excluded: chain N residue 90 MET Chi-restraints excluded: chain N residue 115 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 317 optimal weight: 5.9990 chunk 141 optimal weight: 0.8980 chunk 286 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 320 optimal weight: 5.9990 chunk 241 optimal weight: 0.0670 chunk 36 optimal weight: 2.9990 chunk 122 optimal weight: 0.0000 chunk 262 optimal weight: 0.7980 overall best weight: 0.5522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 103 ASN I 120 GLN I1244 HIS J 364 HIS ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.155863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.123779 restraints weight = 37892.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.122200 restraints weight = 34176.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.123215 restraints weight = 29543.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.123847 restraints weight = 23852.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.123984 restraints weight = 20985.463| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 27401 Z= 0.115 Angle : 0.580 12.209 37264 Z= 0.304 Chirality : 0.043 0.307 4253 Planarity : 0.004 0.067 4665 Dihedral : 13.244 89.612 4260 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.60 % Favored : 94.37 % Rotamer: Outliers : 1.90 % Allowed : 14.51 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.90 (0.15), residues: 3249 helix: 1.31 (0.16), residues: 1122 sheet: -0.83 (0.25), residues: 434 loop : -1.95 (0.14), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I1223 TYR 0.017 0.001 TYR I1231 PHE 0.031 0.001 PHE I 390 TRP 0.012 0.001 TRP J 115 HIS 0.007 0.001 HIS J 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (27394) covalent geometry : angle 0.57950 / 0.30 (37258) hydrogen bonds : bond 0.03673 / 4.00 ( 1079) hydrogen bonds : angle 4.23504 / 4.73 ( 2985) metal coordination : bond 0.00307 / 0.30 ( 7) metal coordination : angle 1.30411 / 2.30 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 285 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 133 LEU cc_start: 0.8215 (mt) cc_final: 0.7929 (mt) REVERT: H 170 ARG cc_start: 0.7282 (ttm170) cc_final: 0.6494 (ptp-170) REVERT: I 47 TYR cc_start: 0.5195 (m-80) cc_final: 0.4717 (m-80) REVERT: I 215 TYR cc_start: 0.8418 (OUTLIER) cc_final: 0.8038 (m-10) REVERT: I 383 SER cc_start: 0.8662 (m) cc_final: 0.8335 (p) REVERT: I 403 MET cc_start: 0.8570 (tmm) cc_final: 0.8275 (tmm) REVERT: I 559 CYS cc_start: 0.9240 (t) cc_final: 0.8971 (t) REVERT: I 1056 VAL cc_start: 0.9021 (OUTLIER) cc_final: 0.8801 (m) REVERT: I 1119 MET cc_start: 0.8206 (tpt) cc_final: 0.7960 (tpp) REVERT: J 200 GLN cc_start: 0.7874 (tp40) cc_final: 0.7558 (tt0) REVERT: J 205 LEU cc_start: 0.6956 (OUTLIER) cc_final: 0.6637 (mm) REVERT: J 505 ASP cc_start: 0.8789 (OUTLIER) cc_final: 0.8146 (t0) REVERT: J 544 LEU cc_start: 0.9037 (tp) cc_final: 0.8814 (tt) REVERT: J 582 ILE cc_start: 0.8864 (mt) cc_final: 0.8587 (mt) REVERT: J 697 MET cc_start: 0.8301 (tmm) cc_final: 0.7824 (tmm) REVERT: J 1188 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7161 (mt-10) REVERT: K 58 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7840 (pp) REVERT: N 27 ARG cc_start: 0.7378 (tpp80) cc_final: 0.7143 (mtt-85) REVERT: N 32 LEU cc_start: 0.8891 (tp) cc_final: 0.8503 (tt) REVERT: N 36 GLU cc_start: 0.8247 (tp30) cc_final: 0.8027 (tp30) outliers start: 53 outliers final: 39 residues processed: 321 average time/residue: 0.1619 time to fit residues: 86.0295 Evaluate side-chains 316 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 271 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 215 TYR Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 575 LEU Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 819 SER Chi-restraints excluded: chain I residue 851 THR Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1154 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain J residue 1188 GLU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain N residue 73 MET Chi-restraints excluded: chain N residue 90 MET Chi-restraints excluded: chain N residue 106 LYS Chi-restraints excluded: chain N residue 115 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 291 optimal weight: 8.9990 chunk 258 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 110 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 214 optimal weight: 3.9990 chunk 0 optimal weight: 40.0000 chunk 160 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 127 GLN I 120 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1244 HIS ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.153408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.121258 restraints weight = 37971.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.122186 restraints weight = 40309.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.122888 restraints weight = 29883.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.122524 restraints weight = 24119.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.122730 restraints weight = 22594.148| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 27401 Z= 0.143 Angle : 0.601 11.968 37264 Z= 0.313 Chirality : 0.044 0.296 4253 Planarity : 0.004 0.067 4665 Dihedral : 13.227 85.704 4260 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.76 % Favored : 94.21 % Rotamer: Outliers : 1.87 % Allowed : 14.58 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.15), residues: 3249 helix: 1.33 (0.16), residues: 1123 sheet: -0.82 (0.25), residues: 434 loop : -1.93 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 143 TYR 0.014 0.001 TYR I 70 PHE 0.014 0.001 PHE I 514 TRP 0.013 0.001 TRP J 115 HIS 0.007 0.001 HIS G 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (27394) covalent geometry : angle 0.60075 / 0.31 (37258) hydrogen bonds : bond 0.03829 / 4.16 ( 1079) hydrogen bonds : angle 4.24361 / 4.74 ( 2985) metal coordination : bond 0.00519 / 0.48 ( 7) metal coordination : angle 1.51254 / 2.69 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 276 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 133 LEU cc_start: 0.8281 (mt) cc_final: 0.7996 (mt) REVERT: H 170 ARG cc_start: 0.7314 (ttm170) cc_final: 0.6483 (ptp-170) REVERT: I 47 TYR cc_start: 0.5245 (m-80) cc_final: 0.4724 (m-80) REVERT: I 215 TYR cc_start: 0.8490 (OUTLIER) cc_final: 0.8018 (m-10) REVERT: I 383 SER cc_start: 0.8466 (m) cc_final: 0.8121 (p) REVERT: I 559 CYS cc_start: 0.9293 (t) cc_final: 0.9017 (t) REVERT: I 1056 VAL cc_start: 0.9065 (OUTLIER) cc_final: 0.8814 (m) REVERT: I 1119 MET cc_start: 0.8141 (tpt) cc_final: 0.7854 (tpp) REVERT: J 200 GLN cc_start: 0.7827 (tp40) cc_final: 0.7502 (tt0) REVERT: J 205 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6606 (mm) REVERT: J 505 ASP cc_start: 0.8936 (OUTLIER) cc_final: 0.8285 (t0) REVERT: J 582 ILE cc_start: 0.8919 (mt) cc_final: 0.8643 (mt) REVERT: J 697 MET cc_start: 0.8319 (tmm) cc_final: 0.7863 (tmm) REVERT: J 983 LYS cc_start: 0.8113 (mmmm) cc_final: 0.7894 (mmmm) REVERT: J 1188 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7124 (mt-10) REVERT: K 58 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7924 (pp) REVERT: N 27 ARG cc_start: 0.7409 (tpp80) cc_final: 0.7134 (mtt-85) REVERT: N 32 LEU cc_start: 0.8872 (tp) cc_final: 0.8503 (tt) REVERT: N 75 MET cc_start: 0.8194 (tpp) cc_final: 0.7550 (tpp) outliers start: 52 outliers final: 42 residues processed: 307 average time/residue: 0.1634 time to fit residues: 82.9405 Evaluate side-chains 318 residues out of total 2789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 270 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 127 GLN Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 84 GLU Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 215 TYR Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 575 LEU Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 819 SER Chi-restraints excluded: chain I residue 851 THR Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 285 LEU Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain J residue 1188 GLU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain N residue 73 MET Chi-restraints excluded: chain N residue 90 MET Chi-restraints excluded: chain N residue 106 LYS Chi-restraints excluded: chain N residue 115 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 69 optimal weight: 5.9990 chunk 287 optimal weight: 10.0000 chunk 296 optimal weight: 20.0000 chunk 144 optimal weight: 9.9990 chunk 244 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 chunk 88 optimal weight: 0.0050 chunk 155 optimal weight: 0.0370 chunk 271 optimal weight: 10.0000 chunk 206 optimal weight: 3.9990 chunk 196 optimal weight: 1.9990 overall best weight: 1.0076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 103 ASN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1244 HIS ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.154863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.122451 restraints weight = 37793.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.122984 restraints weight = 40579.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.124557 restraints weight = 28780.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.123807 restraints weight = 20896.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.124265 restraints weight = 21320.526| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.216 27401 Z= 0.177 Angle : 0.718 59.200 37264 Z= 0.399 Chirality : 0.043 0.280 4253 Planarity : 0.004 0.067 4665 Dihedral : 13.227 85.675 4260 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.76 % Favored : 94.21 % Rotamer: Outliers : 1.87 % Allowed : 14.51 % Favored : 83.63 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.15), residues: 3249 helix: 1.34 (0.16), residues: 1123 sheet: -0.82 (0.25), residues: 434 loop : -1.95 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG I 694 TYR 0.012 0.001 TYR G 177 PHE 0.015 0.001 PHE I 514 TRP 0.012 0.001 TRP J 115 HIS 0.006 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 (27394) covalent geometry : angle 0.71815 / 0.40 (37258) hydrogen bonds : bond 0.03818 / 4.15 ( 1079) hydrogen bonds : angle 4.24376 / 4.74 ( 2985) metal coordination : bond 0.00478 / 0.45 ( 7) metal coordination : angle 1.50583 / 2.68 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3965.86 seconds wall clock time: 69 minutes 43.54 seconds (4183.54 seconds total)