Starting phenix.real_space_refine on Tue Feb 20 04:51:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c6u_7351/02_2024/6c6u_7351_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c6u_7351/02_2024/6c6u_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c6u_7351/02_2024/6c6u_7351.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c6u_7351/02_2024/6c6u_7351.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c6u_7351/02_2024/6c6u_7351_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c6u_7351/02_2024/6c6u_7351_neut.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Residue "I ARG 268": "NH1" <-> "NH2" Residue "I ARG 332": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/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: {'GLN:plan1': 1, 'ARG:plan': 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: 14.00, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 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: 9.82 Conformation dependent library (CDL) restraints added in 4.6 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: 9.28 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: 12.99 Time building geometry restraints manager: 10.70 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=" C ARG G 166 " pdb=" N PRO G 167 " ideal model delta sigma weight residual 1.326 1.372 -0.046 1.44e-02 4.82e+03 1.03e+01 bond pdb=" C ARG J1148 " pdb=" N ARG J1149 " ideal model delta sigma weight residual 1.331 1.266 0.065 2.07e-02 2.33e+03 9.72e+00 bond pdb=" CB VAL J1255 " pdb=" CG1 VAL J1255 " ideal model delta sigma weight residual 1.521 1.450 0.071 3.30e-02 9.18e+02 4.62e+00 bond pdb=" CG LEU I 817 " pdb=" CD1 LEU I 817 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.47e+00 bond pdb=" CB VAL J 801 " pdb=" CG2 VAL J 801 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.16e+00 ... (remaining 27389 not shown) Histogram of bond angle deviations from ideal: 95.12 - 103.18: 371 103.18 - 111.23: 10925 111.23 - 119.29: 12311 119.29 - 127.34: 13362 127.34 - 135.40: 289 Bond angle restraints: 37258 Sorted by residual: 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 angle pdb=" C GLY J 852 " pdb=" N THR J 853 " pdb=" CA THR J 853 " ideal model delta sigma weight residual 121.31 128.63 -7.32 1.49e+00 4.50e-01 2.41e+01 angle pdb=" C HIS N 33 " pdb=" N ASN N 34 " pdb=" CA ASN N 34 " ideal model delta sigma weight residual 121.54 130.62 -9.08 1.91e+00 2.74e-01 2.26e+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: 3900 0.107 - 0.214: 334 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 2.440 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 2.440 ... (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 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: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 7.980 Check model and map are aligned: 0.420 Set scattering table: 0.250 Process input model: 81.500 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.110 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 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 : 0.008 0.071 27394 Z= 0.533 Angle : 1.043 12.774 37258 Z= 0.570 Chirality : 0.062 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.043 0.004 TRP I 183 HIS 0.016 0.002 HIS J 777 PHE 0.038 0.003 PHE J 620 TYR 0.038 0.003 TYR I1229 ARG 0.019 0.001 ARG J 352 *********************** 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 fitting. rotamer outliers: 8 poor density : 605 time to evaluate : 2.887 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: 0.4495 (m-80) REVERT: I 339 ASN cc_start: 0.7844 (t0) cc_final: 0.7438 (t0) REVERT: I 383 SER cc_start: 0.8402 (m) cc_final: 0.7980 (p) REVERT: I 496 LYS cc_start: 0.8756 (mmtt) cc_final: 0.8555 (tppt) REVERT: I 516 ASP cc_start: 0.6864 (p0) cc_final: 0.6517 (p0) REVERT: I 559 CYS cc_start: 0.9326 (t) cc_final: 0.8981 (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: 0.6362 (mt-10) REVERT: J 372 MET cc_start: 0.9020 (mtp) cc_final: 0.8795 (ttm) REVERT: J 521 LYS cc_start: 0.8740 (mttt) cc_final: 0.8460 (mtpp) REVERT: J 582 ILE cc_start: 0.8849 (mt) cc_final: 0.8582 (mt) REVERT: J 821 MET cc_start: 0.7697 (tpp) cc_final: 0.7367 (mtp) REVERT: J 1243 LEU cc_start: 0.8640 (tp) cc_final: 0.8367 (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: 0.4452 time to fit residues: 406.7781 Evaluate side-chains 316 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 315 time to evaluate : 3.099 ------------------------------------------------------------------------------- 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 277 optimal weight: 0.2980 chunk 249 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 168 optimal weight: 0.7980 chunk 133 optimal weight: 0.9990 chunk 257 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 156 optimal weight: 0.6980 chunk 191 optimal weight: 1.9990 chunk 298 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN G 147 GLN H 103 ASN H 117 HIS I 69 GLN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 150 HIS I 214 ASN ** I 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 330 HIS I 580 GLN I 604 HIS ** I 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 834 GLN ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1313 HIS J 157 GLN J 365 GLN J 910 ASN J1108 GLN J1326 GLN ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1367 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.153 27394 Z= 0.193 Angle : 0.606 8.901 37258 Z= 0.322 Chirality : 0.043 0.339 4253 Planarity : 0.005 0.059 4665 Dihedral : 14.041 131.866 4261 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.20 % Favored : 94.71 % Rotamer: Outliers : 2.12 % Allowed : 8.65 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.13), residues: 3249 helix: -0.63 (0.15), residues: 1112 sheet: -1.74 (0.24), residues: 428 loop : -2.67 (0.13), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 183 HIS 0.010 0.001 HIS G 23 PHE 0.014 0.001 PHE J 620 TYR 0.018 0.001 TYR G 177 ARG 0.006 0.000 ARG N 84 *********************** 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 453 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 394 time to evaluate : 2.996 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: 0.7930 (mmm) cc_final: 0.7690 (mtp) REVERT: H 150 ARG cc_start: 0.7337 (mtt90) cc_final: 0.7111 (ttm-80) REVERT: H 170 ARG cc_start: 0.7020 (ttm170) cc_final: 0.6234 (ptp-170) REVERT: H 226 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7405 (mm-30) REVERT: I 47 TYR cc_start: 0.4746 (m-80) cc_final: 0.4321 (m-80) REVERT: I 337 PHE cc_start: 0.6840 (t80) cc_final: 0.6540 (t80) REVERT: I 339 ASN cc_start: 0.7752 (t0) cc_final: 0.7473 (t0) REVERT: I 383 SER cc_start: 0.8448 (m) cc_final: 0.8075 (p) REVERT: I 496 LYS cc_start: 0.8921 (mmtt) cc_final: 0.8711 (tppt) REVERT: I 559 CYS cc_start: 0.9296 (t) cc_final: 0.9000 (t) REVERT: I 1304 MET cc_start: 0.8834 (tpp) cc_final: 0.8572 (tpp) REVERT: J 29 MET cc_start: 0.7396 (tpp) cc_final: 0.6858 (mpp) REVERT: J 200 GLN cc_start: 0.7708 (tp40) cc_final: 0.7186 (tt0) REVERT: J 372 MET cc_start: 0.8873 (mtp) cc_final: 0.8456 (ttm) REVERT: J 505 ASP cc_start: 0.8722 (OUTLIER) cc_final: 0.8134 (t0) REVERT: J 521 LYS cc_start: 0.8691 (mttt) cc_final: 0.8467 (mtpp) REVERT: J 582 ILE cc_start: 0.8864 (mt) cc_final: 0.8570 (mt) REVERT: J 666 GLU cc_start: 0.6506 (mt-10) cc_final: 0.6186 (tm-30) REVERT: J 1254 GLU cc_start: 0.7577 (mt-10) cc_final: 0.6864 (mt-10) REVERT: J 1281 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7216 (mp0) REVERT: N 32 LEU cc_start: 0.8861 (tp) cc_final: 0.8608 (tt) outliers start: 59 outliers final: 29 residues processed: 430 average time/residue: 0.3819 time to fit residues: 260.2538 Evaluate side-chains 324 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 293 time to evaluate : 2.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain H residue 14 VAL 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 205 MET Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 412 GLU Chi-restraints excluded: chain I residue 417 SER Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 524 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 878 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 1254 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 517 CYS Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 1281 GLU Chi-restraints excluded: chain K residue 58 LEU 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 166 optimal weight: 3.9990 chunk 92 optimal weight: 0.1980 chunk 248 optimal weight: 4.9990 chunk 203 optimal weight: 6.9990 chunk 82 optimal weight: 0.0030 chunk 299 optimal weight: 0.8980 chunk 323 optimal weight: 1.9990 chunk 266 optimal weight: 7.9990 chunk 296 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 240 optimal weight: 2.9990 overall best weight: 1.2194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 23 HIS G 103 ASN G 137 ASN H 37 HIS H 103 ASN H 127 GLN H 128 HIS ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 214 ASN ** I 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 580 GLN I 658 GLN I1108 ASN ** I1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN J 450 HIS J1010 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.158 27394 Z= 0.222 Angle : 0.587 10.219 37258 Z= 0.309 Chirality : 0.043 0.333 4253 Planarity : 0.004 0.054 4665 Dihedral : 13.685 129.955 4260 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.12 % Favored : 93.78 % Rotamer: Outliers : 3.05 % Allowed : 10.84 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.14), residues: 3249 helix: 0.28 (0.15), residues: 1123 sheet: -1.36 (0.24), residues: 419 loop : -2.46 (0.13), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 183 HIS 0.009 0.001 HIS G 23 PHE 0.013 0.001 PHE J 620 TYR 0.018 0.001 TYR G 177 ARG 0.004 0.000 ARG I1301 *********************** 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 403 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 318 time to evaluate : 3.056 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: 0.7206 (ttm170) cc_final: 0.6335 (ptp-170) REVERT: H 226 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7533 (mm-30) REVERT: I 47 TYR cc_start: 0.4932 (m-80) cc_final: 0.4386 (m-80) REVERT: I 239 MET cc_start: 0.5204 (ppp) cc_final: 0.4441 (ppp) REVERT: I 383 SER cc_start: 0.8562 (m) cc_final: 0.8168 (p) REVERT: I 496 LYS cc_start: 0.8960 (mmtt) cc_final: 0.8717 (tppt) REVERT: I 559 CYS cc_start: 0.9278 (t) cc_final: 0.9022 (t) REVERT: I 817 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9149 (tp) REVERT: I 917 SER cc_start: 0.8696 (p) cc_final: 0.8432 (t) REVERT: J 171 GLU cc_start: 0.7771 (mp0) cc_final: 0.7568 (mp0) REVERT: J 200 GLN cc_start: 0.7732 (tp40) cc_final: 0.7256 (tt0) REVERT: J 205 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6730 (mm) REVERT: J 372 MET cc_start: 0.8943 (mtp) cc_final: 0.8715 (ttm) REVERT: J 431 ARG cc_start: 0.9157 (OUTLIER) cc_final: 0.8945 (ptt90) REVERT: J 505 ASP cc_start: 0.8768 (OUTLIER) cc_final: 0.8124 (t0) REVERT: J 521 LYS cc_start: 0.8883 (mttt) cc_final: 0.8597 (mtpp) REVERT: J 581 MET cc_start: 0.8847 (mtp) cc_final: 0.8607 (mtp) REVERT: J 582 ILE cc_start: 0.8901 (mt) cc_final: 0.8587 (mt) REVERT: J 800 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8824 (mm) REVERT: J 1143 ASP cc_start: 0.7712 (t0) cc_final: 0.7487 (t0) REVERT: J 1281 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7243 (mp0) REVERT: N 36 GLU cc_start: 0.8259 (tp30) cc_final: 0.7967 (tp30) outliers start: 85 outliers final: 48 residues processed: 377 average time/residue: 0.3921 time to fit residues: 234.5864 Evaluate side-chains 339 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 285 time to evaluate : 2.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain H residue 14 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 173 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 81 ASP 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 604 HIS Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 817 LEU 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 1250 SER 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 180 MET 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 507 VAL Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 800 LEU Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain J residue 1281 GLU Chi-restraints excluded: chain J residue 1329 THR Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain N residue 73 MET Chi-restraints excluded: chain N residue 90 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 295 optimal weight: 7.9990 chunk 225 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 33 optimal weight: 9.9990 chunk 142 optimal weight: 9.9990 chunk 200 optimal weight: 0.0670 chunk 300 optimal weight: 0.5980 chunk 318 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 chunk 284 optimal weight: 40.0000 chunk 85 optimal weight: 8.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 103 ASN G 137 ASN H 127 GLN H 227 GLN I 120 GLN ** I 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1108 ASN ** I1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 27394 Z= 0.162 Angle : 0.549 11.613 37258 Z= 0.288 Chirality : 0.042 0.292 4253 Planarity : 0.004 0.054 4665 Dihedral : 13.420 128.782 4260 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.29 % Favored : 94.61 % Rotamer: Outliers : 2.76 % Allowed : 12.10 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.14), residues: 3249 helix: 0.82 (0.16), residues: 1130 sheet: -1.23 (0.25), residues: 419 loop : -2.22 (0.14), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 9 HIS 0.006 0.001 HIS J 865 PHE 0.012 0.001 PHE I 337 TYR 0.014 0.001 TYR G 177 ARG 0.004 0.000 ARG H 12 *********************** 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 409 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 332 time to evaluate : 3.057 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: 0.7299 (ttm170) cc_final: 0.6387 (ptp-170) REVERT: I 47 TYR cc_start: 0.4804 (m-80) cc_final: 0.4327 (m-80) REVERT: I 337 PHE cc_start: 0.6664 (t80) cc_final: 0.6416 (t80) REVERT: I 339 ASN cc_start: 0.7733 (t0) cc_final: 0.7349 (t0) REVERT: I 383 SER cc_start: 0.8522 (m) cc_final: 0.8138 (p) REVERT: I 496 LYS cc_start: 0.8960 (mmtt) cc_final: 0.8697 (tppt) REVERT: I 559 CYS cc_start: 0.9280 (t) cc_final: 0.9033 (t) REVERT: I 1304 MET cc_start: 0.8924 (tpp) cc_final: 0.8626 (tpp) REVERT: J 29 MET cc_start: 0.7283 (tpp) cc_final: 0.6927 (mpp) REVERT: J 200 GLN cc_start: 0.7695 (tp40) cc_final: 0.7268 (tt0) REVERT: J 205 LEU cc_start: 0.6907 (OUTLIER) cc_final: 0.6635 (mm) REVERT: J 505 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.8001 (t0) REVERT: J 521 LYS cc_start: 0.8916 (mttt) cc_final: 0.8613 (mtpp) REVERT: J 582 ILE cc_start: 0.8975 (mt) cc_final: 0.8682 (mt) REVERT: J 800 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8740 (mm) REVERT: J 992 LYS cc_start: 0.6985 (tppt) cc_final: 0.6078 (mmtm) REVERT: J 1144 LEU cc_start: 0.9203 (mt) cc_final: 0.8969 (tp) REVERT: K 58 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7774 (pp) REVERT: N 36 GLU cc_start: 0.8196 (tp30) cc_final: 0.7683 (mp0) outliers start: 77 outliers final: 40 residues processed: 382 average time/residue: 0.3742 time to fit residues: 230.7484 Evaluate side-chains 333 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 289 time to evaluate : 2.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain H residue 14 VAL 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 146 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 210 THR 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 524 ILE Chi-restraints excluded: chain I residue 604 HIS Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 819 SER Chi-restraints excluded: chain I residue 851 THR Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 180 MET 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 800 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 264 optimal weight: 0.9990 chunk 180 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 236 optimal weight: 3.9990 chunk 131 optimal weight: 6.9990 chunk 271 optimal weight: 7.9990 chunk 219 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 162 optimal weight: 0.6980 chunk 285 optimal weight: 10.0000 chunk 80 optimal weight: 40.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 132 HIS ** G 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 127 GLN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 658 GLN ** I 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1108 ASN ** I1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN J1326 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 27394 Z= 0.346 Angle : 0.652 10.654 37258 Z= 0.339 Chirality : 0.045 0.296 4253 Planarity : 0.005 0.052 4665 Dihedral : 13.502 128.773 4260 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.08 % Favored : 92.83 % Rotamer: Outliers : 3.70 % Allowed : 12.89 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.14), residues: 3249 helix: 0.82 (0.15), residues: 1136 sheet: -1.13 (0.25), residues: 415 loop : -2.26 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP N 9 HIS 0.012 0.001 HIS J 777 PHE 0.017 0.002 PHE J 620 TYR 0.018 0.002 TYR G 177 ARG 0.006 0.001 ARG J 312 *********************** 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 399 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 296 time to evaluate : 2.940 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: 0.7411 (ttm170) cc_final: 0.6478 (ptp-170) REVERT: I 47 TYR cc_start: 0.5418 (m-80) cc_final: 0.4708 (m-80) REVERT: I 339 ASN cc_start: 0.7849 (t0) cc_final: 0.7528 (t0) REVERT: I 383 SER cc_start: 0.8530 (m) cc_final: 0.8162 (p) REVERT: I 496 LYS cc_start: 0.9007 (mmtt) cc_final: 0.8781 (tppt) REVERT: I 559 CYS cc_start: 0.9242 (t) cc_final: 0.9020 (t) REVERT: J 171 GLU cc_start: 0.7782 (mp0) cc_final: 0.7359 (mp0) REVERT: J 205 LEU cc_start: 0.7088 (OUTLIER) cc_final: 0.6712 (mm) REVERT: J 505 ASP cc_start: 0.8855 (OUTLIER) cc_final: 0.7991 (t0) REVERT: J 521 LYS cc_start: 0.8925 (mttt) cc_final: 0.8588 (mtpp) REVERT: J 582 ILE cc_start: 0.8950 (mt) cc_final: 0.8703 (mt) REVERT: J 740 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8711 (mp) REVERT: J 800 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8919 (mm) REVERT: J 1143 ASP cc_start: 0.7780 (t0) cc_final: 0.7555 (t0) REVERT: J 1144 LEU cc_start: 0.9237 (mt) cc_final: 0.8977 (tp) REVERT: J 1243 LEU cc_start: 0.8810 (tp) cc_final: 0.8546 (tp) REVERT: K 58 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8016 (pp) REVERT: N 32 LEU cc_start: 0.8849 (tp) cc_final: 0.8456 (tt) REVERT: N 36 GLU cc_start: 0.8270 (tp30) cc_final: 0.7931 (tp30) outliers start: 103 outliers final: 73 residues processed: 369 average time/residue: 0.3806 time to fit residues: 226.7436 Evaluate side-chains 353 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 275 time to evaluate : 2.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 222 THR Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 54 CYS 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 173 VAL Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 210 THR 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 424 ASP Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 503 LYS 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 589 THR Chi-restraints excluded: chain I residue 604 HIS Chi-restraints excluded: chain I residue 620 ASN Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 785 ASP 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 878 THR Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1239 VAL Chi-restraints excluded: chain I residue 1250 SER 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 114 ILE Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 263 SER 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 624 ILE Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 800 LEU Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1329 THR Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 73 MET Chi-restraints excluded: chain N residue 86 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 106 optimal weight: 0.8980 chunk 286 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 186 optimal weight: 2.9990 chunk 78 optimal weight: 0.0020 chunk 318 optimal weight: 5.9990 chunk 264 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 103 ASN ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 ASN H 127 GLN I 120 GLN ** I 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 658 GLN I1108 ASN ** I1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 805 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.183 27394 Z= 0.186 Angle : 0.547 10.184 37258 Z= 0.286 Chirality : 0.042 0.274 4253 Planarity : 0.004 0.056 4665 Dihedral : 13.263 126.841 4260 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.36 % Favored : 94.55 % Rotamer: Outliers : 2.69 % Allowed : 14.76 % Favored : 82.55 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.15), residues: 3249 helix: 1.20 (0.16), residues: 1128 sheet: -1.00 (0.25), residues: 419 loop : -2.10 (0.14), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 80 HIS 0.006 0.001 HIS J 865 PHE 0.011 0.001 PHE I 390 TYR 0.012 0.001 TYR G 177 ARG 0.004 0.000 ARG H 12 *********************** 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 376 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 301 time to evaluate : 3.270 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 170 ARG cc_start: 0.7400 (ttm170) cc_final: 0.6366 (ptp-170) REVERT: I 47 TYR cc_start: 0.5396 (m-80) cc_final: 0.4718 (m-80) REVERT: I 215 TYR cc_start: 0.8536 (OUTLIER) cc_final: 0.7976 (m-10) REVERT: I 383 SER cc_start: 0.8525 (m) cc_final: 0.8143 (p) REVERT: I 403 MET cc_start: 0.8675 (tmm) cc_final: 0.8368 (tmm) REVERT: I 496 LYS cc_start: 0.8962 (mmtt) cc_final: 0.8726 (tppt) REVERT: I 559 CYS cc_start: 0.9257 (t) cc_final: 0.9020 (t) REVERT: I 1304 MET cc_start: 0.8896 (tpp) cc_final: 0.8581 (tpp) REVERT: J 171 GLU cc_start: 0.7719 (mp0) cc_final: 0.7282 (mp0) REVERT: J 188 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8204 (tt) REVERT: J 205 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6683 (mm) REVERT: J 237 MET cc_start: 0.8583 (mtt) cc_final: 0.8364 (mtt) REVERT: J 505 ASP cc_start: 0.8771 (OUTLIER) cc_final: 0.8155 (t0) REVERT: J 521 LYS cc_start: 0.8911 (mttt) cc_final: 0.8583 (mtpp) REVERT: J 582 ILE cc_start: 0.9000 (mt) cc_final: 0.8716 (mt) REVERT: J 740 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8701 (mp) REVERT: J 800 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8716 (mm) REVERT: J 1143 ASP cc_start: 0.7734 (t0) cc_final: 0.7409 (t0) REVERT: J 1144 LEU cc_start: 0.9193 (mt) cc_final: 0.8897 (tp) REVERT: J 1243 LEU cc_start: 0.8746 (tp) cc_final: 0.8372 (tp) REVERT: J 1254 GLU cc_start: 0.7323 (mt-10) cc_final: 0.7056 (mt-10) REVERT: K 58 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7878 (pp) REVERT: N 32 LEU cc_start: 0.8834 (tp) cc_final: 0.8517 (tt) REVERT: N 36 GLU cc_start: 0.8200 (tp30) cc_final: 0.7849 (tp30) REVERT: N 75 MET cc_start: 0.7859 (tpp) cc_final: 0.7452 (tpp) outliers start: 75 outliers final: 52 residues processed: 353 average time/residue: 0.3826 time to fit residues: 221.0162 Evaluate side-chains 334 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 275 time to evaluate : 3.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 178 SER 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 14 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 139 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 210 THR 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 215 TYR Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 503 LYS Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 690 VAL 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 1041 ASP 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 1298 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 263 SER 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 708 ASN Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 800 LEU Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 73 MET Chi-restraints excluded: chain N residue 90 MET Chi-restraints excluded: chain N residue 106 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 306 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 181 optimal weight: 2.9990 chunk 232 optimal weight: 4.9990 chunk 180 optimal weight: 0.1980 chunk 267 optimal weight: 6.9990 chunk 177 optimal weight: 5.9990 chunk 317 optimal weight: 5.9990 chunk 198 optimal weight: 4.9990 chunk 193 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 103 ASN ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 127 GLN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 658 GLN ** I 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1108 ASN I1268 GLN J 805 GLN J1218 HIS J1326 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.145 27394 Z= 0.292 Angle : 0.602 10.342 37258 Z= 0.314 Chirality : 0.043 0.254 4253 Planarity : 0.004 0.052 4665 Dihedral : 13.316 126.623 4260 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.65 % Favored : 93.26 % Rotamer: Outliers : 3.38 % Allowed : 14.69 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.15), residues: 3249 helix: 1.19 (0.16), residues: 1130 sheet: -0.99 (0.25), residues: 426 loop : -2.09 (0.14), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 80 HIS 0.009 0.001 HIS J 777 PHE 0.013 0.001 PHE J 620 TYR 0.020 0.001 TYR I 70 ARG 0.003 0.000 ARG J 271 *********************** 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 373 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 279 time to evaluate : 3.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 170 ARG cc_start: 0.7388 (ttm170) cc_final: 0.6523 (ptp-170) REVERT: I 47 TYR cc_start: 0.5428 (m-80) cc_final: 0.4827 (m-80) REVERT: I 215 TYR cc_start: 0.8595 (OUTLIER) cc_final: 0.7799 (m-10) REVERT: I 383 SER cc_start: 0.8549 (m) cc_final: 0.8162 (p) REVERT: I 496 LYS cc_start: 0.8991 (mmtt) cc_final: 0.8747 (tppt) REVERT: I 559 CYS cc_start: 0.9265 (t) cc_final: 0.9050 (t) REVERT: I 1217 THR cc_start: 0.8762 (m) cc_final: 0.8553 (p) REVERT: J 188 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8372 (tt) REVERT: J 200 GLN cc_start: 0.7735 (tp40) cc_final: 0.7383 (tt0) REVERT: J 205 LEU cc_start: 0.7009 (OUTLIER) cc_final: 0.6607 (mm) REVERT: J 505 ASP cc_start: 0.8866 (OUTLIER) cc_final: 0.8010 (t0) REVERT: J 521 LYS cc_start: 0.8905 (mttt) cc_final: 0.8555 (mtpp) REVERT: J 582 ILE cc_start: 0.8976 (mt) cc_final: 0.8714 (mt) REVERT: J 740 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8724 (mp) REVERT: J 800 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8804 (mm) REVERT: J 1143 ASP cc_start: 0.7772 (t0) cc_final: 0.7462 (t0) REVERT: J 1144 LEU cc_start: 0.9200 (mt) cc_final: 0.8951 (tp) REVERT: J 1188 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7294 (mt-10) REVERT: K 58 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7985 (pp) REVERT: N 36 GLU cc_start: 0.8207 (tp30) cc_final: 0.7884 (tp30) outliers start: 94 outliers final: 67 residues processed: 346 average time/residue: 0.3683 time to fit residues: 207.3141 Evaluate side-chains 346 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 271 time to evaluate : 2.892 ------------------------------------------------------------------------------- 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 69 SER Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 178 SER 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 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 54 CYS 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 173 VAL Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain I residue 81 ASP 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 215 TYR Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 503 LYS Chi-restraints excluded: chain I residue 508 SER Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 620 ASN Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 785 ASP 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 1041 ASP 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 1233 LEU Chi-restraints excluded: chain I residue 1239 VAL 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 120 LEU Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 194 LEU Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 263 SER Chi-restraints excluded: chain J residue 330 MET 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 641 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 800 LEU Chi-restraints excluded: chain J residue 805 GLN 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 106 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 196 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 189 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 201 optimal weight: 0.8980 chunk 216 optimal weight: 3.9990 chunk 156 optimal weight: 0.2980 chunk 29 optimal weight: 0.8980 chunk 249 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 103 ASN ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 127 GLN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 658 GLN ** I1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 805 GLN J1326 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.136 27394 Z= 0.173 Angle : 0.546 11.310 37258 Z= 0.285 Chirality : 0.041 0.249 4253 Planarity : 0.004 0.057 4665 Dihedral : 13.161 125.292 4260 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.20 % Favored : 94.71 % Rotamer: Outliers : 2.69 % Allowed : 15.37 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.15), residues: 3249 helix: 1.41 (0.16), residues: 1128 sheet: -1.02 (0.26), residues: 416 loop : -1.96 (0.14), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 115 HIS 0.006 0.001 HIS J 865 PHE 0.011 0.001 PHE I 390 TYR 0.013 0.001 TYR J 631 ARG 0.005 0.000 ARG H 12 *********************** 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 362 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 287 time to evaluate : 2.802 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 170 ARG cc_start: 0.7446 (ttm170) cc_final: 0.6469 (ptp-170) REVERT: I 47 TYR cc_start: 0.5329 (m-80) cc_final: 0.4777 (m-80) REVERT: I 215 TYR cc_start: 0.8564 (OUTLIER) cc_final: 0.8033 (m-10) REVERT: I 383 SER cc_start: 0.8529 (m) cc_final: 0.8146 (p) REVERT: I 403 MET cc_start: 0.8701 (tmm) cc_final: 0.8386 (tmm) REVERT: I 496 LYS cc_start: 0.8986 (mmtt) cc_final: 0.8747 (tppt) REVERT: I 559 CYS cc_start: 0.9242 (t) cc_final: 0.9029 (t) REVERT: I 917 SER cc_start: 0.8649 (p) cc_final: 0.8366 (t) REVERT: I 1217 THR cc_start: 0.8548 (m) cc_final: 0.8224 (p) REVERT: J 188 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8278 (tt) REVERT: J 200 GLN cc_start: 0.7725 (tp40) cc_final: 0.7404 (tt0) REVERT: J 205 LEU cc_start: 0.6922 (OUTLIER) cc_final: 0.6563 (mm) REVERT: J 237 MET cc_start: 0.8600 (mtt) cc_final: 0.8347 (mtt) REVERT: J 505 ASP cc_start: 0.8827 (OUTLIER) cc_final: 0.8200 (t0) REVERT: J 521 LYS cc_start: 0.8887 (mttt) cc_final: 0.8506 (mtpp) REVERT: J 582 ILE cc_start: 0.8926 (mt) cc_final: 0.8676 (mt) REVERT: J 740 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8726 (mp) REVERT: J 743 MET cc_start: 0.8903 (ptp) cc_final: 0.8686 (ptm) REVERT: J 800 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8661 (mm) REVERT: J 1143 ASP cc_start: 0.7723 (t0) cc_final: 0.7390 (t0) REVERT: J 1144 LEU cc_start: 0.9171 (mt) cc_final: 0.8894 (tp) REVERT: J 1254 GLU cc_start: 0.7300 (mt-10) cc_final: 0.7073 (mt-10) REVERT: K 58 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7913 (pp) REVERT: N 36 GLU cc_start: 0.8144 (tp30) cc_final: 0.7938 (tp30) REVERT: N 75 MET cc_start: 0.7719 (tpp) cc_final: 0.7273 (tpp) outliers start: 75 outliers final: 52 residues processed: 337 average time/residue: 0.3804 time to fit residues: 206.9087 Evaluate side-chains 326 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 267 time to evaluate : 3.013 ------------------------------------------------------------------------------- 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 69 SER Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 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 174 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain I residue 81 ASP 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 215 TYR Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 503 LYS Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 620 ASN 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 1041 ASP 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 180 MET Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 194 LEU Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 224 LEU Chi-restraints excluded: chain J residue 263 SER 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 740 LEU Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 800 LEU Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 848 VAL 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 25 SER Chi-restraints excluded: chain N residue 73 MET Chi-restraints excluded: chain N residue 90 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 288 optimal weight: 10.0000 chunk 303 optimal weight: 0.9990 chunk 277 optimal weight: 0.8980 chunk 295 optimal weight: 6.9990 chunk 177 optimal weight: 1.9990 chunk 128 optimal weight: 0.2980 chunk 232 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 267 optimal weight: 4.9990 chunk 279 optimal weight: 1.9990 chunk 294 optimal weight: 10.0000 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 103 ASN H 127 GLN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 658 GLN ** I1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 805 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.131 27394 Z= 0.213 Angle : 0.566 10.456 37258 Z= 0.294 Chirality : 0.042 0.305 4253 Planarity : 0.004 0.051 4665 Dihedral : 13.164 125.556 4260 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.91 % Favored : 94.00 % Rotamer: Outliers : 2.91 % Allowed : 15.40 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.15), residues: 3249 helix: 1.45 (0.16), residues: 1129 sheet: -0.74 (0.26), residues: 398 loop : -1.95 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 115 HIS 0.006 0.001 HIS J 113 PHE 0.010 0.001 PHE J 620 TYR 0.024 0.001 TYR I 70 ARG 0.005 0.000 ARG J 312 *********************** 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 365 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 284 time to evaluate : 2.761 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: 0.7485 (ttm170) cc_final: 0.6530 (ptp-170) REVERT: I 47 TYR cc_start: 0.5404 (m-80) cc_final: 0.4829 (m-80) REVERT: I 215 TYR cc_start: 0.8582 (OUTLIER) cc_final: 0.7943 (m-10) REVERT: I 383 SER cc_start: 0.8546 (m) cc_final: 0.8152 (p) REVERT: I 403 MET cc_start: 0.8720 (tmm) cc_final: 0.8369 (tmm) REVERT: I 496 LYS cc_start: 0.8982 (mmtt) cc_final: 0.8742 (tppt) REVERT: J 188 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8350 (tt) REVERT: J 200 GLN cc_start: 0.7567 (tp40) cc_final: 0.7367 (tt0) REVERT: J 205 LEU cc_start: 0.7001 (OUTLIER) cc_final: 0.6632 (mm) REVERT: J 237 MET cc_start: 0.8659 (mtt) cc_final: 0.8420 (mtt) REVERT: J 505 ASP cc_start: 0.8859 (OUTLIER) cc_final: 0.8249 (t0) REVERT: J 521 LYS cc_start: 0.8873 (mttt) cc_final: 0.8499 (mtpp) REVERT: J 582 ILE cc_start: 0.8947 (mt) cc_final: 0.8709 (mt) REVERT: J 740 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8739 (mp) REVERT: J 800 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8718 (mm) REVERT: J 1143 ASP cc_start: 0.7721 (t0) cc_final: 0.7379 (t0) REVERT: J 1144 LEU cc_start: 0.9196 (mt) cc_final: 0.8929 (tp) REVERT: K 58 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7922 (pp) REVERT: N 32 LEU cc_start: 0.8830 (tp) cc_final: 0.8433 (tt) REVERT: N 36 GLU cc_start: 0.8154 (tp30) cc_final: 0.7940 (tp30) REVERT: N 75 MET cc_start: 0.7805 (tpp) cc_final: 0.7338 (tpp) outliers start: 81 outliers final: 67 residues processed: 339 average time/residue: 0.4009 time to fit residues: 222.0432 Evaluate side-chains 347 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 273 time to evaluate : 3.104 ------------------------------------------------------------------------------- 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 69 SER Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 117 HIS Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 57 THR 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 139 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 84 GLU 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 215 TYR Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 503 LYS Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 620 ASN Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 690 VAL 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 1041 ASP 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 1239 VAL 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 180 MET Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 194 LEU Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 224 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 641 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 800 LEU Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain J residue 1329 THR Chi-restraints excluded: chain J residue 1370 MET Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain N residue 16 SER Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 73 MET Chi-restraints excluded: chain N residue 86 VAL Chi-restraints excluded: chain N residue 90 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 194 optimal weight: 6.9990 chunk 312 optimal weight: 1.9990 chunk 190 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 217 optimal weight: 0.9990 chunk 327 optimal weight: 0.0170 chunk 301 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 201 optimal weight: 0.9980 chunk 160 optimal weight: 0.9990 overall best weight: 0.8022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 103 ASN H 127 GLN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 805 GLN J1197 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.127 27394 Z= 0.179 Angle : 0.556 10.530 37258 Z= 0.289 Chirality : 0.042 0.318 4253 Planarity : 0.004 0.052 4665 Dihedral : 13.127 125.453 4260 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.45 % Favored : 94.49 % Rotamer: Outliers : 2.76 % Allowed : 15.62 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.15), residues: 3249 helix: 1.53 (0.16), residues: 1131 sheet: -0.73 (0.27), residues: 393 loop : -1.89 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 80 HIS 0.006 0.001 HIS J 865 PHE 0.010 0.001 PHE J 116 TYR 0.018 0.001 TYR J 140 ARG 0.005 0.000 ARG J 312 ********************** 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 362 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 285 time to evaluate : 3.166 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: 0.7486 (ttm170) cc_final: 0.6517 (ptp-170) REVERT: I 47 TYR cc_start: 0.5361 (m-80) cc_final: 0.4811 (m-80) REVERT: I 215 TYR cc_start: 0.8566 (OUTLIER) cc_final: 0.7945 (m-10) REVERT: I 383 SER cc_start: 0.8536 (m) cc_final: 0.8152 (p) REVERT: I 403 MET cc_start: 0.8706 (tmm) cc_final: 0.8388 (tmm) REVERT: I 496 LYS cc_start: 0.8986 (mmtt) cc_final: 0.8741 (tppt) REVERT: I 1119 MET cc_start: 0.8211 (tpt) cc_final: 0.7299 (ttp) REVERT: J 188 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8343 (tt) REVERT: J 205 LEU cc_start: 0.6867 (OUTLIER) cc_final: 0.6480 (mm) REVERT: J 237 MET cc_start: 0.8658 (mtt) cc_final: 0.8413 (mtt) REVERT: J 505 ASP cc_start: 0.8834 (OUTLIER) cc_final: 0.8215 (t0) REVERT: J 521 LYS cc_start: 0.8881 (mttt) cc_final: 0.8511 (mtpp) REVERT: J 582 ILE cc_start: 0.8921 (mt) cc_final: 0.8689 (mt) REVERT: J 740 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8767 (mp) REVERT: J 800 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8684 (mm) REVERT: J 983 LYS cc_start: 0.8053 (mmmm) cc_final: 0.7816 (mmmm) REVERT: J 1143 ASP cc_start: 0.7710 (t0) cc_final: 0.7362 (t0) REVERT: J 1144 LEU cc_start: 0.9165 (mt) cc_final: 0.8879 (tp) REVERT: K 58 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7886 (pp) REVERT: N 32 LEU cc_start: 0.8818 (tp) cc_final: 0.8442 (tt) REVERT: N 36 GLU cc_start: 0.8166 (tp30) cc_final: 0.7882 (tp30) REVERT: N 75 MET cc_start: 0.7589 (tpp) cc_final: 0.7236 (tpp) outliers start: 77 outliers final: 65 residues processed: 337 average time/residue: 0.3740 time to fit residues: 205.4663 Evaluate side-chains 346 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 274 time to evaluate : 2.934 ------------------------------------------------------------------------------- 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 69 SER Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 57 THR 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 139 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 84 GLU 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 215 TYR Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 503 LYS Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 620 ASN Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 690 VAL 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 1041 ASP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1109 ILE Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1239 VAL 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 180 MET Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 194 LEU Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 224 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 641 ILE Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 800 LEU Chi-restraints excluded: chain J residue 805 GLN Chi-restraints excluded: chain J residue 848 VAL Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain J residue 1329 THR Chi-restraints excluded: chain J residue 1370 MET Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain N residue 16 SER Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 73 MET Chi-restraints excluded: chain N residue 90 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 207 optimal weight: 0.9990 chunk 278 optimal weight: 4.9990 chunk 79 optimal weight: 8.9990 chunk 240 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 72 optimal weight: 0.4980 chunk 261 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 268 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 127 GLN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 805 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.149636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.116298 restraints weight = 38082.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.116743 restraints weight = 33860.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.117854 restraints weight = 29973.065| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.120 27394 Z= 0.211 Angle : 0.569 10.538 37258 Z= 0.294 Chirality : 0.042 0.305 4253 Planarity : 0.004 0.050 4665 Dihedral : 13.127 125.832 4260 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.91 % Favored : 94.03 % Rotamer: Outliers : 2.80 % Allowed : 15.80 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.15), residues: 3249 helix: 1.52 (0.16), residues: 1131 sheet: -0.73 (0.27), residues: 400 loop : -1.88 (0.14), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 80 HIS 0.007 0.001 HIS J 113 PHE 0.010 0.001 PHE J 620 TYR 0.038 0.001 TYR I 70 ARG 0.004 0.000 ARG J 312 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5325.95 seconds wall clock time: 97 minutes 37.72 seconds (5857.72 seconds total)