Starting phenix.real_space_refine on Sat Feb 7 08:51:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9msh_48589/02_2026/9msh_48589.cif Found real_map, /net/cci-nas-00/data/ceres_data/9msh_48589/02_2026/9msh_48589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9msh_48589/02_2026/9msh_48589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9msh_48589/02_2026/9msh_48589.map" model { file = "/net/cci-nas-00/data/ceres_data/9msh_48589/02_2026/9msh_48589.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9msh_48589/02_2026/9msh_48589.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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 100 5.49 5 Mg 1 5.21 5 S 116 5.16 5 C 18964 2.51 5 N 5403 2.21 5 O 6475 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31061 Number of models: 1 Model: "" Number of chains: 18 Chain: "G" Number of atoms: 2382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2382 Classifications: {'peptide': 307} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 292} Chain breaks: 2 Chain: "H" Number of atoms: 1718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1718 Classifications: {'peptide': 223} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 213} Chain breaks: 1 Chain: "I" Number of atoms: 10567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10567 Classifications: {'peptide': 1340} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Chain: "J" Number of atoms: 10508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1350, 10508 Classifications: {'peptide': 1350} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1294} Chain breaks: 2 Chain: "K" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "M" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2917 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 351} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "U" Number of atoms: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1018 Classifications: {'DNA': 49} Link IDs: {'rna3p': 48} Chain: "V" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 991 Classifications: {'DNA': 49} Link IDs: {'rna3p': 48} Chain: "I" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'POP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "H" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "I" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 151 Classifications: {'water': 151} Link IDs: {None: 150} Chain: "J" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 117 Classifications: {'water': 117} Link IDs: {None: 116} Chain: "K" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "M" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "U" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "V" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15232 SG CYS J 70 47.451 61.205 130.716 1.00 74.30 S ATOM 15246 SG CYS J 72 49.300 62.103 133.863 1.00 91.25 S ATOM 15354 SG CYS J 85 45.900 63.091 133.688 1.00 95.41 S ATOM 15378 SG CYS J 88 48.463 64.863 131.680 1.00 79.75 S ATOM 21066 SG CYS J 814 27.339 87.764 69.708 1.00 56.20 S ATOM 21631 SG CYS J 888 30.649 87.260 71.660 1.00 50.41 S ATOM 21682 SG CYS J 895 28.935 84.611 69.812 1.00 53.54 S ATOM 21703 SG CYS J 898 30.440 87.036 67.884 1.00 66.59 S Time building chain proxies: 6.55, per 1000 atoms: 0.21 Number of scatterers: 31061 At special positions: 0 Unit cell: (157.38, 160.82, 171.14, 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 116 16.00 P 100 15.00 Mg 1 11.99 O 6475 8.00 N 5403 7.00 C 18964 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " Number of angles added : 12 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6794 Finding SS restraints... Secondary structure from input PDB file: 137 helices and 52 sheets defined 41.3% alpha, 16.0% beta 39 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 4.09 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.763A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.723A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 212 through 228 Processing helix chain 'G' and resid 229 through 231 No H-bonds generated for 'chain 'G' and resid 229 through 231' Processing helix chain 'G' and resid 250 through 255 removed outlier: 3.879A pdb=" N LEU G 254 " --> pdb=" O ASP G 250 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG G 255 " --> pdb=" O PRO G 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 250 through 255' Processing helix chain 'G' and resid 256 through 260 Processing helix chain 'G' and resid 263 through 273 Processing helix chain 'G' and resid 277 through 284 removed outlier: 3.648A pdb=" N GLN G 283 " --> pdb=" O GLY G 279 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG G 284 " --> pdb=" O ASP G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 285 through 292 Processing helix chain 'G' and resid 296 through 309 Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.629A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 removed outlier: 3.626A 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 228 removed outlier: 3.534A pdb=" N GLN H 227 " --> pdb=" O ILE H 223 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 9 removed outlier: 3.599A pdb=" N LYS I 9 " --> pdb=" O TYR I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.565A pdb=" N LEU I 32 " --> pdb=" O LEU I 28 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 57 removed outlier: 3.894A pdb=" N ALA I 51 " --> pdb=" O TYR I 47 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA I 52 " --> pdb=" O GLY I 48 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL I 56 " --> pdb=" O ALA I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 4.208A 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 Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 288 through 293 Processing helix chain 'I' and resid 318 through 327 removed outlier: 3.757A pdb=" N GLN I 327 " --> pdb=" O ALA I 323 " (cutoff:3.500A) Processing helix chain 'I' and resid 346 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 4.242A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 removed outlier: 3.619A pdb=" N ARG I 402 " --> pdb=" O SER I 398 " (cutoff:3.500A) Processing helix chain 'I' and resid 421 through 437 Processing helix chain 'I' and resid 455 through 480 removed outlier: 3.861A pdb=" N ARG I 470 " --> pdb=" O VAL I 466 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER I 480 " --> pdb=" O LYS I 476 " (cutoff:3.500A) Processing helix chain 'I' and resid 488 through 492 Processing helix chain 'I' and resid 495 through 509 removed outlier: 4.166A pdb=" N ALA I 501 " --> pdb=" O PRO I 497 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER I 509 " --> pdb=" O PHE I 505 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.646A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 608 through 612 removed outlier: 3.660A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 612' Processing helix chain 'I' and resid 664 through 668 removed outlier: 3.522A pdb=" N ILE I 668 " --> pdb=" O ALA I 665 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 686 Processing helix chain 'I' and resid 687 through 689 No H-bonds generated for 'chain 'I' and resid 687 through 689' Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 860 through 865 removed outlier: 4.471A pdb=" N LYS I 864 " --> pdb=" O ALA I 861 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU I 865 " --> pdb=" O LEU I 862 " (cutoff:3.500A) Processing helix chain 'I' and resid 896 through 907 Processing helix chain 'I' and resid 942 through 982 removed outlier: 3.769A pdb=" N ASP I 959 " --> pdb=" O GLN I 955 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA I 981 " --> pdb=" O ALA I 977 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY I 982 " --> pdb=" O VAL I 978 " (cutoff:3.500A) Processing helix chain 'I' and resid 985 through 992 Processing helix chain 'I' and resid 993 through 999 Processing helix chain 'I' and resid 1005 through 1037 removed outlier: 4.137A pdb=" N ASN I1009 " --> pdb=" O GLU I1005 " (cutoff:3.500A) Processing helix chain 'I' and resid 1081 through 1085 removed outlier: 3.615A pdb=" N MET I1085 " --> pdb=" O ILE I1082 " (cutoff:3.500A) Processing helix chain 'I' and resid 1099 through 1103 removed outlier: 3.687A pdb=" N GLY I1102 " --> pdb=" O ASN I1099 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.513A pdb=" N LEU I1113 " --> pdb=" O ILE I1109 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN I1134 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1150 Processing helix chain 'I' and resid 1165 through 1176 Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1242 Processing helix chain 'I' and resid 1271 through 1282 Processing helix chain 'I' and resid 1283 through 1292 Processing helix chain 'I' and resid 1297 through 1311 Processing helix chain 'I' and resid 1320 through 1332 removed outlier: 3.862A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 11 removed outlier: 3.840A pdb=" N GLN J 11 " --> pdb=" O PHE J 7 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 34 Processing helix chain 'J' and resid 58 through 63 Processing helix chain 'J' and resid 77 through 81 removed outlier: 3.528A pdb=" N ARG J 81 " --> pdb=" O LEU J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.793A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG J 98 " --> pdb=" O THR J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 removed outlier: 3.623A pdb=" N SER J 119 " --> pdb=" O TRP J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 173 Processing helix chain 'J' and resid 181 through 192 Processing helix chain 'J' and resid 194 through 208 Processing helix chain 'J' and resid 211 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 286 Processing helix chain 'J' and resid 288 through 308 removed outlier: 4.192A pdb=" N ASN J 294 " --> pdb=" O ILE J 290 " (cutoff:3.500A) Processing helix chain 'J' and resid 326 through 332 Processing helix chain 'J' and resid 336 through 341 Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 405 through 416 removed outlier: 4.154A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 450 through 452 No H-bonds generated for 'chain 'J' and resid 450 through 452' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 485 through 489 removed outlier: 3.513A pdb=" N ASN J 489 " --> pdb=" O SER J 486 " (cutoff:3.500A) Processing helix chain 'J' and resid 504 through 514 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 580 Processing helix chain 'J' and resid 581 through 583 No H-bonds generated for 'chain 'J' and resid 581 through 583' Processing helix chain 'J' and resid 588 through 592 Processing helix chain 'J' and resid 597 through 613 Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.791A pdb=" N ILE J 619 " --> pdb=" O LYS J 615 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 644 removed outlier: 3.774A pdb=" N MET J 644 " --> pdb=" O ILE J 641 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 702 Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 Processing helix chain 'J' and resid 768 through 805 removed outlier: 4.075A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU J 783 " --> pdb=" O ALA J 779 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA J 784 " --> pdb=" O ARG J 780 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR J 795 " --> pdb=" O ALA J 791 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 876 Processing helix chain 'J' and resid 896 through 900 Processing helix chain 'J' and resid 914 through 925 removed outlier: 3.688A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 930 Processing helix chain 'J' and resid 1137 through 1147 Processing helix chain 'J' and resid 1216 through 1225 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 3.912A pdb=" N LEU J1243 " --> pdb=" O ASP J1239 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.355A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE J1256 " --> pdb=" O HIS J1252 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1294 removed outlier: 3.678A pdb=" N ALA J1294 " --> pdb=" O ARG J1290 " (cutoff:3.500A) Processing helix chain 'J' and resid 1308 through 1314 Processing helix chain 'J' and resid 1318 through 1324 Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1353 removed outlier: 3.632A pdb=" N ASN J1350 " --> pdb=" O GLY J1346 " (cutoff:3.500A) Processing helix chain 'J' and resid 1359 through 1361 No H-bonds generated for 'chain 'J' and resid 1359 through 1361' Processing helix chain 'J' and resid 1362 through 1373 removed outlier: 3.802A pdb=" N ASP J1368 " --> pdb=" O ALA J1364 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG J1369 " --> pdb=" O TYR J1365 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 15 through 32 removed outlier: 3.772A pdb=" N VAL K 20 " --> pdb=" O ARG K 16 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 removed outlier: 3.573A pdb=" N LEU K 51 " --> pdb=" O THR K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 76 Processing helix chain 'M' and resid 119 through 130 removed outlier: 3.639A pdb=" N LEU M 130 " --> pdb=" O TRP M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 134 through 147 removed outlier: 3.651A pdb=" N ALA M 147 " --> pdb=" O SER M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 157 through 166 removed outlier: 4.005A pdb=" N GLY M 166 " --> pdb=" O LEU M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 171 through 183 removed outlier: 4.172A pdb=" N VAL M 175 " --> pdb=" O ASP M 171 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 204 Processing helix chain 'M' and resid 212 through 223 removed outlier: 3.821A pdb=" N ALA M 216 " --> pdb=" O TRP M 212 " (cutoff:3.500A) Processing helix chain 'M' and resid 224 through 229 removed outlier: 3.572A pdb=" N ALA M 228 " --> pdb=" O LEU M 224 " (cutoff:3.500A) Processing helix chain 'M' and resid 233 through 240 Processing helix chain 'M' and resid 242 through 254 removed outlier: 3.611A pdb=" N LEU M 246 " --> pdb=" O LYS M 242 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 263 Processing helix chain 'M' and resid 323 through 351 removed outlier: 3.739A pdb=" N TRP M 328 " --> pdb=" O GLN M 324 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU M 329 " --> pdb=" O ASP M 325 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS M 331 " --> pdb=" O LYS M 327 " (cutoff:3.500A) Processing helix chain 'M' and resid 351 through 358 removed outlier: 4.025A pdb=" N PHE M 355 " --> pdb=" O GLN M 351 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU M 356 " --> pdb=" O GLN M 352 " (cutoff:3.500A) Processing helix chain 'M' and resid 366 through 375 removed outlier: 3.710A pdb=" N ILE M 370 " --> pdb=" O VAL M 366 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 385 Processing helix chain 'M' and resid 400 through 403 Processing helix chain 'M' and resid 417 through 430 Processing helix chain 'M' and resid 438 through 449 removed outlier: 3.799A pdb=" N GLN M 449 " --> pdb=" O LEU M 445 " (cutoff:3.500A) Processing helix chain 'M' and resid 455 through 465 Processing helix chain 'M' and resid 469 through 474 removed outlier: 4.054A pdb=" N LYS M 474 " --> pdb=" O ASN M 471 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 12 through 18 removed outlier: 5.088A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LYS G 200 " --> pdb=" O VAL G 187 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL G 187 " --> pdb=" O LYS G 200 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL G 202 " --> pdb=" O TYR G 185 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N TYR G 185 " --> pdb=" O VAL G 202 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLU G 204 " --> pdb=" O ILE G 183 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE G 183 " --> pdb=" O GLU G 204 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLU G 206 " --> pdb=" O GLU G 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 97 through 105 removed outlier: 7.491A pdb=" N SER G 141 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ILE G 61 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'G' and resid 108 through 111 removed outlier: 6.561A pdb=" N GLY G 108 " --> pdb=" O HIS G 132 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N HIS G 132 " --> pdb=" O GLY G 108 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL G 110 " --> pdb=" O ILE G 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'H' and resid 15 through 18 removed outlier: 6.420A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 97 through 105 removed outlier: 7.797A pdb=" N SER H 141 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ILE H 61 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (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 Processing sheet with id=AB1, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.576A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'I' and resid 59 through 60 removed outlier: 5.422A pdb=" N SER I 66 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TYR I 105 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 136 through 138 Processing sheet with id=AB5, first strand: chain 'I' and resid 451 through 454 removed outlier: 3.664A pdb=" N SER I 147 " --> pdb=" O ARG I 529 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 154 through 159 removed outlier: 5.197A pdb=" N TYR I 172 " --> pdb=" O PHE I 188 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 227 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: 7.677A pdb=" N ILE I 255 " --> pdb=" O TYR I 262 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 296 through 297 removed outlier: 4.298A pdb=" N MET I 315 " --> pdb=" O VAL I 297 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 301 through 302 removed outlier: 7.396A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.237A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N THR I 595 " --> pdb=" O THR I 600 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N THR I 600 " --> pdb=" O THR I 595 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 641 through 646 Processing sheet with id=AC5, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.466A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.765A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AC8, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.052A pdb=" N ILE I 816 " --> pdb=" O LYS I1078 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ASN I1080 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL I 818 " --> pdb=" O ASN I1080 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 830 through 840 removed outlier: 3.840A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 842 through 843 Processing sheet with id=AD2, first strand: chain 'I' and resid 849 through 850 Processing sheet with id=AD3, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.822A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AD5, first strand: chain 'I' and resid 1268 through 1270 removed outlier: 3.791A pdb=" N GLN I1268 " --> pdb=" O VAL J 347 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 1335 through 1340 removed outlier: 3.584A pdb=" N ALA J 19 " --> pdb=" O GLU I1340 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 103 through 112 removed outlier: 10.159A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.394A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 159 through 160 removed outlier: 7.071A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 253 through 254 Processing sheet with id=AE1, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AE2, first strand: chain 'J' and resid 703 through 707 Processing sheet with id=AE3, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AE4, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE5, first strand: chain 'J' and resid 825 through 827 removed outlier: 6.416A pdb=" N VAL J 825 " --> pdb=" O LYS J 832 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 848 through 849 removed outlier: 6.595A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 949 through 951 removed outlier: 6.661A pdb=" N ILE J 950 " --> pdb=" O VAL J1017 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 991 through 996 removed outlier: 3.936A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL J1011 " --> pdb=" O GLY J 956 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 1024 through 1028 Processing sheet with id=AF1, first strand: chain 'J' and resid 1034 through 1038 Processing sheet with id=AF2, first strand: chain 'J' and resid 1046 through 1048 Processing sheet with id=AF3, first strand: chain 'J' and resid 1155 through 1156 removed outlier: 6.489A pdb=" N ILE J1155 " --> pdb=" O ILE J1210 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 1162 through 1165 Processing sheet with id=AF5, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 6.965A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 284 through 289 removed outlier: 3.510A pdb=" N VAL M 276 " --> pdb=" O TYR M 389 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 406 through 408 1238 hydrogen bonds defined for protein. 3462 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 93 hydrogen bonds 186 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 8.52 Time building geometry restraints manager: 3.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 9410 1.33 - 1.45: 4337 1.45 - 1.57: 17239 1.57 - 1.69: 196 1.69 - 1.81: 201 Bond restraints: 31383 Sorted by residual: bond pdb=" O POP I1401 " pdb=" P2 POP I1401 " ideal model delta sigma weight residual 1.661 1.608 0.053 2.00e-02 2.50e+03 6.93e+00 bond pdb=" O POP I1401 " pdb=" P1 POP I1401 " ideal model delta sigma weight residual 1.660 1.609 0.051 2.00e-02 2.50e+03 6.53e+00 bond pdb=" C3' DT V 29 " pdb=" O3' DT V 29 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.70e+00 bond pdb=" C3' DT V 60 " pdb=" O3' DT V 60 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.68e+00 bond pdb=" O1 POP I1401 " pdb=" P1 POP I1401 " ideal model delta sigma weight residual 1.531 1.508 0.023 2.00e-02 2.50e+03 1.36e+00 ... (remaining 31378 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.53: 42786 3.53 - 7.06: 43 7.06 - 10.59: 6 10.59 - 14.12: 0 14.12 - 17.65: 1 Bond angle restraints: 42836 Sorted by residual: angle pdb=" P1 POP I1401 " pdb=" O POP I1401 " pdb=" P2 POP I1401 " ideal model delta sigma weight residual 139.66 122.01 17.65 3.00e+00 1.11e-01 3.46e+01 angle pdb=" C LYS J1170 " pdb=" CA LYS J1170 " pdb=" CB LYS J1170 " ideal model delta sigma weight residual 110.42 115.87 -5.45 1.99e+00 2.53e-01 7.51e+00 angle pdb=" CA LEU G 83 " pdb=" CB LEU G 83 " pdb=" CG LEU G 83 " ideal model delta sigma weight residual 116.30 125.12 -8.82 3.50e+00 8.16e-02 6.35e+00 angle pdb=" CA LEU I 237 " pdb=" CB LEU I 237 " pdb=" CG LEU I 237 " ideal model delta sigma weight residual 116.30 124.95 -8.65 3.50e+00 8.16e-02 6.11e+00 angle pdb=" C4' DA V 40 " pdb=" O4' DA V 40 " pdb=" C1' DA V 40 " ideal model delta sigma weight residual 109.70 106.08 3.62 1.50e+00 4.44e-01 5.83e+00 ... (remaining 42831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 18432 35.72 - 71.45: 609 71.45 - 107.17: 26 107.17 - 142.89: 0 142.89 - 178.61: 7 Dihedral angle restraints: 19074 sinusoidal: 8531 harmonic: 10543 Sorted by residual: dihedral pdb=" CA ARG H 191 " pdb=" C ARG H 191 " pdb=" N VAL H 192 " pdb=" CA VAL H 192 " ideal model delta harmonic sigma weight residual 180.00 157.76 22.24 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA SER G 49 " pdb=" C SER G 49 " pdb=" N SER G 50 " pdb=" CA SER G 50 " ideal model delta harmonic sigma weight residual -180.00 -158.38 -21.62 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" C4' DT V 60 " pdb=" C3' DT V 60 " pdb=" O3' DT V 60 " pdb=" P DT V 61 " ideal model delta sinusoidal sigma weight residual -140.00 38.61 -178.61 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 19071 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 3179 0.033 - 0.066: 1173 0.066 - 0.098: 340 0.098 - 0.131: 188 0.131 - 0.164: 21 Chirality restraints: 4901 Sorted by residual: chirality pdb=" CB VAL J1255 " pdb=" CA VAL J1255 " pdb=" CG1 VAL J1255 " pdb=" CG2 VAL J1255 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.72e-01 chirality pdb=" P DA U 53 " pdb=" OP1 DA U 53 " pdb=" OP2 DA U 53 " pdb=" O5' DA U 53 " both_signs ideal model delta sigma weight residual True 2.35 -2.50 -0.15 2.00e-01 2.50e+01 5.87e-01 chirality pdb=" P DA U 52 " pdb=" OP1 DA U 52 " pdb=" OP2 DA U 52 " pdb=" O5' DA U 52 " both_signs ideal model delta sigma weight residual True 2.35 -2.49 -0.15 2.00e-01 2.50e+01 5.31e-01 ... (remaining 4898 not shown) Planarity restraints: 5252 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER M 392 " -0.031 5.00e-02 4.00e+02 4.66e-02 3.48e+00 pdb=" N PRO M 393 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO M 393 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO M 393 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER J 492 " -0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO J 493 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO J 493 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO J 493 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR I 589 " 0.028 5.00e-02 4.00e+02 4.17e-02 2.79e+00 pdb=" N PRO I 590 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO I 590 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO I 590 " 0.023 5.00e-02 4.00e+02 ... (remaining 5249 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 688 2.68 - 3.24: 27926 3.24 - 3.79: 46223 3.79 - 4.35: 65053 4.35 - 4.90: 106418 Nonbonded interactions: 246308 Sorted by model distance: nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1501 " model vdw 2.126 2.170 nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1501 " model vdw 2.136 2.170 nonbonded pdb="MG MG J1501 " pdb=" O HOH J1630 " model vdw 2.141 2.170 nonbonded pdb="MG MG J1501 " pdb=" O HOH J1644 " model vdw 2.155 2.170 nonbonded pdb=" OG SER M 382 " pdb=" OP2 DT U 45 " model vdw 2.178 3.040 ... (remaining 246303 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.940 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: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 34.980 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 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 : 0.004 0.305 31391 Z= 0.171 Angle : 0.526 17.647 42848 Z= 0.282 Chirality : 0.042 0.164 4901 Planarity : 0.004 0.047 5252 Dihedral : 15.871 178.614 12280 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.74 % Allowed : 6.35 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.14), residues: 3640 helix: 1.26 (0.15), residues: 1357 sheet: 0.23 (0.24), residues: 490 loop : -0.73 (0.14), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 731 TYR 0.013 0.001 TYR J 631 PHE 0.011 0.001 PHE J 338 TRP 0.008 0.001 TRP J 409 HIS 0.004 0.001 HIS I 447 Details of bonding type rmsd covalent geometry : bond 0.00340 (31383) covalent geometry : angle 0.52635 (42836) hydrogen bonds : bond 0.15044 ( 1331) hydrogen bonds : angle 5.56154 ( 3648) metal coordination : bond 0.15972 ( 8) metal coordination : angle 0.07214 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 242 time to evaluate : 1.264 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 228 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8846 (mt) REVERT: J 217 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8758 (mt) REVERT: J 891 ASP cc_start: 0.8774 (OUTLIER) cc_final: 0.8548 (p0) REVERT: J 1101 LEU cc_start: 0.7425 (mt) cc_final: 0.7175 (pp) REVERT: J 1334 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8232 (mp0) REVERT: M 118 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7493 (tt0) REVERT: M 212 TRP cc_start: 0.8619 (m-90) cc_final: 0.8199 (m-10) REVERT: M 462 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.7798 (tmm160) outliers start: 86 outliers final: 32 residues processed: 322 average time/residue: 0.7537 time to fit residues: 282.0718 Evaluate side-chains 201 residues out of total 3141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 163 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 370 MET Chi-restraints excluded: chain I residue 894 GLN Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain J residue 206 ASN Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 638 SER Chi-restraints excluded: chain J residue 790 THR Chi-restraints excluded: chain J residue 830 ASP Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 952 VAL Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1181 ASP Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1334 GLU Chi-restraints excluded: chain M residue 118 GLN Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 462 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.1980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 ASN I 165 HIS I 490 GLN I 510 GLN I1220 GLN J 954 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.088950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.053821 restraints weight = 76216.220| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.71 r_work: 0.2694 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 31391 Z= 0.150 Angle : 0.535 10.885 42848 Z= 0.285 Chirality : 0.041 0.148 4901 Planarity : 0.004 0.047 5252 Dihedral : 16.942 176.162 5176 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.62 % Allowed : 9.76 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.14), residues: 3640 helix: 1.62 (0.14), residues: 1377 sheet: 0.30 (0.23), residues: 507 loop : -0.68 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 473 TYR 0.014 0.001 TYR J1363 PHE 0.011 0.001 PHE I 405 TRP 0.016 0.001 TRP J1193 HIS 0.007 0.001 HIS J 651 Details of bonding type rmsd covalent geometry : bond 0.00350 (31383) covalent geometry : angle 0.53299 (42836) hydrogen bonds : bond 0.04610 ( 1331) hydrogen bonds : angle 4.36278 ( 3648) metal coordination : bond 0.00662 ( 8) metal coordination : angle 2.82227 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 179 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 95 LYS cc_start: 0.8945 (tptp) cc_final: 0.8680 (tptp) REVERT: H 125 LYS cc_start: 0.8483 (tttm) cc_final: 0.8168 (tppt) REVERT: I 124 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.8703 (mmm) REVERT: I 239 MET cc_start: 0.5651 (tpp) cc_final: 0.4850 (tpp) REVERT: I 287 VAL cc_start: 0.7485 (OUTLIER) cc_final: 0.7212 (t) REVERT: I 515 MET cc_start: 0.9392 (ttp) cc_final: 0.9158 (ttp) REVERT: I 1200 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.9060 (ttmm) REVERT: J 322 ARG cc_start: 0.8742 (ptp-170) cc_final: 0.8524 (mtm-85) REVERT: J 846 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7666 (pm20) REVERT: J 1095 MET cc_start: 0.8556 (mpp) cc_final: 0.8287 (mpp) REVERT: J 1101 LEU cc_start: 0.6916 (mt) cc_final: 0.6471 (pp) REVERT: J 1334 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8085 (mp0) REVERT: K 56 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8132 (tm-30) REVERT: K 62 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8081 (tm-30) REVERT: K 72 GLN cc_start: 0.8869 (tm-30) cc_final: 0.8643 (tm-30) REVERT: K 76 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7388 (mm-30) REVERT: M 212 TRP cc_start: 0.8831 (m-90) cc_final: 0.8083 (m-10) outliers start: 82 outliers final: 31 residues processed: 239 average time/residue: 0.6869 time to fit residues: 193.6068 Evaluate side-chains 194 residues out of total 3141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 157 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 595 THR Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1200 LYS Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 331 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 790 THR Chi-restraints excluded: chain J residue 846 GLU Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 952 VAL Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1334 GLU Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 62 GLN Chi-restraints excluded: chain M residue 275 ASP Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 348 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 38 optimal weight: 6.9990 chunk 267 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 202 optimal weight: 4.9990 chunk 350 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 91 optimal weight: 0.0570 chunk 47 optimal weight: 4.9990 chunk 291 optimal weight: 20.0000 chunk 52 optimal weight: 0.7980 chunk 282 optimal weight: 6.9990 overall best weight: 2.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 165 HIS I 214 ASN I 490 GLN J 430 HIS M 282 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.087688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.052209 restraints weight = 75753.254| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 2.66 r_work: 0.2641 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2514 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 31391 Z= 0.197 Angle : 0.545 10.510 42848 Z= 0.288 Chirality : 0.042 0.146 4901 Planarity : 0.004 0.047 5252 Dihedral : 16.978 176.110 5139 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.36 % Allowed : 10.81 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.14), residues: 3640 helix: 1.62 (0.14), residues: 1398 sheet: 0.33 (0.24), residues: 494 loop : -0.72 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I1034 TYR 0.014 0.001 TYR J 631 PHE 0.017 0.001 PHE J1325 TRP 0.016 0.001 TRP M 88 HIS 0.006 0.001 HIS J 651 Details of bonding type rmsd covalent geometry : bond 0.00471 (31383) covalent geometry : angle 0.54336 (42836) hydrogen bonds : bond 0.04927 ( 1331) hydrogen bonds : angle 4.26153 ( 3648) metal coordination : bond 0.00950 ( 8) metal coordination : angle 2.64772 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 159 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 93 GLN cc_start: 0.8963 (tp40) cc_final: 0.8620 (tm-30) REVERT: G 191 ARG cc_start: 0.8328 (tpm170) cc_final: 0.7726 (tpm-80) REVERT: I 241 LEU cc_start: 0.8117 (mm) cc_final: 0.7897 (mm) REVERT: I 287 VAL cc_start: 0.7670 (OUTLIER) cc_final: 0.7404 (t) REVERT: I 369 MET cc_start: 0.8965 (ttp) cc_final: 0.8667 (tmm) REVERT: I 431 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8876 (tptp) REVERT: I 1329 GLU cc_start: 0.9249 (OUTLIER) cc_final: 0.9014 (mt-10) REVERT: J 788 LEU cc_start: 0.8624 (tp) cc_final: 0.8418 (tm) REVERT: J 932 MET cc_start: 0.6415 (ttm) cc_final: 0.5969 (ttm) REVERT: J 1101 LEU cc_start: 0.7004 (mt) cc_final: 0.6641 (pp) REVERT: K 56 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8290 (tm-30) REVERT: K 62 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8209 (tm-30) REVERT: K 70 GLN cc_start: 0.8435 (tm-30) cc_final: 0.8217 (tm-30) REVERT: M 118 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.7830 (tt0) REVERT: M 212 TRP cc_start: 0.8882 (m-90) cc_final: 0.8125 (m-10) REVERT: M 279 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.7488 (ppp80) outliers start: 74 outliers final: 33 residues processed: 220 average time/residue: 0.7485 time to fit residues: 192.9355 Evaluate side-chains 192 residues out of total 3141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 153 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 431 LYS Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 595 THR Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 331 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 790 THR Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 952 VAL Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 978 ARG Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 62 GLN Chi-restraints excluded: chain M residue 118 GLN Chi-restraints excluded: chain M residue 275 ASP Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 279 ARG Chi-restraints excluded: chain M residue 323 LEU Chi-restraints excluded: chain M residue 348 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 313 optimal weight: 9.9990 chunk 351 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 309 optimal weight: 3.9990 chunk 364 optimal weight: 10.0000 chunk 229 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 178 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 147 GLN I 165 HIS I 490 GLN J 430 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.087892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.052614 restraints weight = 74834.434| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 2.64 r_work: 0.2650 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2524 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 31391 Z= 0.169 Angle : 0.517 11.012 42848 Z= 0.274 Chirality : 0.041 0.142 4901 Planarity : 0.004 0.046 5252 Dihedral : 16.948 175.601 5134 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.49 % Allowed : 11.77 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.14), residues: 3640 helix: 1.75 (0.14), residues: 1389 sheet: 0.31 (0.23), residues: 509 loop : -0.63 (0.14), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I1034 TYR 0.014 0.001 TYR J 631 PHE 0.012 0.001 PHE J 988 TRP 0.019 0.001 TRP M 88 HIS 0.006 0.001 HIS J 651 Details of bonding type rmsd covalent geometry : bond 0.00403 (31383) covalent geometry : angle 0.51586 (42836) hydrogen bonds : bond 0.04506 ( 1331) hydrogen bonds : angle 4.12287 ( 3648) metal coordination : bond 0.00781 ( 8) metal coordination : angle 2.47616 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 158 time to evaluate : 1.024 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: G 93 GLN cc_start: 0.8999 (tp40) cc_final: 0.8572 (tm-30) REVERT: G 191 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7953 (tpm-80) REVERT: I 241 LEU cc_start: 0.8313 (mm) cc_final: 0.8113 (mm) REVERT: I 253 PHE cc_start: 0.8081 (p90) cc_final: 0.7719 (p90) REVERT: I 287 VAL cc_start: 0.7629 (OUTLIER) cc_final: 0.7302 (t) REVERT: I 431 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8888 (tptp) REVERT: I 488 MET cc_start: 0.8864 (mmm) cc_final: 0.8597 (mmm) REVERT: I 515 MET cc_start: 0.9538 (ttp) cc_final: 0.9302 (ttp) REVERT: I 1329 GLU cc_start: 0.9227 (OUTLIER) cc_final: 0.8987 (mt-10) REVERT: J 314 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7613 (ttp-110) REVERT: J 788 LEU cc_start: 0.8553 (tp) cc_final: 0.8311 (tm) REVERT: J 846 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.7948 (pm20) REVERT: J 932 MET cc_start: 0.5872 (ttm) cc_final: 0.5606 (ttm) REVERT: J 988 PHE cc_start: 0.8768 (m-80) cc_final: 0.8389 (m-10) REVERT: J 1101 LEU cc_start: 0.7006 (mt) cc_final: 0.6667 (pp) REVERT: J 1190 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7866 (mp) REVERT: K 56 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8265 (tm-30) REVERT: K 62 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8228 (tm-30) REVERT: M 212 TRP cc_start: 0.8906 (m-90) cc_final: 0.8202 (m-10) outliers start: 78 outliers final: 31 residues processed: 220 average time/residue: 0.7140 time to fit residues: 184.8467 Evaluate side-chains 193 residues out of total 3141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 154 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 103 ASN Chi-restraints excluded: chain G residue 191 ARG Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 431 LYS Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 985 GLU Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain J residue 314 ARG Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 331 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 790 THR Chi-restraints excluded: chain J residue 846 GLU Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 952 VAL Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 978 ARG Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1190 ILE Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 62 GLN Chi-restraints excluded: chain M residue 106 ASP Chi-restraints excluded: chain M residue 275 ASP Chi-restraints excluded: chain M residue 348 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 323 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 236 optimal weight: 0.7980 chunk 315 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 274 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 371 optimal weight: 10.0000 chunk 116 optimal weight: 7.9990 chunk 224 optimal weight: 0.9980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 165 HIS I 490 GLN J 430 HIS M 282 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.087905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.052391 restraints weight = 75306.003| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 2.67 r_work: 0.2650 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2522 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 31391 Z= 0.162 Angle : 0.511 10.664 42848 Z= 0.270 Chirality : 0.041 0.142 4901 Planarity : 0.004 0.047 5252 Dihedral : 16.932 175.694 5130 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.30 % Allowed : 12.57 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.14), residues: 3640 helix: 1.79 (0.14), residues: 1393 sheet: 0.34 (0.23), residues: 508 loop : -0.60 (0.14), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I1034 TYR 0.014 0.001 TYR J 631 PHE 0.011 0.001 PHE I 405 TRP 0.006 0.001 TRP J 409 HIS 0.005 0.001 HIS J 651 Details of bonding type rmsd covalent geometry : bond 0.00385 (31383) covalent geometry : angle 0.50994 (42836) hydrogen bonds : bond 0.04413 ( 1331) hydrogen bonds : angle 4.06271 ( 3648) metal coordination : bond 0.00743 ( 8) metal coordination : angle 2.39709 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 160 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 93 GLN cc_start: 0.9012 (tp40) cc_final: 0.8530 (tm-30) REVERT: G 191 ARG cc_start: 0.8364 (tpm170) cc_final: 0.7986 (tpm-80) REVERT: H 25 LYS cc_start: 0.8912 (mtpm) cc_final: 0.8686 (mtpt) REVERT: H 95 LYS cc_start: 0.9335 (mtpp) cc_final: 0.8898 (tptp) REVERT: I 253 PHE cc_start: 0.8051 (p90) cc_final: 0.7688 (p90) REVERT: I 287 VAL cc_start: 0.7635 (OUTLIER) cc_final: 0.7290 (t) REVERT: I 431 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8890 (tptp) REVERT: I 490 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8822 (mm-40) REVERT: I 515 MET cc_start: 0.9530 (ttp) cc_final: 0.9322 (ttp) REVERT: I 1329 GLU cc_start: 0.9223 (OUTLIER) cc_final: 0.8985 (mt-10) REVERT: J 314 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7640 (ttp-110) REVERT: J 788 LEU cc_start: 0.8546 (tp) cc_final: 0.8309 (tm) REVERT: J 846 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.7989 (pm20) REVERT: J 932 MET cc_start: 0.6058 (ttm) cc_final: 0.5773 (ttm) REVERT: J 988 PHE cc_start: 0.8769 (m-80) cc_final: 0.8368 (m-10) REVERT: J 1101 LEU cc_start: 0.7004 (mt) cc_final: 0.6692 (pp) REVERT: K 56 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8271 (tm-30) REVERT: K 62 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8220 (tm-30) REVERT: M 118 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.7848 (tt0) REVERT: M 212 TRP cc_start: 0.8904 (m-90) cc_final: 0.8195 (m-10) outliers start: 72 outliers final: 37 residues processed: 219 average time/residue: 0.7072 time to fit residues: 182.0655 Evaluate side-chains 201 residues out of total 3141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 156 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 103 ASN Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 431 LYS Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 490 GLN Chi-restraints excluded: chain I residue 595 THR Chi-restraints excluded: chain I residue 661 VAL Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 975 ILE Chi-restraints excluded: chain I residue 985 GLU Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 294 ASN Chi-restraints excluded: chain J residue 314 ARG Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 331 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 790 THR Chi-restraints excluded: chain J residue 846 GLU Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 952 VAL Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 62 GLN Chi-restraints excluded: chain M residue 106 ASP Chi-restraints excluded: chain M residue 118 GLN Chi-restraints excluded: chain M residue 225 ASP Chi-restraints excluded: chain M residue 275 ASP Chi-restraints excluded: chain M residue 348 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 190 optimal weight: 8.9990 chunk 250 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 367 optimal weight: 10.0000 chunk 361 optimal weight: 6.9990 chunk 210 optimal weight: 1.9990 chunk 352 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 327 optimal weight: 2.9990 chunk 265 optimal weight: 4.9990 chunk 342 optimal weight: 7.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 147 GLN I 165 HIS I 214 ASN ** I 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 430 HIS J1218 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.086514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.050944 restraints weight = 75203.098| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 2.66 r_work: 0.2614 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2487 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 31391 Z= 0.279 Angle : 0.589 11.019 42848 Z= 0.310 Chirality : 0.044 0.194 4901 Planarity : 0.004 0.048 5252 Dihedral : 17.043 176.103 5130 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.30 % Allowed : 13.11 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.14), residues: 3640 helix: 1.63 (0.14), residues: 1392 sheet: 0.35 (0.23), residues: 498 loop : -0.74 (0.14), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I1034 TYR 0.015 0.001 TYR J 631 PHE 0.015 0.001 PHE I 405 TRP 0.008 0.001 TRP J1193 HIS 0.005 0.001 HIS J 651 Details of bonding type rmsd covalent geometry : bond 0.00673 (31383) covalent geometry : angle 0.58721 (42836) hydrogen bonds : bond 0.05425 ( 1331) hydrogen bonds : angle 4.28147 ( 3648) metal coordination : bond 0.01187 ( 8) metal coordination : angle 2.68583 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 157 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 93 GLN cc_start: 0.9060 (tp40) cc_final: 0.8485 (tm-30) REVERT: G 191 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7966 (tpm-80) REVERT: G 302 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8536 (tp30) REVERT: H 95 LYS cc_start: 0.9374 (mtpp) cc_final: 0.8983 (tptp) REVERT: H 228 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9116 (mt) REVERT: I 124 MET cc_start: 0.9200 (OUTLIER) cc_final: 0.8888 (mmt) REVERT: I 253 PHE cc_start: 0.8024 (p90) cc_final: 0.7646 (p90) REVERT: I 287 VAL cc_start: 0.7651 (OUTLIER) cc_final: 0.7353 (t) REVERT: I 431 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8907 (tptp) REVERT: I 1329 GLU cc_start: 0.9257 (OUTLIER) cc_final: 0.9026 (mt-10) REVERT: J 314 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7383 (ttp-110) REVERT: J 788 LEU cc_start: 0.8732 (tp) cc_final: 0.8515 (tm) REVERT: J 846 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8013 (pm20) REVERT: J 932 MET cc_start: 0.6410 (ttm) cc_final: 0.6089 (ttm) REVERT: J 988 PHE cc_start: 0.8711 (m-80) cc_final: 0.8296 (m-10) REVERT: J 1101 LEU cc_start: 0.7071 (mt) cc_final: 0.6772 (pp) REVERT: K 41 GLU cc_start: 0.8421 (tm-30) cc_final: 0.8087 (tm-30) REVERT: K 56 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8244 (tm-30) REVERT: K 62 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8240 (tm-30) REVERT: M 212 TRP cc_start: 0.8873 (m-90) cc_final: 0.8265 (m-10) outliers start: 72 outliers final: 38 residues processed: 217 average time/residue: 0.6572 time to fit residues: 168.5440 Evaluate side-chains 202 residues out of total 3141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 154 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 103 ASN Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 191 ARG Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain G residue 302 GLU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 431 LYS Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 595 THR Chi-restraints excluded: chain I residue 661 VAL Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 975 ILE Chi-restraints excluded: chain I residue 985 GLU Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1329 GLU Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 314 ARG Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 331 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 790 THR Chi-restraints excluded: chain J residue 846 GLU Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 952 VAL Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 62 GLN Chi-restraints excluded: chain M residue 106 ASP Chi-restraints excluded: chain M residue 275 ASP Chi-restraints excluded: chain M residue 348 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 147 optimal weight: 7.9990 chunk 369 optimal weight: 6.9990 chunk 330 optimal weight: 0.9980 chunk 209 optimal weight: 0.5980 chunk 160 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 247 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 314 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 165 HIS I 490 GLN J 430 HIS ** J1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.088587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.053295 restraints weight = 75386.966| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 2.67 r_work: 0.2673 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2545 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31391 Z= 0.116 Angle : 0.502 11.464 42848 Z= 0.262 Chirality : 0.040 0.152 4901 Planarity : 0.003 0.048 5252 Dihedral : 16.900 176.698 5128 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.79 % Allowed : 13.88 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.14), residues: 3640 helix: 1.90 (0.14), residues: 1393 sheet: 0.42 (0.24), residues: 498 loop : -0.53 (0.15), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG I1034 TYR 0.013 0.001 TYR J 631 PHE 0.010 0.001 PHE J1319 TRP 0.029 0.001 TRP J1193 HIS 0.005 0.001 HIS J 651 Details of bonding type rmsd covalent geometry : bond 0.00264 (31383) covalent geometry : angle 0.50102 (42836) hydrogen bonds : bond 0.03824 ( 1331) hydrogen bonds : angle 3.96262 ( 3648) metal coordination : bond 0.00500 ( 8) metal coordination : angle 2.27137 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 157 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 93 GLN cc_start: 0.8996 (tp40) cc_final: 0.8525 (tm-30) REVERT: G 191 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.8019 (tpm-80) REVERT: H 95 LYS cc_start: 0.9331 (mtpp) cc_final: 0.8982 (tptp) REVERT: H 228 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9156 (mt) REVERT: I 253 PHE cc_start: 0.8004 (p90) cc_final: 0.7617 (p90) REVERT: I 287 VAL cc_start: 0.7606 (OUTLIER) cc_final: 0.7252 (t) REVERT: I 321 LEU cc_start: 0.9023 (mt) cc_final: 0.8652 (mp) REVERT: I 431 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8894 (tptp) REVERT: I 490 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.8834 (mm-40) REVERT: I 515 MET cc_start: 0.9525 (ttp) cc_final: 0.9294 (ttp) REVERT: I 1200 LYS cc_start: 0.9331 (OUTLIER) cc_final: 0.9130 (ttmm) REVERT: J 846 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8028 (pm20) REVERT: J 988 PHE cc_start: 0.8712 (m-80) cc_final: 0.8310 (m-10) REVERT: J 1101 LEU cc_start: 0.6975 (mt) cc_final: 0.6684 (pp) REVERT: K 56 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8249 (tm-30) REVERT: K 62 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8261 (tm-30) REVERT: M 212 TRP cc_start: 0.8892 (m-90) cc_final: 0.8222 (m-10) outliers start: 56 outliers final: 25 residues processed: 199 average time/residue: 0.7545 time to fit residues: 176.2247 Evaluate side-chains 186 residues out of total 3141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 191 ARG Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 431 LYS Chi-restraints excluded: chain I residue 490 GLN Chi-restraints excluded: chain I residue 595 THR Chi-restraints excluded: chain I residue 661 VAL Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 975 ILE Chi-restraints excluded: chain I residue 985 GLU Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1200 LYS Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 331 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 846 GLU Chi-restraints excluded: chain J residue 952 VAL Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain K residue 62 GLN Chi-restraints excluded: chain M residue 106 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 87 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 234 optimal weight: 4.9990 chunk 212 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 210 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 180 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 165 HIS I 214 ASN I 490 GLN J 294 ASN J 430 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.087530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.052103 restraints weight = 75449.288| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 2.66 r_work: 0.2641 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 31391 Z= 0.181 Angle : 0.539 10.936 42848 Z= 0.281 Chirality : 0.042 0.143 4901 Planarity : 0.004 0.048 5252 Dihedral : 16.947 178.554 5127 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.95 % Allowed : 14.07 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.14), residues: 3640 helix: 1.84 (0.14), residues: 1393 sheet: 0.45 (0.24), residues: 495 loop : -0.56 (0.15), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG I1034 TYR 0.039 0.001 TYR M 303 PHE 0.012 0.001 PHE I 405 TRP 0.025 0.001 TRP J1193 HIS 0.008 0.001 HIS M 302 Details of bonding type rmsd covalent geometry : bond 0.00433 (31383) covalent geometry : angle 0.53740 (42836) hydrogen bonds : bond 0.04572 ( 1331) hydrogen bonds : angle 4.06435 ( 3648) metal coordination : bond 0.00807 ( 8) metal coordination : angle 2.29674 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 155 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 93 GLN cc_start: 0.9022 (tp40) cc_final: 0.8443 (tm-30) REVERT: G 191 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.8001 (tpm-80) REVERT: H 95 LYS cc_start: 0.9320 (mtpp) cc_final: 0.8976 (tptp) REVERT: H 228 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9107 (mt) REVERT: I 253 PHE cc_start: 0.8009 (p90) cc_final: 0.7625 (p90) REVERT: I 287 VAL cc_start: 0.7712 (OUTLIER) cc_final: 0.7381 (t) REVERT: I 321 LEU cc_start: 0.9045 (mt) cc_final: 0.8662 (mp) REVERT: I 431 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8900 (tptp) REVERT: I 515 MET cc_start: 0.9539 (ttp) cc_final: 0.9337 (ttp) REVERT: J 314 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7328 (ttp-110) REVERT: J 846 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8027 (pm20) REVERT: J 988 PHE cc_start: 0.8725 (m-80) cc_final: 0.8311 (m-10) REVERT: J 1101 LEU cc_start: 0.7002 (mt) cc_final: 0.6717 (pp) REVERT: J 1189 MET cc_start: 0.8387 (tpp) cc_final: 0.8186 (tpp) REVERT: J 1370 MET cc_start: 0.8596 (ttm) cc_final: 0.8246 (ttm) REVERT: K 56 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8261 (tm-30) REVERT: K 62 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8274 (tm-30) REVERT: M 118 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.7874 (tt0) REVERT: M 212 TRP cc_start: 0.8914 (m-90) cc_final: 0.8252 (m-10) outliers start: 61 outliers final: 35 residues processed: 203 average time/residue: 0.7101 time to fit residues: 169.3308 Evaluate side-chains 196 residues out of total 3141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 153 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 103 ASN Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 191 ARG Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 431 LYS Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 595 THR Chi-restraints excluded: chain I residue 661 VAL Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 975 ILE Chi-restraints excluded: chain I residue 985 GLU Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 314 ARG Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 331 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 846 GLU Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 952 VAL Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 62 GLN Chi-restraints excluded: chain M residue 88 TRP Chi-restraints excluded: chain M residue 106 ASP Chi-restraints excluded: chain M residue 118 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 189 optimal weight: 2.9990 chunk 232 optimal weight: 0.8980 chunk 146 optimal weight: 7.9990 chunk 263 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 chunk 329 optimal weight: 3.9990 chunk 312 optimal weight: 6.9990 chunk 241 optimal weight: 0.9990 chunk 217 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 147 GLN I 165 HIS J 294 ASN J 430 HIS ** M 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.088374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.052913 restraints weight = 75321.121| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 2.68 r_work: 0.2666 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2538 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31391 Z= 0.128 Angle : 0.517 11.851 42848 Z= 0.268 Chirality : 0.040 0.141 4901 Planarity : 0.004 0.048 5252 Dihedral : 16.876 179.092 5127 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.72 % Allowed : 14.45 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.14), residues: 3640 helix: 1.92 (0.14), residues: 1392 sheet: 0.49 (0.24), residues: 498 loop : -0.47 (0.15), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG I1034 TYR 0.015 0.001 TYR M 303 PHE 0.011 0.001 PHE J1319 TRP 0.023 0.001 TRP J1193 HIS 0.005 0.001 HIS J 651 Details of bonding type rmsd covalent geometry : bond 0.00302 (31383) covalent geometry : angle 0.51614 (42836) hydrogen bonds : bond 0.03957 ( 1331) hydrogen bonds : angle 3.94623 ( 3648) metal coordination : bond 0.00553 ( 8) metal coordination : angle 2.13470 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 3141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 154 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 93 GLN cc_start: 0.8997 (tp40) cc_final: 0.8449 (tm-30) REVERT: G 191 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.8032 (tpm-80) REVERT: H 25 LYS cc_start: 0.8883 (mtpm) cc_final: 0.8673 (mtpt) REVERT: H 95 LYS cc_start: 0.9308 (mtpp) cc_final: 0.8964 (tptp) REVERT: H 228 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9159 (mt) REVERT: I 253 PHE cc_start: 0.8029 (p90) cc_final: 0.7638 (p90) REVERT: I 287 VAL cc_start: 0.7696 (OUTLIER) cc_final: 0.7361 (t) REVERT: I 321 LEU cc_start: 0.9031 (mt) cc_final: 0.8671 (mp) REVERT: I 431 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8888 (tptp) REVERT: J 846 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8035 (pm20) REVERT: J 988 PHE cc_start: 0.8712 (m-80) cc_final: 0.8333 (m-10) REVERT: J 1101 LEU cc_start: 0.6986 (mt) cc_final: 0.6707 (pp) REVERT: J 1370 MET cc_start: 0.8590 (ttm) cc_final: 0.8244 (ttm) REVERT: K 56 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8249 (tm-30) REVERT: K 62 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8268 (tm-30) REVERT: M 106 ASP cc_start: 0.5030 (OUTLIER) cc_final: 0.4810 (m-30) REVERT: M 118 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.7888 (tt0) REVERT: M 212 TRP cc_start: 0.8897 (m-90) cc_final: 0.8274 (m-10) outliers start: 54 outliers final: 31 residues processed: 198 average time/residue: 0.6530 time to fit residues: 152.9927 Evaluate side-chains 190 residues out of total 3141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 151 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 191 ARG Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 431 LYS Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 595 THR Chi-restraints excluded: chain I residue 661 VAL Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 975 ILE Chi-restraints excluded: chain I residue 985 GLU Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 331 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 846 GLU Chi-restraints excluded: chain J residue 952 VAL Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 978 ARG Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 62 GLN Chi-restraints excluded: chain M residue 106 ASP Chi-restraints excluded: chain M residue 118 GLN Chi-restraints excluded: chain M residue 223 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 163 optimal weight: 3.9990 chunk 360 optimal weight: 9.9990 chunk 298 optimal weight: 2.9990 chunk 270 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 336 optimal weight: 8.9990 chunk 193 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 147 GLN I 165 HIS J 294 ASN J 430 HIS ** M 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.087710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.052329 restraints weight = 74896.772| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 2.66 r_work: 0.2648 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2522 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 31391 Z= 0.169 Angle : 0.549 16.234 42848 Z= 0.283 Chirality : 0.041 0.140 4901 Planarity : 0.004 0.049 5252 Dihedral : 16.895 179.616 5127 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.59 % Allowed : 14.70 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.14), residues: 3640 helix: 1.87 (0.14), residues: 1393 sheet: 0.45 (0.24), residues: 499 loop : -0.50 (0.15), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG I1034 TYR 0.014 0.001 TYR J 631 PHE 0.011 0.001 PHE I 405 TRP 0.022 0.001 TRP J1193 HIS 0.005 0.001 HIS J 651 Details of bonding type rmsd covalent geometry : bond 0.00403 (31383) covalent geometry : angle 0.54826 (42836) hydrogen bonds : bond 0.04410 ( 1331) hydrogen bonds : angle 4.03414 ( 3648) metal coordination : bond 0.00743 ( 8) metal coordination : angle 2.24296 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 153 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 93 GLN cc_start: 0.9018 (tp40) cc_final: 0.8517 (tm-30) REVERT: G 191 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.8018 (tpm-80) REVERT: H 25 LYS cc_start: 0.8924 (mtpm) cc_final: 0.8705 (mtpt) REVERT: H 95 LYS cc_start: 0.9311 (mtpp) cc_final: 0.8977 (tptp) REVERT: H 228 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9106 (mt) REVERT: I 253 PHE cc_start: 0.8021 (p90) cc_final: 0.7654 (p90) REVERT: I 287 VAL cc_start: 0.7693 (OUTLIER) cc_final: 0.7353 (t) REVERT: I 321 LEU cc_start: 0.9043 (mt) cc_final: 0.8693 (mp) REVERT: I 431 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8903 (tptp) REVERT: J 846 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8028 (pm20) REVERT: J 988 PHE cc_start: 0.8709 (m-80) cc_final: 0.8331 (m-10) REVERT: J 1101 LEU cc_start: 0.6940 (mt) cc_final: 0.6659 (pp) REVERT: J 1370 MET cc_start: 0.8601 (ttm) cc_final: 0.8256 (ttm) REVERT: K 56 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8284 (tm-30) REVERT: K 62 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8266 (tm-30) REVERT: M 106 ASP cc_start: 0.5116 (OUTLIER) cc_final: 0.4885 (m-30) REVERT: M 118 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.7934 (tt0) REVERT: M 212 TRP cc_start: 0.8893 (m-90) cc_final: 0.8211 (m-10) outliers start: 50 outliers final: 33 residues processed: 196 average time/residue: 0.8037 time to fit residues: 185.4838 Evaluate side-chains 193 residues out of total 3141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 152 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 103 ASN Chi-restraints excluded: chain G residue 191 ARG Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 431 LYS Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 595 THR Chi-restraints excluded: chain I residue 661 VAL Chi-restraints excluded: chain I residue 896 THR Chi-restraints excluded: chain I residue 975 ILE Chi-restraints excluded: chain I residue 985 GLU Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 331 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 846 GLU Chi-restraints excluded: chain J residue 952 VAL Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 978 ARG Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 62 GLN Chi-restraints excluded: chain M residue 106 ASP Chi-restraints excluded: chain M residue 118 GLN Chi-restraints excluded: chain M residue 223 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 207 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 221 optimal weight: 0.8980 chunk 270 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 309 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 200 optimal weight: 0.9980 chunk 27 optimal weight: 0.0010 chunk 11 optimal weight: 3.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 165 HIS J 430 HIS ** J1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 352 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.088611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.053357 restraints weight = 74929.520| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 2.66 r_work: 0.2675 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2548 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31391 Z= 0.121 Angle : 0.531 16.266 42848 Z= 0.270 Chirality : 0.040 0.204 4901 Planarity : 0.003 0.047 5252 Dihedral : 16.813 179.868 5127 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.53 % Allowed : 14.77 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.14), residues: 3640 helix: 1.96 (0.14), residues: 1392 sheet: 0.52 (0.24), residues: 498 loop : -0.43 (0.15), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG I1034 TYR 0.013 0.001 TYR J 631 PHE 0.011 0.001 PHE J1319 TRP 0.021 0.001 TRP J1193 HIS 0.004 0.001 HIS J 651 Details of bonding type rmsd covalent geometry : bond 0.00285 (31383) covalent geometry : angle 0.52953 (42836) hydrogen bonds : bond 0.03832 ( 1331) hydrogen bonds : angle 3.92346 ( 3648) metal coordination : bond 0.00530 ( 8) metal coordination : angle 2.10630 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14353.28 seconds wall clock time: 243 minutes 57.03 seconds (14637.03 seconds total)