Starting phenix.real_space_refine on Sat Aug 8 20:12:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8urw_42502/08_2026/8urw_42502.cif Found real_map, /net/cci-nas-00/data/ceres_data/8urw_42502/08_2026/8urw_42502.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8urw_42502/08_2026/8urw_42502.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8urw_42502/08_2026/8urw_42502.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8urw_42502/08_2026/8urw_42502.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8urw_42502/08_2026/8urw_42502.cif" model { file = "/net/cci-nas-00/data/ceres_data/8urw_42502/08_2026/8urw_42502.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8urw_42502/08_2026/8urw_42502.cif" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.035 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 97 5.49 5 Mg 1 5.21 5 S 85 5.16 5 C 18400 2.51 5 N 5353 2.21 5 O 5958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29896 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1738 Classifications: {'peptide': 227} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 216} Chain: "B" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1738 Classifications: {'peptide': 227} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 216} Chain: "C" Number of atoms: 8529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1080, 8529 Classifications: {'peptide': 1080} Link IDs: {'PTRANS': 61, 'TRANS': 1018} Chain: "D" Number of atoms: 4961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4961 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 32, 'TRANS': 587} Chain: "E" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 529 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "Z" Number of atoms: 9461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1235, 9461 Classifications: {'peptide': 1235} Link IDs: {'PTRANS': 46, 'TRANS': 1188} Chain: "G" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 957 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 8, 'TRANS': 111} Chain: "N" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 825 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain: "T" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 815 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain: "R" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 311 Classifications: {'RNAv2': 14} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 9, 'rna3p_pyr': 1} Link IDs: {'rna2p': 3, 'rna3p': 10} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'CTP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12545 SG CYS D 70 93.293 111.943 114.118 1.00128.39 S ATOM 12561 SG CYS D 72 92.762 114.242 116.793 1.00123.83 S ATOM 12670 SG CYS D 85 96.125 112.281 116.665 1.00129.15 S ATOM 12696 SG CYS D 88 92.929 110.499 117.687 1.00131.04 S ATOM 19221 SG CYS Z 221 97.479 47.868 86.292 1.00 73.95 S ATOM 19777 SG CYS Z 295 94.501 49.797 87.703 1.00 59.75 S ATOM 19826 SG CYS Z 302 95.949 50.640 84.234 1.00 54.28 S ATOM 19850 SG CYS Z 305 93.943 47.566 84.704 1.00 63.60 S Time building chain proxies: 5.55, per 1000 atoms: 0.19 Number of scatterers: 29896 At special positions: 0 Unit cell: (126.54, 152.19, 231.705, 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 85 16.00 P 97 15.00 Mg 1 11.99 O 5958 8.00 N 5353 7.00 C 18400 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: 2.23 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 702 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 70 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 72 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 85 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 88 " pdb=" ZN Z1401 " pdb="ZN ZN Z1401 " - pdb=" SG CYS Z 302 " pdb="ZN ZN Z1401 " - pdb=" SG CYS Z 305 " pdb="ZN ZN Z1401 " - pdb=" SG CYS Z 221 " pdb="ZN ZN Z1401 " - pdb=" SG CYS Z 295 " Number of angles added : 12 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6580 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 50 sheets defined 31.6% alpha, 17.5% beta 36 base pairs and 69 stacking pairs defined. Time for finding SS restraints: 3.04 Creating SS restraints... Processing helix chain 'A' and resid 30 through 46 removed outlier: 4.016A pdb=" N THR A 34 " --> pdb=" O GLY A 30 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A 38 " --> pdb=" O THR A 34 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 45 " --> pdb=" O ARG A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 83 removed outlier: 3.718A pdb=" N GLU A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 204 through 221 Processing helix chain 'A' and resid 222 through 224 No H-bonds generated for 'chain 'A' and resid 222 through 224' Processing helix chain 'B' and resid 30 through 46 removed outlier: 3.860A pdb=" N THR B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER B 45 " --> pdb=" O ARG B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 82 Processing helix chain 'B' and resid 109 through 111 No H-bonds generated for 'chain 'B' and resid 109 through 111' Processing helix chain 'B' and resid 204 through 221 Processing helix chain 'B' and resid 222 through 224 No H-bonds generated for 'chain 'B' and resid 222 through 224' Processing helix chain 'C' and resid 18 through 38 removed outlier: 3.802A pdb=" N ARG C 22 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N LEU C 33 " --> pdb=" O LEU C 29 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ILE C 34 " --> pdb=" O GLU C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 74 Processing helix chain 'C' and resid 182 through 189 Processing helix chain 'C' and resid 192 through 199 removed outlier: 3.699A pdb=" N LYS C 199 " --> pdb=" O GLU C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 214 removed outlier: 4.152A pdb=" N TYR C 206 " --> pdb=" O HIS C 202 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN C 207 " --> pdb=" O PRO C 203 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LYS C 208 " --> pdb=" O GLU C 204 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N THR C 209 " --> pdb=" O TYR C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 230 Processing helix chain 'C' and resid 236 through 249 Processing helix chain 'C' and resid 256 through 269 removed outlier: 3.788A pdb=" N GLY C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 296 removed outlier: 3.589A pdb=" N ILE C 284 " --> pdb=" O THR C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 310 No H-bonds generated for 'chain 'C' and resid 308 through 310' Processing helix chain 'C' and resid 316 through 343 removed outlier: 3.729A pdb=" N ASN C 323 " --> pdb=" O GLU C 319 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN C 324 " --> pdb=" O LEU C 320 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG C 334 " --> pdb=" O ASN C 330 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE C 335 " --> pdb=" O ARG C 331 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER C 343 " --> pdb=" O ARG C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 354 removed outlier: 3.945A pdb=" N VAL C 354 " --> pdb=" O ALA C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 369 removed outlier: 3.999A pdb=" N VAL C 360 " --> pdb=" O PRO C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 388 removed outlier: 3.639A pdb=" N LYS C 388 " --> pdb=" O GLU C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.623A pdb=" N ASP C 410 " --> pdb=" O ALA C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 416 removed outlier: 3.834A pdb=" N TYR C 416 " --> pdb=" O PRO C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 531 removed outlier: 3.503A pdb=" N LEU C 530 " --> pdb=" O ALA C 527 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE C 531 " --> pdb=" O THR C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 537 Processing helix chain 'C' and resid 538 through 550 removed outlier: 3.886A pdb=" N ARG C 550 " --> pdb=" O SER C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 574 Processing helix chain 'C' and resid 676 through 681 Processing helix chain 'C' and resid 714 through 718 removed outlier: 3.503A pdb=" N ALA C 717 " --> pdb=" O GLY C 714 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 763 removed outlier: 4.246A pdb=" N LYS C 756 " --> pdb=" O PRO C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 857 through 863 removed outlier: 4.153A pdb=" N SER C 861 " --> pdb=" O LEU C 857 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 865 through 881 removed outlier: 3.846A pdb=" N PHE C 869 " --> pdb=" O VAL C 865 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA C 876 " --> pdb=" O MET C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 889 through 894 removed outlier: 4.211A pdb=" N MET C 892 " --> pdb=" O PHE C 889 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR C 893 " --> pdb=" O ASP C 890 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 914 Processing helix chain 'C' and resid 915 through 919 removed outlier: 3.569A pdb=" N VAL C 918 " --> pdb=" O GLN C 915 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N PHE C 919 " --> pdb=" O PRO C 916 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 915 through 919' Processing helix chain 'C' and resid 955 through 959 Processing helix chain 'C' and resid 978 through 982 removed outlier: 3.505A pdb=" N GLN C 981 " --> pdb=" O GLY C 978 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN C 982 " --> pdb=" O LYS C 979 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 978 through 982' Processing helix chain 'C' and resid 988 through 999 Processing helix chain 'C' and resid 1000 through 1009 removed outlier: 3.847A pdb=" N LEU C1004 " --> pdb=" O ALA C1000 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1028 removed outlier: 3.533A pdb=" N GLU C1020 " --> pdb=" O GLN C1016 " (cutoff:3.500A) Processing helix chain 'C' and resid 1037 through 1049 removed outlier: 3.962A pdb=" N LYS C1041 " --> pdb=" O PRO C1037 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 25 removed outlier: 3.695A pdb=" N GLY D 25 " --> pdb=" O ILE D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.893A pdb=" N VAL D 97 " --> pdb=" O GLU D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 139 Processing helix chain 'D' and resid 162 through 174 Processing helix chain 'D' and resid 191 through 198 removed outlier: 3.840A pdb=" N LEU D 195 " --> pdb=" O ALA D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 214 removed outlier: 4.172A pdb=" N ALA D 213 " --> pdb=" O ARG D 209 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLU D 214 " --> pdb=" O GLN D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 236 removed outlier: 3.632A pdb=" N LEU D 223 " --> pdb=" O LYS D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 242 Processing helix chain 'D' and resid 252 through 256 Processing helix chain 'D' and resid 269 through 291 removed outlier: 3.945A pdb=" N ASP D 273 " --> pdb=" O SER D 269 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE D 291 " --> pdb=" O ARG D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 314 Processing helix chain 'D' and resid 333 through 337 removed outlier: 3.523A pdb=" N ILE D 336 " --> pdb=" O LEU D 333 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE D 337 " --> pdb=" O SER D 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 333 through 337' Processing helix chain 'D' and resid 342 through 348 removed outlier: 3.625A pdb=" N LEU D 348 " --> pdb=" O PHE D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 383 removed outlier: 3.748A pdb=" N GLU D 381 " --> pdb=" O GLU D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 394 Processing helix chain 'D' and resid 399 through 410 Processing helix chain 'D' and resid 412 through 422 removed outlier: 3.834A pdb=" N ASP D 416 " --> pdb=" O PRO D 412 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU D 420 " --> pdb=" O ASP D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 438 No H-bonds generated for 'chain 'D' and resid 436 through 438' Processing helix chain 'D' and resid 456 through 458 No H-bonds generated for 'chain 'D' and resid 456 through 458' Processing helix chain 'D' and resid 459 through 464 Processing helix chain 'D' and resid 479 through 490 removed outlier: 3.518A pdb=" N MET D 490 " --> pdb=" O ALA D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 520 removed outlier: 3.733A pdb=" N LEU D 514 " --> pdb=" O GLN D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 546 removed outlier: 3.826A pdb=" N ILE D 541 " --> pdb=" O LEU D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 622 Processing helix chain 'E' and resid 8 through 22 removed outlier: 3.758A pdb=" N LEU E 12 " --> pdb=" O ASP E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 47 removed outlier: 3.612A pdb=" N ASN E 47 " --> pdb=" O GLU E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 69 removed outlier: 3.633A pdb=" N LEU E 68 " --> pdb=" O MET E 64 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN E 69 " --> pdb=" O SER E 65 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 31 Processing helix chain 'Z' and resid 34 through 55 removed outlier: 4.032A pdb=" N VAL Z 38 " --> pdb=" O ALA Z 34 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR Z 52 " --> pdb=" O PHE Z 48 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG Z 53 " --> pdb=" O ARG Z 49 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA Z 54 " --> pdb=" O TYR Z 50 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY Z 55 " --> pdb=" O ALA Z 51 " (cutoff:3.500A) Processing helix chain 'Z' and resid 68 through 90 removed outlier: 3.869A pdb=" N LEU Z 72 " --> pdb=" O SER Z 68 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY Z 90 " --> pdb=" O ARG Z 86 " (cutoff:3.500A) Processing helix chain 'Z' and resid 93 through 124 removed outlier: 3.726A pdb=" N ASP Z 124 " --> pdb=" O PHE Z 120 " (cutoff:3.500A) Processing helix chain 'Z' and resid 127 through 134 Processing helix chain 'Z' and resid 140 through 149 removed outlier: 3.559A pdb=" N VAL Z 144 " --> pdb=" O ASN Z 140 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN Z 146 " --> pdb=" O SER Z 142 " (cutoff:3.500A) Processing helix chain 'Z' and resid 175 through 194 removed outlier: 3.920A pdb=" N TYR Z 184 " --> pdb=" O ILE Z 180 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLY Z 185 " --> pdb=" O ILE Z 181 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA Z 194 " --> pdb=" O LEU Z 190 " (cutoff:3.500A) Processing helix chain 'Z' and resid 196 through 211 removed outlier: 4.407A pdb=" N SER Z 200 " --> pdb=" O ARG Z 196 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER Z 211 " --> pdb=" O LEU Z 207 " (cutoff:3.500A) Processing helix chain 'Z' and resid 241 through 246 removed outlier: 3.879A pdb=" N ARG Z 245 " --> pdb=" O PRO Z 241 " (cutoff:3.500A) Processing helix chain 'Z' and resid 272 through 282 Processing helix chain 'Z' and resid 291 through 295 removed outlier: 3.757A pdb=" N CYS Z 295 " --> pdb=" O PRO Z 292 " (cutoff:3.500A) Processing helix chain 'Z' and resid 302 through 307 removed outlier: 3.562A pdb=" N GLY Z 307 " --> pdb=" O GLN Z 303 " (cutoff:3.500A) Processing helix chain 'Z' and resid 321 through 331 removed outlier: 3.869A pdb=" N ILE Z 325 " --> pdb=" O ALA Z 321 " (cutoff:3.500A) Processing helix chain 'Z' and resid 331 through 339 removed outlier: 3.882A pdb=" N THR Z 335 " --> pdb=" O GLY Z 331 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET Z 339 " --> pdb=" O THR Z 335 " (cutoff:3.500A) Processing helix chain 'Z' and resid 340 through 345 removed outlier: 3.504A pdb=" N HIS Z 343 " --> pdb=" O ARG Z 340 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR Z 344 " --> pdb=" O THR Z 341 " (cutoff:3.500A) Processing helix chain 'Z' and resid 990 through 993 Processing helix chain 'Z' and resid 994 through 1003 removed outlier: 3.551A pdb=" N ILE Z 998 " --> pdb=" O GLY Z 994 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1025 through 1029 removed outlier: 3.945A pdb=" N ASP Z1028 " --> pdb=" O SER Z1025 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1072 through 1088 removed outlier: 3.605A pdb=" N LEU Z1076 " --> pdb=" O ASN Z1072 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU Z1077 " --> pdb=" O PRO Z1073 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU Z1078 " --> pdb=" O HIS Z1074 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1091 through 1117 removed outlier: 4.137A pdb=" N GLN Z1117 " --> pdb=" O VAL Z1113 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1122 through 1132 removed outlier: 4.293A pdb=" N ILE Z1126 " --> pdb=" O SER Z1122 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN Z1132 " --> pdb=" O VAL Z1128 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1155 through 1166 Processing helix chain 'Z' and resid 1181 through 1187 removed outlier: 3.792A pdb=" N SER Z1186 " --> pdb=" O ILE Z1182 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU Z1187 " --> pdb=" O THR Z1183 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1191 through 1197 removed outlier: 3.501A pdb=" N ALA Z1195 " --> pdb=" O SER Z1191 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1200 through 1212 Processing helix chain 'Z' and resid 1222 through 1227 Processing helix chain 'Z' and resid 1232 through 1236 removed outlier: 3.618A pdb=" N GLY Z1235 " --> pdb=" O ALA Z1232 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 47 Processing helix chain 'G' and resid 91 through 100 Processing helix chain 'G' and resid 129 through 137 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 12 removed outlier: 6.840A pdb=" N ARG A 21 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N SER A 10 " --> pdb=" O TYR A 19 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N TYR A 19 " --> pdb=" O SER A 10 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASP A 191 " --> pdb=" O PRO A 26 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 101 removed outlier: 3.923A pdb=" N GLN A 94 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A 141 " --> pdb=" O GLN A 94 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA A 54 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLU A 142 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N VAL A 52 " --> pdb=" O GLU A 142 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLY A 144 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N THR A 50 " --> pdb=" O GLY A 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 88 Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 107 Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 148 Processing sheet with id=AA6, first strand: chain 'B' and resid 4 through 12 removed outlier: 6.834A pdb=" N ARG B 21 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N SER B 10 " --> pdb=" O TYR B 19 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N TYR B 19 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASP B 191 " --> pdb=" O PRO B 26 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 95 through 101 removed outlier: 7.257A pdb=" N GLU B 136 " --> pdb=" O ILE B 57 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ILE B 57 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLU B 138 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL B 55 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LYS B 140 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA B 51 " --> pdb=" O GLU B 142 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AA9, first strand: chain 'B' and resid 105 through 107 removed outlier: 6.885A pdb=" N VAL B 106 " --> pdb=" O ILE B 126 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 148 Processing sheet with id=AB2, first strand: chain 'C' and resid 52 through 54 Processing sheet with id=AB3, first strand: chain 'C' and resid 52 through 54 removed outlier: 4.031A pdb=" N GLY C 104 " --> pdb=" O MET C 82 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL C 84 " --> pdb=" O PHE C 102 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N PHE C 102 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR C 86 " --> pdb=" O GLU C 100 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N GLU C 100 " --> pdb=" O THR C 86 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 115 through 117 Processing sheet with id=AB5, first strand: chain 'C' and resid 312 through 315 removed outlier: 6.419A pdb=" N ASN C 126 " --> pdb=" O SER C 392 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 133 through 141 removed outlier: 6.665A pdb=" N GLY C 133 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU C 152 " --> pdb=" O GLY C 133 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TYR C 135 " --> pdb=" O ALA C 150 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ALA C 150 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS C 137 " --> pdb=" O HIS C 148 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N HIS C 148 " --> pdb=" O LYS C 137 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLU C 139 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU C 146 " --> pdb=" O GLU C 139 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N HIS C 148 " --> pdb=" O THR C 164 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS C 161 " --> pdb=" O ARG C 173 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 441 through 442 Processing sheet with id=AB8, first strand: chain 'C' and resid 459 through 460 Processing sheet with id=AB9, first strand: chain 'C' and resid 497 through 501 Processing sheet with id=AC1, first strand: chain 'C' and resid 579 through 580 removed outlier: 6.771A pdb=" N ILE C 579 " --> pdb=" O ILE C 639 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 585 through 591 removed outlier: 6.628A pdb=" N GLU C 596 " --> pdb=" O SER C 588 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL C 590 " --> pdb=" O HIS C 594 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N HIS C 594 " --> pdb=" O VAL C 590 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 613 through 614 Processing sheet with id=AC4, first strand: chain 'C' and resid 926 through 927 removed outlier: 7.310A pdb=" N ILE C 672 " --> pdb=" O SER C 833 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE C 835 " --> pdb=" O ILE C 672 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE C 674 " --> pdb=" O ILE C 835 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU C 673 " --> pdb=" O VAL C 853 " (cutoff:3.500A) removed outlier: 9.419A pdb=" N ILE C 852 " --> pdb=" O ASN C 655 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU C 657 " --> pdb=" O ILE C 852 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N LEU C 854 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA C 659 " --> pdb=" O LEU C 854 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N THR C 943 " --> pdb=" O TYR C 660 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 686 through 697 removed outlier: 6.523A pdb=" N SER C 686 " --> pdb=" O LYS C 813 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS C 813 " --> pdb=" O SER C 686 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N HIS C 688 " --> pdb=" O ALA C 811 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ALA C 811 " --> pdb=" O HIS C 688 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLU C 690 " --> pdb=" O TYR C 809 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR C 809 " --> pdb=" O GLU C 690 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N PHE C 692 " --> pdb=" O ARG C 807 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ARG C 807 " --> pdb=" O PHE C 692 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE C 694 " --> pdb=" O VAL C 805 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL C 805 " --> pdb=" O ILE C 694 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA C 696 " --> pdb=" O ASN C 803 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP C 786 " --> pdb=" O TYR C 809 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ALA C 811 " --> pdb=" O VAL C 784 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N VAL C 784 " --> pdb=" O ALA C 811 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N LYS C 813 " --> pdb=" O GLY C 782 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N GLY C 782 " --> pdb=" O LYS C 813 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 705 through 706 Processing sheet with id=AC7, first strand: chain 'C' and resid 721 through 722 removed outlier: 3.781A pdb=" N ILE C 726 " --> pdb=" O ASP C 722 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 738 through 740 removed outlier: 3.607A pdb=" N VAL C 740 " --> pdb=" O LEU C 774 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 961 through 963 Processing sheet with id=AD1, first strand: chain 'C' and resid 985 through 987 removed outlier: 3.937A pdb=" N GLN C 985 " --> pdb=" O VAL D 353 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1068 through 1069 Processing sheet with id=AD3, first strand: chain 'D' and resid 27 through 28 Processing sheet with id=AD4, first strand: chain 'D' and resid 103 through 112 removed outlier: 10.419A pdb=" N LEU D 107 " --> pdb=" O PRO D 249 " (cutoff:3.500A) removed outlier: 10.544A pdb=" N ALA D 109 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL D 247 " --> pdb=" O ALA D 109 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 160 through 161 removed outlier: 3.675A pdb=" N TYR D 144 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL D 185 " --> pdb=" O LEU D 147 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 533 through 534 removed outlier: 6.833A pdb=" N ARG D 593 " --> pdb=" O LEU D 601 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLN D 603 " --> pdb=" O ARG D 591 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ARG D 591 " --> pdb=" O GLN D 603 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR D 582 " --> pdb=" O ALA D 578 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 563 through 565 removed outlier: 6.687A pdb=" N GLU D 564 " --> pdb=" O ASN Z 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'Z' and resid 227 through 229 Processing sheet with id=AD9, first strand: chain 'Z' and resid 232 through 234 removed outlier: 6.696A pdb=" N MET Z 232 " --> pdb=" O LEU Z 239 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Z' and resid 255 through 256 removed outlier: 3.910A pdb=" N ALA Z 265 " --> pdb=" O VAL Z 255 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Z' and resid 354 through 357 removed outlier: 6.414A pdb=" N ARG Z 354 " --> pdb=" O GLU Z 427 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU Z 427 " --> pdb=" O ARG Z 354 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU Z 356 " --> pdb=" O LEU Z 425 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Z' and resid 400 through 405 Processing sheet with id=AE4, first strand: chain 'Z' and resid 441 through 446 removed outlier: 6.581A pdb=" N ALA Z 441 " --> pdb=" O VAL Z 982 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL Z 982 " --> pdb=" O ALA Z 441 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LYS Z 443 " --> pdb=" O LEU Z 980 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU Z 980 " --> pdb=" O LYS Z 443 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL Z 445 " --> pdb=" O LEU Z 978 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Z' and resid 903 through 906 removed outlier: 6.757A pdb=" N GLN Z 949 " --> pdb=" O ARG Z 941 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Z' and resid 903 through 906 removed outlier: 6.378A pdb=" N ILE Z 952 " --> pdb=" O ALA Z 484 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Z' and resid 459 through 464 removed outlier: 6.342A pdb=" N VAL Z 459 " --> pdb=" O GLN Z 475 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Z' and resid 486 through 489 removed outlier: 3.702A pdb=" N GLY Z 880 " --> pdb=" O VAL Z 504 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Z' and resid 495 through 496 removed outlier: 6.836A pdb=" N ILE Z 874 " --> pdb=" O LEU Z 510 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER Z 850 " --> pdb=" O GLN Z 875 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Z' and resid 1020 through 1021 Processing sheet with id=AF2, first strand: chain 'Z' and resid 1152 through 1154 Processing sheet with id=AF3, first strand: chain 'G' and resid 53 through 57 removed outlier: 3.625A pdb=" N GLN G 55 " --> pdb=" O ARG G 87 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ALA G 25 " --> pdb=" O PHE G 107 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N PHE G 107 " --> pdb=" O ALA G 25 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N GLN G 27 " --> pdb=" O ILE G 105 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 60 through 63 Processing sheet with id=AF5, first strand: chain 'G' and resid 109 through 110 977 hydrogen bonds defined for protein. 2682 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 98 hydrogen bonds 196 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 69 stacking parallelities Total time for adding SS restraints: 6.73 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8816 1.33 - 1.45: 4895 1.45 - 1.57: 16553 1.57 - 1.70: 190 1.70 - 1.82: 142 Bond restraints: 30596 Sorted by residual: bond pdb=" C3' DG T 3 " pdb=" C2' DG T 3 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.29e+01 bond pdb=" C3' DC T 22 " pdb=" C2' DC T 22 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DG N 18 " pdb=" C2' DG N 18 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.00e+01 bond pdb=" C3' DG T 6 " pdb=" C2' DG T 6 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.23e+00 bond pdb=" C3' DC T 23 " pdb=" C2' DC T 23 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.79e+00 ... (remaining 30591 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 41442 2.43 - 4.87: 400 4.87 - 7.30: 22 7.30 - 9.74: 6 9.74 - 12.17: 6 Bond angle restraints: 41876 Sorted by residual: angle pdb=" N VAL Z 588 " pdb=" CA VAL Z 588 " pdb=" C VAL Z 588 " ideal model delta sigma weight residual 113.71 108.95 4.76 9.50e-01 1.11e+00 2.51e+01 angle pdb=" O4' DT T 19 " pdb=" C4' DT T 19 " pdb=" C3' DT T 19 " ideal model delta sigma weight residual 106.00 103.00 3.00 6.00e-01 2.78e+00 2.49e+01 angle pdb=" O4' DC T 17 " pdb=" C4' DC T 17 " pdb=" C3' DC T 17 " ideal model delta sigma weight residual 106.00 103.07 2.93 6.00e-01 2.78e+00 2.39e+01 angle pdb=" N3 DT T 24 " pdb=" C4 DT T 24 " pdb=" O4 DT T 24 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT T 13 " pdb=" C4 DT T 13 " pdb=" O4 DT T 13 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 ... (remaining 41871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.80: 16856 32.80 - 65.60: 1463 65.60 - 98.40: 96 98.40 - 131.19: 2 131.19 - 163.99: 4 Dihedral angle restraints: 18421 sinusoidal: 8181 harmonic: 10240 Sorted by residual: dihedral pdb=" C4' A R 9 " pdb=" C3' A R 9 " pdb=" C2' A R 9 " pdb=" C1' A R 9 " ideal model delta sinusoidal sigma weight residual 36.34 -34.55 70.89 1 3.10e+00 1.04e-01 6.72e+02 dihedral pdb=" C4' A R 8 " pdb=" C3' A R 8 " pdb=" C2' A R 8 " pdb=" C1' A R 8 " ideal model delta sinusoidal sigma weight residual 36.34 -34.54 70.89 1 3.10e+00 1.04e-01 6.72e+02 dihedral pdb=" C4' A R 7 " pdb=" C3' A R 7 " pdb=" C2' A R 7 " pdb=" C1' A R 7 " ideal model delta sinusoidal sigma weight residual 36.34 -34.13 70.47 1 3.10e+00 1.04e-01 6.65e+02 ... (remaining 18418 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 4088 0.063 - 0.127: 628 0.127 - 0.190: 28 0.190 - 0.254: 15 0.254 - 0.317: 5 Chirality restraints: 4764 Sorted by residual: chirality pdb=" P A R 11 " pdb=" OP1 A R 11 " pdb=" OP2 A R 11 " pdb=" O5' A R 11 " both_signs ideal model delta sigma weight residual True 2.17 -2.49 -0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" P A R 9 " pdb=" OP1 A R 9 " pdb=" OP2 A R 9 " pdb=" O5' A R 9 " both_signs ideal model delta sigma weight residual True 2.17 -2.49 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" C2' A R 9 " pdb=" C3' A R 9 " pdb=" O2' A R 9 " pdb=" C1' A R 9 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.28 2.00e-01 2.50e+01 2.03e+00 ... (remaining 4761 not shown) Planarity restraints: 5181 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG Z1016 " -0.056 5.00e-02 4.00e+02 8.53e-02 1.16e+01 pdb=" N PRO Z1017 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO Z1017 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO Z1017 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 571 " -0.010 2.00e-02 2.50e+03 2.11e-02 4.47e+00 pdb=" CD GLU D 571 " 0.037 2.00e-02 2.50e+03 pdb=" OE1 GLU D 571 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU D 571 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 580 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.36e+00 pdb=" CG ASP D 580 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASP D 580 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP D 580 " -0.013 2.00e-02 2.50e+03 ... (remaining 5178 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 4255 2.76 - 3.30: 25227 3.30 - 3.83: 46434 3.83 - 4.37: 53288 4.37 - 4.90: 95007 Nonbonded interactions: 224211 Sorted by model distance: nonbonded pdb="MG MG D 701 " pdb=" O1A CTP R 101 " model vdw 2.226 2.170 nonbonded pdb=" O SER C 131 " pdb=" OH TYR C 135 " model vdw 2.235 3.040 nonbonded pdb=" NH2 ARG A 41 " pdb=" OD1 ASP C 840 " model vdw 2.236 3.120 nonbonded pdb=" OE2 GLU C 333 " pdb=" NH2 ARG C 337 " model vdw 2.244 3.120 nonbonded pdb=" NH1 ARG C 614 " pdb=" OD1 ASP C 618 " model vdw 2.246 3.120 ... (remaining 224206 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 4.000 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: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 32.610 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 44.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9099 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 : 0.003 0.062 30604 Z= 0.209 Angle : 0.598 12.175 41888 Z= 0.358 Chirality : 0.046 0.317 4764 Planarity : 0.004 0.085 5181 Dihedral : 21.051 163.992 11841 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.12 % Favored : 93.54 % Rotamer: Outliers : 4.41 % Allowed : 31.97 % Favored : 63.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.96 (0.14), residues: 3560 helix: 1.63 (0.17), residues: 951 sheet: 0.16 (0.22), residues: 536 loop : -2.10 (0.12), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 334 TYR 0.016 0.001 TYR B 125 PHE 0.014 0.001 PHE A 169 TRP 0.009 0.001 TRP C 875 HIS 0.003 0.000 HIS A 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.21 (30596) covalent geometry : angle 0.59515 / 0.36 (41876) hydrogen bonds : bond 0.15977 / 10.70 ( 1069) hydrogen bonds : angle 5.34101 / 3.68 ( 2878) metal coordination : bond 0.00305 / 0.15 ( 8) metal coordination : angle 3.57541 / 1.89 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 227 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ARG cc_start: 0.7387 (ttm170) cc_final: 0.6838 (ttm170) REVERT: C 45 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7700 (p0) REVERT: C 63 ARG cc_start: 0.5901 (tpt170) cc_final: 0.5446 (mmp-170) REVERT: C 99 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.8069 (pm20) REVERT: C 302 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8739 (mp0) REVERT: C 333 GLU cc_start: 0.8678 (tt0) cc_final: 0.8396 (tm-30) REVERT: C 403 ARG cc_start: 0.8343 (ttm-80) cc_final: 0.7979 (ttt90) REVERT: Z 466 ARG cc_start: 0.8246 (ttp80) cc_final: 0.7802 (ptt90) REVERT: Z 633 TRP cc_start: 0.1701 (OUTLIER) cc_final: 0.0291 (t-100) REVERT: G 42 GLN cc_start: 0.9290 (tm-30) cc_final: 0.9085 (tm-30) REVERT: G 46 THR cc_start: 0.9046 (OUTLIER) cc_final: 0.8832 (t) outliers start: 133 outliers final: 97 residues processed: 354 average time/residue: 0.6080 time to fit residues: 254.5083 Evaluate side-chains 298 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 196 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 496 THR Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain C residue 565 THR Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 828 ASN Chi-restraints excluded: chain C residue 881 ASP Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 1012 SER Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 511 ASP Chi-restraints excluded: chain D residue 536 ASN Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 602 SER Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain Z residue 168 THR Chi-restraints excluded: chain Z residue 200 SER Chi-restraints excluded: chain Z residue 270 ASP Chi-restraints excluded: chain Z residue 300 SER Chi-restraints excluded: chain Z residue 316 VAL Chi-restraints excluded: chain Z residue 341 THR Chi-restraints excluded: chain Z residue 363 THR Chi-restraints excluded: chain Z residue 389 ASN Chi-restraints excluded: chain Z residue 410 THR Chi-restraints excluded: chain Z residue 437 THR Chi-restraints excluded: chain Z residue 448 ASP Chi-restraints excluded: chain Z residue 498 VAL Chi-restraints excluded: chain Z residue 533 THR Chi-restraints excluded: chain Z residue 609 VAL Chi-restraints excluded: chain Z residue 633 TRP Chi-restraints excluded: chain Z residue 645 ILE Chi-restraints excluded: chain Z residue 647 LEU Chi-restraints excluded: chain Z residue 684 ARG Chi-restraints excluded: chain Z residue 693 VAL Chi-restraints excluded: chain Z residue 695 VAL Chi-restraints excluded: chain Z residue 717 VAL Chi-restraints excluded: chain Z residue 756 VAL Chi-restraints excluded: chain Z residue 789 VAL Chi-restraints excluded: chain Z residue 797 THR Chi-restraints excluded: chain Z residue 923 VAL Chi-restraints excluded: chain Z residue 1028 ASP Chi-restraints excluded: chain Z residue 1040 THR Chi-restraints excluded: chain Z residue 1055 SER Chi-restraints excluded: chain Z residue 1091 ASP Chi-restraints excluded: chain Z residue 1098 SER Chi-restraints excluded: chain Z residue 1112 SER Chi-restraints excluded: chain Z residue 1123 ASP Chi-restraints excluded: chain Z residue 1145 THR Chi-restraints excluded: chain Z residue 1161 SER Chi-restraints excluded: chain Z residue 1182 ILE Chi-restraints excluded: chain Z residue 1183 THR Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 55 GLN Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 72 ARG Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 116 TYR Chi-restraints excluded: chain G residue 129 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 0.0770 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 225 ASN C 712 ASN C 826 HIS D 260 GLN ** D 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 ASN G 112 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.122081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.072007 restraints weight = 54480.675| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.98 r_work: 0.2790 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.0761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 30604 Z= 0.128 Angle : 0.619 14.442 41888 Z= 0.321 Chirality : 0.049 0.838 4764 Planarity : 0.005 0.105 5181 Dihedral : 16.505 162.608 5139 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.18 % Favored : 93.51 % Rotamer: Outliers : 4.77 % Allowed : 30.25 % Favored : 64.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.80 (0.14), residues: 3560 helix: 1.74 (0.17), residues: 983 sheet: 0.19 (0.21), residues: 566 loop : -2.05 (0.12), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG Z 535 TYR 0.015 0.001 TYR C 680 PHE 0.015 0.001 PHE B 64 TRP 0.008 0.001 TRP C 875 HIS 0.011 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 (30596) covalent geometry : angle 0.61512 / 0.32 (41876) hydrogen bonds : bond 0.05029 / 3.32 ( 1069) hydrogen bonds : angle 4.37921 / 2.99 ( 2878) metal coordination : bond 0.00537 / 0.27 ( 8) metal coordination : angle 3.93312 / 2.10 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 207 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7133 (pp-130) cc_final: 0.6674 (ppp) REVERT: A 29 ARG cc_start: 0.7314 (tpp-160) cc_final: 0.7001 (tpp-160) REVERT: A 183 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.7121 (ttm170) REVERT: B 73 ASP cc_start: 0.7947 (p0) cc_final: 0.7629 (p0) REVERT: C 63 ARG cc_start: 0.5446 (tpt170) cc_final: 0.4886 (mmp-170) REVERT: C 245 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8658 (tm-30) REVERT: C 302 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8436 (mp0) REVERT: C 333 GLU cc_start: 0.8575 (tt0) cc_final: 0.8332 (tm-30) REVERT: D 44 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.8265 (pp) REVERT: Z 466 ARG cc_start: 0.8416 (ttp80) cc_final: 0.8131 (ptt90) REVERT: Z 508 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7751 (m-30) REVERT: Z 990 ASP cc_start: 0.6784 (OUTLIER) cc_final: 0.6484 (p0) REVERT: Z 999 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7821 (tm-30) REVERT: Z 1016 ARG cc_start: 0.8439 (tpp80) cc_final: 0.7958 (tpp80) REVERT: G 132 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8112 (mt-10) outliers start: 144 outliers final: 73 residues processed: 339 average time/residue: 0.6344 time to fit residues: 256.4239 Evaluate side-chains 269 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 191 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 496 THR Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 712 ASN Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 771 ASP Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 953 VAL Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain Z residue 120 PHE Chi-restraints excluded: chain Z residue 168 THR Chi-restraints excluded: chain Z residue 341 THR Chi-restraints excluded: chain Z residue 437 THR Chi-restraints excluded: chain Z residue 448 ASP Chi-restraints excluded: chain Z residue 498 VAL Chi-restraints excluded: chain Z residue 506 VAL Chi-restraints excluded: chain Z residue 508 ASP Chi-restraints excluded: chain Z residue 533 THR Chi-restraints excluded: chain Z residue 582 VAL Chi-restraints excluded: chain Z residue 609 VAL Chi-restraints excluded: chain Z residue 645 ILE Chi-restraints excluded: chain Z residue 647 LEU Chi-restraints excluded: chain Z residue 693 VAL Chi-restraints excluded: chain Z residue 695 VAL Chi-restraints excluded: chain Z residue 717 VAL Chi-restraints excluded: chain Z residue 749 VAL Chi-restraints excluded: chain Z residue 789 VAL Chi-restraints excluded: chain Z residue 906 LEU Chi-restraints excluded: chain Z residue 923 VAL Chi-restraints excluded: chain Z residue 928 LEU Chi-restraints excluded: chain Z residue 990 ASP Chi-restraints excluded: chain Z residue 1040 THR Chi-restraints excluded: chain Z residue 1112 SER Chi-restraints excluded: chain Z residue 1182 ILE Chi-restraints excluded: chain Z residue 1183 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 72 ARG Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 90 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 259 optimal weight: 5.9990 chunk 230 optimal weight: 5.9990 chunk 203 optimal weight: 5.9990 chunk 333 optimal weight: 5.9990 chunk 149 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 201 optimal weight: 0.0040 chunk 237 optimal weight: 0.9980 chunk 73 optimal weight: 0.1980 overall best weight: 1.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 712 ASN ** D 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 ASN G 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.120688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.070526 restraints weight = 54831.564| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.92 r_work: 0.2747 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 30604 Z= 0.149 Angle : 0.591 10.090 41888 Z= 0.309 Chirality : 0.047 0.525 4764 Planarity : 0.004 0.094 5181 Dihedral : 16.237 162.777 5060 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.43 % Favored : 93.26 % Rotamer: Outliers : 4.41 % Allowed : 30.75 % Favored : 64.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.80 (0.14), residues: 3560 helix: 1.84 (0.17), residues: 984 sheet: 0.09 (0.21), residues: 562 loop : -2.07 (0.12), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG Z 535 TYR 0.017 0.001 TYR C 680 PHE 0.015 0.001 PHE A 169 TRP 0.009 0.001 TRP C 875 HIS 0.010 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (30596) covalent geometry : angle 0.58715 / 0.31 (41876) hydrogen bonds : bond 0.05099 / 3.40 ( 1069) hydrogen bonds : angle 4.21532 / 2.87 ( 2878) metal coordination : bond 0.00475 / 0.24 ( 8) metal coordination : angle 3.76477 / 1.99 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 198 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7322 (OUTLIER) cc_final: 0.6869 (ppp) REVERT: A 183 ARG cc_start: 0.7412 (ttm170) cc_final: 0.7079 (ttm170) REVERT: B 73 ASP cc_start: 0.7984 (p0) cc_final: 0.7604 (p0) REVERT: C 63 ARG cc_start: 0.5167 (tpt170) cc_final: 0.4564 (mmp-170) REVERT: C 302 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8473 (mp0) REVERT: C 333 GLU cc_start: 0.8670 (tt0) cc_final: 0.8390 (tm-30) REVERT: C 746 LYS cc_start: 0.8591 (mttt) cc_final: 0.8267 (ptpt) REVERT: D 210 GLN cc_start: 0.9291 (OUTLIER) cc_final: 0.8874 (tm-30) REVERT: Z 462 GLU cc_start: 0.9170 (OUTLIER) cc_final: 0.8625 (mm-30) REVERT: Z 466 ARG cc_start: 0.8422 (ttp80) cc_final: 0.8039 (ptm160) REVERT: Z 467 GLN cc_start: 0.8810 (mm-40) cc_final: 0.8549 (mm-40) REVERT: Z 470 THR cc_start: 0.8991 (OUTLIER) cc_final: 0.7889 (t) REVERT: Z 508 ASP cc_start: 0.8075 (OUTLIER) cc_final: 0.7826 (m-30) REVERT: Z 999 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7886 (tm-30) REVERT: Z 1016 ARG cc_start: 0.8389 (tpp80) cc_final: 0.7831 (tpp-160) REVERT: G 91 ASP cc_start: 0.8928 (t70) cc_final: 0.8556 (p0) outliers start: 133 outliers final: 74 residues processed: 317 average time/residue: 0.6216 time to fit residues: 236.5011 Evaluate side-chains 268 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 189 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 496 THR Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 771 ASP Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 953 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 156 GLN Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 25 ASN Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain Z residue 120 PHE Chi-restraints excluded: chain Z residue 126 LEU Chi-restraints excluded: chain Z residue 168 THR Chi-restraints excluded: chain Z residue 316 VAL Chi-restraints excluded: chain Z residue 320 GLU Chi-restraints excluded: chain Z residue 437 THR Chi-restraints excluded: chain Z residue 462 GLU Chi-restraints excluded: chain Z residue 470 THR Chi-restraints excluded: chain Z residue 498 VAL Chi-restraints excluded: chain Z residue 506 VAL Chi-restraints excluded: chain Z residue 508 ASP Chi-restraints excluded: chain Z residue 574 LEU Chi-restraints excluded: chain Z residue 582 VAL Chi-restraints excluded: chain Z residue 604 LEU Chi-restraints excluded: chain Z residue 609 VAL Chi-restraints excluded: chain Z residue 645 ILE Chi-restraints excluded: chain Z residue 647 LEU Chi-restraints excluded: chain Z residue 693 VAL Chi-restraints excluded: chain Z residue 695 VAL Chi-restraints excluded: chain Z residue 717 VAL Chi-restraints excluded: chain Z residue 749 VAL Chi-restraints excluded: chain Z residue 906 LEU Chi-restraints excluded: chain Z residue 923 VAL Chi-restraints excluded: chain Z residue 928 LEU Chi-restraints excluded: chain Z residue 990 ASP Chi-restraints excluded: chain Z residue 1040 THR Chi-restraints excluded: chain Z residue 1112 SER Chi-restraints excluded: chain Z residue 1182 ILE Chi-restraints excluded: chain Z residue 1189 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 55 GLN Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 90 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 99 optimal weight: 5.9990 chunk 169 optimal weight: 5.9990 chunk 158 optimal weight: 6.9990 chunk 287 optimal weight: 9.9990 chunk 167 optimal weight: 6.9990 chunk 244 optimal weight: 2.9990 chunk 67 optimal weight: 0.3980 chunk 5 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 166 optimal weight: 7.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 398 ASN D 410 ASN ** D 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.119099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.068871 restraints weight = 54262.238| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 2.86 r_work: 0.2698 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 30604 Z= 0.206 Angle : 0.612 9.680 41888 Z= 0.321 Chirality : 0.048 0.423 4764 Planarity : 0.005 0.095 5181 Dihedral : 16.192 162.975 5039 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.85 % Favored : 92.84 % Rotamer: Outliers : 5.24 % Allowed : 29.75 % Favored : 65.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.87 (0.14), residues: 3560 helix: 1.79 (0.17), residues: 981 sheet: 0.03 (0.21), residues: 565 loop : -2.12 (0.12), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Z 535 TYR 0.019 0.001 TYR C 680 PHE 0.019 0.001 PHE A 169 TRP 0.011 0.001 TRP C 875 HIS 0.005 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.21 (30596) covalent geometry : angle 0.60853 / 0.32 (41876) hydrogen bonds : bond 0.05932 / 3.99 ( 1069) hydrogen bonds : angle 4.19706 / 2.86 ( 2878) metal coordination : bond 0.00695 / 0.36 ( 8) metal coordination : angle 4.06419 / 2.11 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 200 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7412 (OUTLIER) cc_final: 0.7021 (ppp) REVERT: A 29 ARG cc_start: 0.7390 (tpp-160) cc_final: 0.7052 (tpm170) REVERT: A 183 ARG cc_start: 0.7348 (OUTLIER) cc_final: 0.7026 (ttm170) REVERT: B 73 ASP cc_start: 0.7930 (p0) cc_final: 0.7562 (p0) REVERT: C 40 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.7395 (p90) REVERT: C 63 ARG cc_start: 0.5092 (tpt170) cc_final: 0.4516 (mmp-170) REVERT: C 302 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8455 (mp0) REVERT: C 333 GLU cc_start: 0.8712 (tt0) cc_final: 0.8412 (tm-30) REVERT: C 746 LYS cc_start: 0.8528 (mttt) cc_final: 0.8281 (mttt) REVERT: D 210 GLN cc_start: 0.9308 (OUTLIER) cc_final: 0.8902 (tm-30) REVERT: D 320 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7711 (ppt170) REVERT: Z 249 ARG cc_start: 0.9086 (OUTLIER) cc_final: 0.7856 (mmt180) REVERT: Z 466 ARG cc_start: 0.8450 (ttp80) cc_final: 0.8040 (ptm160) REVERT: Z 467 GLN cc_start: 0.8781 (mm-40) cc_final: 0.8486 (mm-40) REVERT: Z 508 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.7768 (m-30) REVERT: Z 990 ASP cc_start: 0.7439 (OUTLIER) cc_final: 0.7214 (p0) REVERT: Z 999 GLU cc_start: 0.8305 (tm-30) cc_final: 0.8006 (tm-30) REVERT: Z 1016 ARG cc_start: 0.8345 (tpp80) cc_final: 0.7846 (tpp80) REVERT: G 55 GLN cc_start: 0.6357 (OUTLIER) cc_final: 0.5976 (pm20) REVERT: G 91 ASP cc_start: 0.8913 (t70) cc_final: 0.8519 (p0) REVERT: G 132 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8156 (mt-10) outliers start: 158 outliers final: 78 residues processed: 340 average time/residue: 0.6184 time to fit residues: 252.1301 Evaluate side-chains 274 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 187 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 496 THR Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 771 ASP Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 953 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 156 GLN Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 320 ARG Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 536 ASN Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 25 ASN Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain Z residue 120 PHE Chi-restraints excluded: chain Z residue 168 THR Chi-restraints excluded: chain Z residue 249 ARG Chi-restraints excluded: chain Z residue 316 VAL Chi-restraints excluded: chain Z residue 320 GLU Chi-restraints excluded: chain Z residue 402 THR Chi-restraints excluded: chain Z residue 410 THR Chi-restraints excluded: chain Z residue 437 THR Chi-restraints excluded: chain Z residue 471 THR Chi-restraints excluded: chain Z residue 498 VAL Chi-restraints excluded: chain Z residue 506 VAL Chi-restraints excluded: chain Z residue 508 ASP Chi-restraints excluded: chain Z residue 574 LEU Chi-restraints excluded: chain Z residue 582 VAL Chi-restraints excluded: chain Z residue 609 VAL Chi-restraints excluded: chain Z residue 645 ILE Chi-restraints excluded: chain Z residue 647 LEU Chi-restraints excluded: chain Z residue 693 VAL Chi-restraints excluded: chain Z residue 695 VAL Chi-restraints excluded: chain Z residue 717 VAL Chi-restraints excluded: chain Z residue 749 VAL Chi-restraints excluded: chain Z residue 789 VAL Chi-restraints excluded: chain Z residue 797 THR Chi-restraints excluded: chain Z residue 923 VAL Chi-restraints excluded: chain Z residue 928 LEU Chi-restraints excluded: chain Z residue 990 ASP Chi-restraints excluded: chain Z residue 1040 THR Chi-restraints excluded: chain Z residue 1123 ASP Chi-restraints excluded: chain Z residue 1182 ILE Chi-restraints excluded: chain Z residue 1183 THR Chi-restraints excluded: chain Z residue 1189 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 55 GLN Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 129 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 65 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 274 optimal weight: 6.9990 chunk 129 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 331 optimal weight: 4.9990 chunk 254 optimal weight: 6.9990 chunk 56 optimal weight: 0.0870 chunk 125 optimal weight: 1.9990 chunk 269 optimal weight: 9.9990 chunk 119 optimal weight: 0.0370 overall best weight: 1.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 31 ASN D 398 ASN D 410 ASN ** D 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.121012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.070838 restraints weight = 54433.767| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.96 r_work: 0.2763 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 30604 Z= 0.121 Angle : 0.567 9.863 41888 Z= 0.298 Chirality : 0.045 0.344 4764 Planarity : 0.004 0.098 5181 Dihedral : 16.096 162.844 5035 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.98 % Favored : 93.71 % Rotamer: Outliers : 4.17 % Allowed : 30.85 % Favored : 64.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.75 (0.14), residues: 3560 helix: 1.89 (0.17), residues: 985 sheet: 0.10 (0.22), residues: 550 loop : -2.03 (0.12), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Z 535 TYR 0.017 0.001 TYR Z 623 PHE 0.013 0.001 PHE A 169 TRP 0.010 0.001 TRP C 875 HIS 0.007 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (30596) covalent geometry : angle 0.56475 / 0.30 (41876) hydrogen bonds : bond 0.04479 / 3.00 ( 1069) hydrogen bonds : angle 4.08534 / 2.78 ( 2878) metal coordination : bond 0.00358 / 0.18 ( 8) metal coordination : angle 3.17631 / 1.69 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 194 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.6974 (ppp) REVERT: A 29 ARG cc_start: 0.7247 (tpp-160) cc_final: 0.6921 (tpm170) REVERT: A 183 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.7041 (ttm170) REVERT: B 73 ASP cc_start: 0.7724 (p0) cc_final: 0.7375 (p0) REVERT: B 112 ASP cc_start: 0.8032 (p0) cc_final: 0.7817 (p0) REVERT: C 63 ARG cc_start: 0.4818 (tpt170) cc_final: 0.4391 (mmp-170) REVERT: C 302 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8434 (mp0) REVERT: C 333 GLU cc_start: 0.8610 (tt0) cc_final: 0.8338 (tm-30) REVERT: C 512 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7590 (mtm-85) REVERT: C 734 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7791 (mm-30) REVERT: C 746 LYS cc_start: 0.8464 (mttt) cc_final: 0.8180 (ptpt) REVERT: C 797 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8380 (mp0) REVERT: D 320 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7682 (ppt170) REVERT: D 326 ASN cc_start: 0.7490 (t0) cc_final: 0.7050 (p0) REVERT: D 419 GLU cc_start: 0.9035 (tt0) cc_final: 0.8433 (tm-30) REVERT: Z 120 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.7687 (t80) REVERT: Z 249 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.7654 (mmt180) REVERT: Z 431 SER cc_start: 0.7923 (OUTLIER) cc_final: 0.7720 (t) REVERT: Z 466 ARG cc_start: 0.8468 (ttp80) cc_final: 0.8047 (ptm160) REVERT: Z 467 GLN cc_start: 0.8781 (mm-40) cc_final: 0.8517 (mm-40) REVERT: Z 508 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.7685 (m-30) REVERT: Z 999 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7865 (tm-30) REVERT: Z 1016 ARG cc_start: 0.8309 (tpp80) cc_final: 0.7759 (tpp80) REVERT: G 91 ASP cc_start: 0.8915 (t70) cc_final: 0.8474 (p0) outliers start: 126 outliers final: 67 residues processed: 305 average time/residue: 0.6186 time to fit residues: 225.4720 Evaluate side-chains 264 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 187 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 734 GLU Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 771 ASP Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 156 GLN Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 320 ARG Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain Z residue 120 PHE Chi-restraints excluded: chain Z residue 126 LEU Chi-restraints excluded: chain Z residue 249 ARG Chi-restraints excluded: chain Z residue 316 VAL Chi-restraints excluded: chain Z residue 320 GLU Chi-restraints excluded: chain Z residue 431 SER Chi-restraints excluded: chain Z residue 437 THR Chi-restraints excluded: chain Z residue 471 THR Chi-restraints excluded: chain Z residue 498 VAL Chi-restraints excluded: chain Z residue 506 VAL Chi-restraints excluded: chain Z residue 508 ASP Chi-restraints excluded: chain Z residue 574 LEU Chi-restraints excluded: chain Z residue 582 VAL Chi-restraints excluded: chain Z residue 609 VAL Chi-restraints excluded: chain Z residue 645 ILE Chi-restraints excluded: chain Z residue 647 LEU Chi-restraints excluded: chain Z residue 682 ILE Chi-restraints excluded: chain Z residue 693 VAL Chi-restraints excluded: chain Z residue 695 VAL Chi-restraints excluded: chain Z residue 717 VAL Chi-restraints excluded: chain Z residue 749 VAL Chi-restraints excluded: chain Z residue 789 VAL Chi-restraints excluded: chain Z residue 797 THR Chi-restraints excluded: chain Z residue 833 ILE Chi-restraints excluded: chain Z residue 885 ILE Chi-restraints excluded: chain Z residue 923 VAL Chi-restraints excluded: chain Z residue 928 LEU Chi-restraints excluded: chain Z residue 1040 THR Chi-restraints excluded: chain Z residue 1123 ASP Chi-restraints excluded: chain Z residue 1148 LEU Chi-restraints excluded: chain Z residue 1182 ILE Chi-restraints excluded: chain Z residue 1189 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 90 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 362 optimal weight: 50.0000 chunk 146 optimal weight: 0.5980 chunk 311 optimal weight: 5.9990 chunk 317 optimal weight: 5.9990 chunk 192 optimal weight: 6.9990 chunk 238 optimal weight: 4.9990 chunk 226 optimal weight: 2.9990 chunk 156 optimal weight: 6.9990 chunk 215 optimal weight: 0.9990 chunk 350 optimal weight: 10.0000 chunk 325 optimal weight: 0.9980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 398 ASN D 410 ASN ** D 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 55 GLN G 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.119354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.069189 restraints weight = 54496.050| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.90 r_work: 0.2722 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 30604 Z= 0.176 Angle : 0.592 9.103 41888 Z= 0.310 Chirality : 0.046 0.350 4764 Planarity : 0.004 0.098 5181 Dihedral : 16.052 163.152 5028 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.57 % Favored : 93.12 % Rotamer: Outliers : 4.34 % Allowed : 30.38 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.80 (0.14), residues: 3560 helix: 1.90 (0.17), residues: 982 sheet: 0.05 (0.21), residues: 561 loop : -2.09 (0.12), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Z 535 TYR 0.017 0.001 TYR C 680 PHE 0.020 0.001 PHE A 169 TRP 0.010 0.001 TRP C 875 HIS 0.009 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (30596) covalent geometry : angle 0.58922 / 0.31 (41876) hydrogen bonds : bond 0.05400 / 3.62 ( 1069) hydrogen bonds : angle 4.08129 / 2.78 ( 2878) metal coordination : bond 0.00577 / 0.30 ( 8) metal coordination : angle 3.65784 / 1.93 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 191 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.7019 (ppp) REVERT: A 183 ARG cc_start: 0.7295 (OUTLIER) cc_final: 0.6984 (ttm170) REVERT: B 73 ASP cc_start: 0.7883 (p0) cc_final: 0.7515 (p0) REVERT: B 112 ASP cc_start: 0.8007 (p0) cc_final: 0.7757 (p0) REVERT: C 40 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.7454 (p90) REVERT: C 63 ARG cc_start: 0.4942 (tpt170) cc_final: 0.4419 (mmp-170) REVERT: C 302 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8490 (mp0) REVERT: C 333 GLU cc_start: 0.8600 (tt0) cc_final: 0.8295 (tm-30) REVERT: C 402 GLU cc_start: 0.7964 (tp30) cc_final: 0.7760 (tp30) REVERT: C 512 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.7743 (mtm-85) REVERT: C 734 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7834 (mm-30) REVERT: C 746 LYS cc_start: 0.8472 (mttt) cc_final: 0.8235 (ptpt) REVERT: D 210 GLN cc_start: 0.9292 (OUTLIER) cc_final: 0.8910 (tm-30) REVERT: D 320 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7687 (ppt170) REVERT: D 326 ASN cc_start: 0.7651 (t0) cc_final: 0.7430 (t0) REVERT: D 419 GLU cc_start: 0.9121 (tt0) cc_final: 0.8538 (tm-30) REVERT: Z 120 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7798 (t80) REVERT: Z 249 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.7826 (mmt180) REVERT: Z 431 SER cc_start: 0.7995 (OUTLIER) cc_final: 0.7793 (t) REVERT: Z 466 ARG cc_start: 0.8491 (ttp80) cc_final: 0.8091 (ptm160) REVERT: Z 508 ASP cc_start: 0.7998 (OUTLIER) cc_final: 0.7770 (m-30) REVERT: Z 999 GLU cc_start: 0.8308 (tm-30) cc_final: 0.8003 (tm-30) REVERT: Z 1016 ARG cc_start: 0.8296 (tpp80) cc_final: 0.7871 (tpp80) REVERT: G 91 ASP cc_start: 0.8913 (t70) cc_final: 0.8479 (p0) outliers start: 131 outliers final: 71 residues processed: 308 average time/residue: 0.6203 time to fit residues: 227.7016 Evaluate side-chains 272 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 189 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 734 GLU Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 771 ASP Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 953 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 156 GLN Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 320 ARG Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain Z residue 61 ASP Chi-restraints excluded: chain Z residue 120 PHE Chi-restraints excluded: chain Z residue 249 ARG Chi-restraints excluded: chain Z residue 316 VAL Chi-restraints excluded: chain Z residue 320 GLU Chi-restraints excluded: chain Z residue 402 THR Chi-restraints excluded: chain Z residue 410 THR Chi-restraints excluded: chain Z residue 431 SER Chi-restraints excluded: chain Z residue 437 THR Chi-restraints excluded: chain Z residue 471 THR Chi-restraints excluded: chain Z residue 498 VAL Chi-restraints excluded: chain Z residue 506 VAL Chi-restraints excluded: chain Z residue 508 ASP Chi-restraints excluded: chain Z residue 574 LEU Chi-restraints excluded: chain Z residue 582 VAL Chi-restraints excluded: chain Z residue 609 VAL Chi-restraints excluded: chain Z residue 645 ILE Chi-restraints excluded: chain Z residue 647 LEU Chi-restraints excluded: chain Z residue 693 VAL Chi-restraints excluded: chain Z residue 695 VAL Chi-restraints excluded: chain Z residue 717 VAL Chi-restraints excluded: chain Z residue 749 VAL Chi-restraints excluded: chain Z residue 789 VAL Chi-restraints excluded: chain Z residue 797 THR Chi-restraints excluded: chain Z residue 833 ILE Chi-restraints excluded: chain Z residue 855 LEU Chi-restraints excluded: chain Z residue 923 VAL Chi-restraints excluded: chain Z residue 928 LEU Chi-restraints excluded: chain Z residue 1123 ASP Chi-restraints excluded: chain Z residue 1148 LEU Chi-restraints excluded: chain Z residue 1182 ILE Chi-restraints excluded: chain Z residue 1189 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 129 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 70 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 209 optimal weight: 9.9990 chunk 183 optimal weight: 0.5980 chunk 27 optimal weight: 8.9990 chunk 260 optimal weight: 5.9990 chunk 176 optimal weight: 0.1980 chunk 321 optimal weight: 0.9980 chunk 240 optimal weight: 0.9990 chunk 201 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 80 HIS D 398 ASN D 410 ASN ** D 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 561 HIS G 112 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.121825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.071670 restraints weight = 54070.359| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.94 r_work: 0.2786 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 30604 Z= 0.109 Angle : 0.553 9.415 41888 Z= 0.290 Chirality : 0.044 0.336 4764 Planarity : 0.004 0.100 5181 Dihedral : 15.968 162.921 5027 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.65 % Favored : 94.10 % Rotamer: Outliers : 3.31 % Allowed : 31.68 % Favored : 65.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.68 (0.14), residues: 3560 helix: 1.97 (0.17), residues: 985 sheet: 0.05 (0.22), residues: 552 loop : -1.97 (0.12), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Z 535 TYR 0.014 0.001 TYR C 680 PHE 0.012 0.001 PHE A 169 TRP 0.010 0.001 TRP C 875 HIS 0.006 0.000 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (30596) covalent geometry : angle 0.55071 / 0.29 (41876) hydrogen bonds : bond 0.03830 / 2.55 ( 1069) hydrogen bonds : angle 3.94662 / 2.69 ( 2878) metal coordination : bond 0.00373 / 0.18 ( 8) metal coordination : angle 3.07758 / 1.61 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 198 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7297 (OUTLIER) cc_final: 0.6967 (ppp) REVERT: A 29 ARG cc_start: 0.7390 (tpm170) cc_final: 0.7141 (tpm170) REVERT: A 183 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.6997 (ttm170) REVERT: A 221 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8302 (tp30) REVERT: A 227 SER cc_start: 0.6369 (OUTLIER) cc_final: 0.6003 (m) REVERT: B 73 ASP cc_start: 0.7723 (p0) cc_final: 0.7364 (p0) REVERT: B 112 ASP cc_start: 0.8053 (p0) cc_final: 0.7847 (p0) REVERT: C 63 ARG cc_start: 0.4824 (tpt170) cc_final: 0.4271 (mmp-170) REVERT: C 302 GLU cc_start: 0.9036 (OUTLIER) cc_final: 0.8440 (mp0) REVERT: C 333 GLU cc_start: 0.8522 (tt0) cc_final: 0.8253 (tm-30) REVERT: C 402 GLU cc_start: 0.7997 (tp30) cc_final: 0.7737 (tp30) REVERT: C 512 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7581 (mtm-85) REVERT: C 734 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7779 (mm-30) REVERT: D 210 GLN cc_start: 0.9320 (OUTLIER) cc_final: 0.8897 (tm-30) REVERT: D 320 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7668 (ppt170) REVERT: D 419 GLU cc_start: 0.9039 (tt0) cc_final: 0.8471 (tm-30) REVERT: Z 466 ARG cc_start: 0.8535 (ttp80) cc_final: 0.8065 (ptm160) REVERT: Z 467 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8317 (mm-40) REVERT: Z 508 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7703 (m-30) REVERT: Z 999 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7856 (tm-30) REVERT: Z 1016 ARG cc_start: 0.8243 (tpp80) cc_final: 0.7771 (tpp80) REVERT: G 91 ASP cc_start: 0.8894 (t70) cc_final: 0.8453 (p0) outliers start: 100 outliers final: 59 residues processed: 287 average time/residue: 0.6242 time to fit residues: 212.7018 Evaluate side-chains 257 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 188 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 727 ILE Chi-restraints excluded: chain C residue 734 GLU Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 771 ASP Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 320 ARG Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain Z residue 61 ASP Chi-restraints excluded: chain Z residue 320 GLU Chi-restraints excluded: chain Z residue 506 VAL Chi-restraints excluded: chain Z residue 508 ASP Chi-restraints excluded: chain Z residue 574 LEU Chi-restraints excluded: chain Z residue 582 VAL Chi-restraints excluded: chain Z residue 609 VAL Chi-restraints excluded: chain Z residue 641 VAL Chi-restraints excluded: chain Z residue 647 LEU Chi-restraints excluded: chain Z residue 682 ILE Chi-restraints excluded: chain Z residue 693 VAL Chi-restraints excluded: chain Z residue 695 VAL Chi-restraints excluded: chain Z residue 749 VAL Chi-restraints excluded: chain Z residue 789 VAL Chi-restraints excluded: chain Z residue 833 ILE Chi-restraints excluded: chain Z residue 906 LEU Chi-restraints excluded: chain Z residue 923 VAL Chi-restraints excluded: chain Z residue 928 LEU Chi-restraints excluded: chain Z residue 1123 ASP Chi-restraints excluded: chain Z residue 1148 LEU Chi-restraints excluded: chain Z residue 1182 ILE Chi-restraints excluded: chain Z residue 1189 THR Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 129 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 3 optimal weight: 5.9990 chunk 328 optimal weight: 0.8980 chunk 147 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 264 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 334 optimal weight: 10.0000 chunk 140 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 323 optimal weight: 0.0870 overall best weight: 2.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 398 ASN D 410 ASN ** D 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 55 GLN G 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.119667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.069650 restraints weight = 54810.188| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.91 r_work: 0.2727 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 30604 Z= 0.179 Angle : 0.594 10.280 41888 Z= 0.310 Chirality : 0.046 0.341 4764 Planarity : 0.004 0.100 5181 Dihedral : 15.956 163.333 5017 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.38 % Favored : 93.37 % Rotamer: Outliers : 3.25 % Allowed : 31.91 % Favored : 64.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.75 (0.14), residues: 3560 helix: 1.92 (0.17), residues: 984 sheet: 0.00 (0.21), residues: 571 loop : -2.03 (0.12), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Z 535 TYR 0.017 0.001 TYR C 680 PHE 0.021 0.001 PHE A 169 TRP 0.009 0.001 TRP C 875 HIS 0.003 0.001 HIS D 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.18 (30596) covalent geometry : angle 0.59088 / 0.31 (41876) hydrogen bonds : bond 0.05133 / 3.44 ( 1069) hydrogen bonds : angle 4.00083 / 2.73 ( 2878) metal coordination : bond 0.00646 / 0.33 ( 8) metal coordination : angle 3.55242 / 1.86 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 189 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7298 (OUTLIER) cc_final: 0.6966 (ppp) REVERT: A 183 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.6964 (ttm170) REVERT: A 227 SER cc_start: 0.6406 (OUTLIER) cc_final: 0.6043 (m) REVERT: B 73 ASP cc_start: 0.7908 (p0) cc_final: 0.7562 (p0) REVERT: B 112 ASP cc_start: 0.8028 (p0) cc_final: 0.7802 (p0) REVERT: C 40 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.7559 (p90) REVERT: C 63 ARG cc_start: 0.4960 (tpt170) cc_final: 0.4298 (mmp-170) REVERT: C 223 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.8847 (tpt) REVERT: C 302 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.8492 (mp0) REVERT: C 333 GLU cc_start: 0.8619 (tt0) cc_final: 0.8296 (tm-30) REVERT: C 402 GLU cc_start: 0.8006 (tp30) cc_final: 0.7763 (tp30) REVERT: C 512 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.7755 (mtm-85) REVERT: C 734 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.7846 (mm-30) REVERT: C 746 LYS cc_start: 0.8509 (mttt) cc_final: 0.8191 (ptpt) REVERT: D 210 GLN cc_start: 0.9293 (OUTLIER) cc_final: 0.8900 (tm-30) REVERT: D 320 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7663 (ppt170) REVERT: D 419 GLU cc_start: 0.9106 (tt0) cc_final: 0.8578 (tm-30) REVERT: Z 249 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.7720 (mmt180) REVERT: Z 466 ARG cc_start: 0.8547 (ttp80) cc_final: 0.8130 (ptm160) REVERT: Z 467 GLN cc_start: 0.8766 (mm-40) cc_final: 0.8283 (mm-40) REVERT: Z 469 ASN cc_start: 0.8543 (m110) cc_final: 0.8312 (m110) REVERT: Z 508 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.7780 (m-30) REVERT: Z 999 GLU cc_start: 0.8334 (tm-30) cc_final: 0.8017 (tm-30) REVERT: Z 1016 ARG cc_start: 0.8278 (tpp80) cc_final: 0.7755 (tpp80) REVERT: G 91 ASP cc_start: 0.8908 (t70) cc_final: 0.8399 (t70) outliers start: 98 outliers final: 66 residues processed: 273 average time/residue: 0.6130 time to fit residues: 198.7220 Evaluate side-chains 266 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 188 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 727 ILE Chi-restraints excluded: chain C residue 734 GLU Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 771 ASP Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 953 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 156 GLN Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 320 ARG Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain Z residue 61 ASP Chi-restraints excluded: chain Z residue 120 PHE Chi-restraints excluded: chain Z residue 249 ARG Chi-restraints excluded: chain Z residue 316 VAL Chi-restraints excluded: chain Z residue 320 GLU Chi-restraints excluded: chain Z residue 498 VAL Chi-restraints excluded: chain Z residue 506 VAL Chi-restraints excluded: chain Z residue 508 ASP Chi-restraints excluded: chain Z residue 574 LEU Chi-restraints excluded: chain Z residue 582 VAL Chi-restraints excluded: chain Z residue 609 VAL Chi-restraints excluded: chain Z residue 641 VAL Chi-restraints excluded: chain Z residue 647 LEU Chi-restraints excluded: chain Z residue 693 VAL Chi-restraints excluded: chain Z residue 695 VAL Chi-restraints excluded: chain Z residue 749 VAL Chi-restraints excluded: chain Z residue 789 VAL Chi-restraints excluded: chain Z residue 797 THR Chi-restraints excluded: chain Z residue 923 VAL Chi-restraints excluded: chain Z residue 928 LEU Chi-restraints excluded: chain Z residue 1123 ASP Chi-restraints excluded: chain Z residue 1148 LEU Chi-restraints excluded: chain Z residue 1182 ILE Chi-restraints excluded: chain Z residue 1189 THR Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 55 GLN Chi-restraints excluded: chain G residue 129 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 325 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 chunk 73 optimal weight: 0.0370 chunk 64 optimal weight: 4.9990 chunk 219 optimal weight: 0.6980 chunk 318 optimal weight: 3.9990 chunk 338 optimal weight: 0.0060 chunk 49 optimal weight: 2.9990 chunk 361 optimal weight: 20.0000 chunk 174 optimal weight: 3.9990 overall best weight: 0.9476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 398 ASN D 410 ASN ** D 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN G 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.121038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.070868 restraints weight = 54246.815| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.98 r_work: 0.2765 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 30604 Z= 0.122 Angle : 0.576 11.800 41888 Z= 0.302 Chirality : 0.044 0.338 4764 Planarity : 0.004 0.100 5181 Dihedral : 15.938 163.701 5017 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.04 % Favored : 93.71 % Rotamer: Outliers : 3.08 % Allowed : 31.84 % Favored : 65.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 3560 helix: 1.94 (0.17), residues: 984 sheet: 0.01 (0.21), residues: 582 loop : -1.99 (0.13), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Z 535 TYR 0.015 0.001 TYR C 680 PHE 0.016 0.001 PHE A 169 TRP 0.010 0.001 TRP C 875 HIS 0.003 0.000 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (30596) covalent geometry : angle 0.57332 / 0.30 (41876) hydrogen bonds : bond 0.04347 / 2.91 ( 1069) hydrogen bonds : angle 3.98990 / 2.72 ( 2878) metal coordination : bond 0.00397 / 0.19 ( 8) metal coordination : angle 3.13703 / 1.63 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 192 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7292 (OUTLIER) cc_final: 0.6987 (ppp) REVERT: A 183 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.6908 (ttm170) REVERT: A 221 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8299 (tp30) REVERT: A 227 SER cc_start: 0.6421 (OUTLIER) cc_final: 0.6046 (m) REVERT: B 73 ASP cc_start: 0.7732 (p0) cc_final: 0.7418 (p0) REVERT: C 63 ARG cc_start: 0.4808 (tpt170) cc_final: 0.4153 (mmp-170) REVERT: C 302 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8435 (mp0) REVERT: C 333 GLU cc_start: 0.8535 (tt0) cc_final: 0.8227 (tm-30) REVERT: C 402 GLU cc_start: 0.7964 (tp30) cc_final: 0.7706 (tp30) REVERT: C 512 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7594 (mtm-85) REVERT: C 734 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7792 (mm-30) REVERT: C 746 LYS cc_start: 0.8481 (mttt) cc_final: 0.8169 (ptpt) REVERT: D 210 GLN cc_start: 0.9324 (OUTLIER) cc_final: 0.8921 (tm-30) REVERT: D 320 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7656 (ppt170) REVERT: D 326 ASN cc_start: 0.7717 (t0) cc_final: 0.7348 (p0) REVERT: D 419 GLU cc_start: 0.9041 (tt0) cc_final: 0.8501 (tm-30) REVERT: Z 249 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.7548 (mmt180) REVERT: Z 466 ARG cc_start: 0.8541 (ttp80) cc_final: 0.8090 (ptm160) REVERT: Z 467 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8278 (mm-40) REVERT: Z 469 ASN cc_start: 0.8493 (m110) cc_final: 0.8264 (m110) REVERT: Z 508 ASP cc_start: 0.7952 (OUTLIER) cc_final: 0.7706 (m-30) REVERT: Z 999 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7901 (tm-30) REVERT: Z 1016 ARG cc_start: 0.8242 (tpp80) cc_final: 0.7672 (tpp80) REVERT: G 91 ASP cc_start: 0.8905 (t70) cc_final: 0.8388 (t70) outliers start: 93 outliers final: 61 residues processed: 270 average time/residue: 0.6717 time to fit residues: 215.0388 Evaluate side-chains 262 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 190 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 727 ILE Chi-restraints excluded: chain C residue 734 GLU Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 771 ASP Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 320 ARG Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain Z residue 61 ASP Chi-restraints excluded: chain Z residue 249 ARG Chi-restraints excluded: chain Z residue 316 VAL Chi-restraints excluded: chain Z residue 320 GLU Chi-restraints excluded: chain Z residue 355 LEU Chi-restraints excluded: chain Z residue 506 VAL Chi-restraints excluded: chain Z residue 508 ASP Chi-restraints excluded: chain Z residue 574 LEU Chi-restraints excluded: chain Z residue 582 VAL Chi-restraints excluded: chain Z residue 609 VAL Chi-restraints excluded: chain Z residue 641 VAL Chi-restraints excluded: chain Z residue 647 LEU Chi-restraints excluded: chain Z residue 682 ILE Chi-restraints excluded: chain Z residue 693 VAL Chi-restraints excluded: chain Z residue 695 VAL Chi-restraints excluded: chain Z residue 749 VAL Chi-restraints excluded: chain Z residue 789 VAL Chi-restraints excluded: chain Z residue 797 THR Chi-restraints excluded: chain Z residue 923 VAL Chi-restraints excluded: chain Z residue 928 LEU Chi-restraints excluded: chain Z residue 1040 THR Chi-restraints excluded: chain Z residue 1123 ASP Chi-restraints excluded: chain Z residue 1148 LEU Chi-restraints excluded: chain Z residue 1182 ILE Chi-restraints excluded: chain Z residue 1189 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 129 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 250 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 78 optimal weight: 0.4980 chunk 120 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 310 optimal weight: 0.0570 chunk 26 optimal weight: 2.9990 overall best weight: 1.3104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 398 ASN ** D 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.121582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.070973 restraints weight = 53890.839| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.88 r_work: 0.2787 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 30604 Z= 0.135 Angle : 0.589 10.619 41888 Z= 0.309 Chirality : 0.045 0.339 4764 Planarity : 0.004 0.100 5181 Dihedral : 15.929 173.107 5016 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.18 % Favored : 93.57 % Rotamer: Outliers : 2.82 % Allowed : 32.21 % Favored : 64.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 3560 helix: 1.95 (0.17), residues: 984 sheet: 0.02 (0.21), residues: 583 loop : -1.99 (0.13), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Z 535 TYR 0.016 0.001 TYR C 680 PHE 0.019 0.001 PHE A 169 TRP 0.010 0.001 TRP C 875 HIS 0.004 0.000 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (30596) covalent geometry : angle 0.58647 / 0.31 (41876) hydrogen bonds : bond 0.04437 / 2.97 ( 1069) hydrogen bonds : angle 3.98485 / 2.72 ( 2878) metal coordination : bond 0.00470 / 0.23 ( 8) metal coordination : angle 3.24389 / 1.68 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 194 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7266 (OUTLIER) cc_final: 0.6971 (ppp) REVERT: A 183 ARG cc_start: 0.7220 (OUTLIER) cc_final: 0.6904 (ttm170) REVERT: A 221 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8272 (tp30) REVERT: A 227 SER cc_start: 0.6439 (OUTLIER) cc_final: 0.6058 (m) REVERT: B 73 ASP cc_start: 0.7742 (p0) cc_final: 0.7407 (p0) REVERT: B 92 GLN cc_start: 0.8413 (pm20) cc_final: 0.8121 (pm20) REVERT: C 63 ARG cc_start: 0.4676 (tpt170) cc_final: 0.4035 (mmp-170) REVERT: C 302 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8430 (mp0) REVERT: C 333 GLU cc_start: 0.8511 (tt0) cc_final: 0.8187 (tm-30) REVERT: C 402 GLU cc_start: 0.7945 (tp30) cc_final: 0.7669 (tp30) REVERT: C 512 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7587 (mtm-85) REVERT: C 734 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7761 (mm-30) REVERT: C 746 LYS cc_start: 0.8490 (mttt) cc_final: 0.8165 (ptpt) REVERT: D 210 GLN cc_start: 0.9325 (OUTLIER) cc_final: 0.8928 (tm-30) REVERT: D 320 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7620 (ppt170) REVERT: D 326 ASN cc_start: 0.7791 (t0) cc_final: 0.7454 (p0) REVERT: D 419 GLU cc_start: 0.9017 (tt0) cc_final: 0.8477 (tm-30) REVERT: Z 249 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.7499 (mmt180) REVERT: Z 466 ARG cc_start: 0.8567 (ttp80) cc_final: 0.8100 (ptm160) REVERT: Z 467 GLN cc_start: 0.8705 (mm-40) cc_final: 0.8269 (mm-40) REVERT: Z 469 ASN cc_start: 0.8495 (m110) cc_final: 0.8274 (m110) REVERT: Z 508 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7678 (m-30) REVERT: Z 999 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7892 (tm-30) REVERT: Z 1016 ARG cc_start: 0.8206 (tpp80) cc_final: 0.7628 (tpp80) REVERT: G 100 ASN cc_start: 0.8647 (m-40) cc_final: 0.8352 (p0) outliers start: 85 outliers final: 62 residues processed: 268 average time/residue: 0.6081 time to fit residues: 192.4086 Evaluate side-chains 265 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 192 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 727 ILE Chi-restraints excluded: chain C residue 734 GLU Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 771 ASP Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 320 ARG Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain Z residue 61 ASP Chi-restraints excluded: chain Z residue 249 ARG Chi-restraints excluded: chain Z residue 316 VAL Chi-restraints excluded: chain Z residue 320 GLU Chi-restraints excluded: chain Z residue 355 LEU Chi-restraints excluded: chain Z residue 498 VAL Chi-restraints excluded: chain Z residue 506 VAL Chi-restraints excluded: chain Z residue 508 ASP Chi-restraints excluded: chain Z residue 574 LEU Chi-restraints excluded: chain Z residue 582 VAL Chi-restraints excluded: chain Z residue 609 VAL Chi-restraints excluded: chain Z residue 641 VAL Chi-restraints excluded: chain Z residue 647 LEU Chi-restraints excluded: chain Z residue 682 ILE Chi-restraints excluded: chain Z residue 693 VAL Chi-restraints excluded: chain Z residue 695 VAL Chi-restraints excluded: chain Z residue 749 VAL Chi-restraints excluded: chain Z residue 789 VAL Chi-restraints excluded: chain Z residue 797 THR Chi-restraints excluded: chain Z residue 923 VAL Chi-restraints excluded: chain Z residue 928 LEU Chi-restraints excluded: chain Z residue 1040 THR Chi-restraints excluded: chain Z residue 1123 ASP Chi-restraints excluded: chain Z residue 1148 LEU Chi-restraints excluded: chain Z residue 1176 THR Chi-restraints excluded: chain Z residue 1182 ILE Chi-restraints excluded: chain Z residue 1189 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 129 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 83 optimal weight: 6.9990 chunk 279 optimal weight: 30.0000 chunk 17 optimal weight: 3.9990 chunk 298 optimal weight: 7.9990 chunk 43 optimal weight: 0.5980 chunk 130 optimal weight: 3.9990 chunk 204 optimal weight: 5.9990 chunk 328 optimal weight: 0.6980 chunk 244 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 398 ASN ** D 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 55 GLN G 112 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.119153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.069015 restraints weight = 54630.166| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.92 r_work: 0.2721 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 30604 Z= 0.211 Angle : 0.636 10.929 41888 Z= 0.333 Chirality : 0.047 0.370 4764 Planarity : 0.005 0.100 5181 Dihedral : 15.975 169.683 5016 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.71 % Favored : 93.01 % Rotamer: Outliers : 3.02 % Allowed : 32.21 % Favored : 64.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 3560 helix: 1.85 (0.17), residues: 981 sheet: -0.05 (0.21), residues: 577 loop : -2.07 (0.12), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Z 535 TYR 0.018 0.001 TYR C 680 PHE 0.023 0.002 PHE A 169 TRP 0.010 0.001 TRP C 875 HIS 0.004 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.21 (30596) covalent geometry : angle 0.63331 / 0.33 (41876) hydrogen bonds : bond 0.05800 / 3.90 ( 1069) hydrogen bonds : angle 4.11402 / 2.81 ( 2878) metal coordination : bond 0.00722 / 0.37 ( 8) metal coordination : angle 3.64380 / 1.87 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11352.42 seconds wall clock time: 193 minutes 28.72 seconds (11608.72 seconds total)