Starting phenix.real_space_refine on Sun Aug 9 07:06:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8u3b_41856/08_2026/8u3b_41856.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u3b_41856/08_2026/8u3b_41856.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8u3b_41856/08_2026/8u3b_41856.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u3b_41856/08_2026/8u3b_41856.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u3b_41856/08_2026/8u3b_41856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u3b_41856/08_2026/8u3b_41856.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8u3b_41856/08_2026/8u3b_41856.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8u3b_41856/08_2026/8u3b_41856.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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 142 5.49 5 Mg 1 5.21 5 S 136 5.16 5 C 20427 2.51 5 N 5918 2.21 5 O 6660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 137 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: 33286 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2381 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 305, 2373 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 290} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 305, 2373 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 290} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 2395 Chain: "B" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1767 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "C" Number of atoms: 10576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10576 Classifications: {'peptide': 1341} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1284} Chain: "D" Number of atoms: 10443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1344, 10443 Classifications: {'peptide': 1344} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1288} Chain breaks: 2 Chain: "E" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 610 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "F" Number of atoms: 3516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3516 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 12, 'TRANS': 418} Chain breaks: 3 Chain: "G" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 547 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "H" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 547 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "1" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1415 Classifications: {'DNA': 69} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 68} Chain: "2" Number of atoms: 1405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1405 Classifications: {'DNA': 69} Link IDs: {'rna3p': 68} Chain: "3" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 76 Unusual residues: {'GTP': 1} Classifications: {'RNAv2': 2, 'undetermined': 1} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1, None: 1} Not linked: pdbres="GTP 3 1 " pdbres=" A 3 2 " Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15182 SG CYS D 70 48.767 128.993 81.345 1.00166.50 S ATOM 15196 SG CYS D 72 50.044 131.107 78.392 1.00175.94 S ATOM 15304 SG CYS D 85 47.532 128.978 77.734 1.00175.67 S ATOM 15328 SG CYS D 88 50.566 127.098 78.460 1.00169.54 S ATOM 21016 SG CYS D 814 25.816 73.390 114.196 1.00 99.14 S ATOM 21581 SG CYS D 888 29.094 75.032 113.221 1.00 89.23 S ATOM 21632 SG CYS D 895 27.446 76.105 116.422 1.00 82.85 S ATOM 21653 SG CYS D 898 28.851 72.888 116.383 1.00 83.62 S Time building chain proxies: 5.99, per 1000 atoms: 0.18 Number of scatterers: 33286 At special positions: 0 Unit cell: (155.819, 214.251, 202.741, 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 136 16.00 P 142 15.00 Mg 1 11.99 O 6660 8.00 N 5918 7.00 C 20427 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.81 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " Number of angles added : 12 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7176 Finding SS restraints... Secondary structure from input PDB file: 149 helices and 48 sheets defined 46.5% alpha, 14.4% beta 16 base pairs and 58 stacking pairs defined. Time for finding SS restraints: 3.12 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.567A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A 42 " --> pdb=" O THR A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 154 through 162 removed outlier: 3.591A pdb=" N ARG A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 234 removed outlier: 4.841A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 3.993A pdb=" N LEU A 254 " --> pdb=" O ASP A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 261 Processing helix chain 'A' and resid 263 through 273 Processing helix chain 'A' and resid 277 through 284 removed outlier: 3.869A pdb=" N GLN A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 291 Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.752A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.700A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 154 through 161 removed outlier: 3.906A pdb=" N ARG B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER B 161 " --> pdb=" O THR B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 233 removed outlier: 4.827A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N PHE B 231 " --> pdb=" O GLN B 227 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ASP B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.856A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 removed outlier: 4.401A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 345 through 354 removed outlier: 3.503A pdb=" N GLU C 349 " --> pdb=" O PRO C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.598A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 482 removed outlier: 3.670A pdb=" N ARG C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY C 482 " --> pdb=" O ARG C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 removed outlier: 3.819A pdb=" N MET C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE C 493 " --> pdb=" O PRO C 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 488 through 493' Processing helix chain 'C' and resid 495 through 509 Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.883A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 612 removed outlier: 4.031A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 656 through 661 removed outlier: 4.342A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 667 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 removed outlier: 4.193A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 860 through 865 removed outlier: 3.854A pdb=" N LYS C 864 " --> pdb=" O ALA C 861 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 865 " --> pdb=" O LEU C 862 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 907 removed outlier: 3.620A pdb=" N LYS C 900 " --> pdb=" O THR C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 980 removed outlier: 4.183A pdb=" N GLU C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU C 967 " --> pdb=" O GLU C 963 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY C 970 " --> pdb=" O ILE C 966 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL C 980 " --> pdb=" O ARG C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 983 No H-bonds generated for 'chain 'C' and resid 981 through 983' Processing helix chain 'C' and resid 985 through 992 removed outlier: 3.696A pdb=" N LEU C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASP C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 994 through 998 removed outlier: 3.825A pdb=" N TRP C 997 " --> pdb=" O ARG C 994 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU C 998 " --> pdb=" O ASP C 995 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 994 through 998' Processing helix chain 'C' and resid 1005 through 1038 removed outlier: 3.810A pdb=" N ASN C1009 " --> pdb=" O GLU C1005 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN C1017 " --> pdb=" O GLN C1013 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR C1018 " --> pdb=" O LEU C1014 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP C1019 " --> pdb=" O ALA C1015 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLU C1020 " --> pdb=" O GLU C1016 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS C1023 " --> pdb=" O ASP C1019 " (cutoff:3.500A) Processing helix chain 'C' and resid 1099 through 1103 removed outlier: 3.517A pdb=" N GLY C1102 " --> pdb=" O ASN C1099 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.514A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 Processing helix chain 'C' and resid 1165 through 1177 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1242 Processing helix chain 'C' and resid 1271 through 1281 Processing helix chain 'C' and resid 1283 through 1292 removed outlier: 3.725A pdb=" N LEU C1287 " --> pdb=" O ALA C1283 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1310 removed outlier: 3.638A pdb=" N ASP C1310 " --> pdb=" O LYS C1306 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 3.652A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 95 through 100 Processing helix chain 'D' and resid 114 through 119 removed outlier: 3.518A pdb=" N SER D 119 " --> pdb=" O TRP D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.550A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 removed outlier: 3.514A pdb=" N LEU D 166 " --> pdb=" O GLU D 162 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU D 171 " --> pdb=" O ASP D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 192 Processing helix chain 'D' and resid 193 through 208 removed outlier: 3.931A pdb=" N GLU D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 removed outlier: 3.843A pdb=" N GLY D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 285 removed outlier: 4.269A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 removed outlier: 3.517A pdb=" N VAL D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 403 Processing helix chain 'D' and resid 405 through 417 removed outlier: 3.586A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG D 417 " --> pdb=" O ASP D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 485 through 489 Processing helix chain 'D' and resid 503 through 515 Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.588A pdb=" N ALA D 533 " --> pdb=" O GLY D 529 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.898A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.592A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 613 removed outlier: 3.715A pdb=" N ILE D 601 " --> pdb=" O GLY D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.582A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 644 Processing helix chain 'D' and resid 649 through 669 removed outlier: 3.692A pdb=" N GLN D 669 " --> pdb=" O GLN D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 removed outlier: 4.187A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.997A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 840 removed outlier: 3.575A pdb=" N LEU D 840 " --> pdb=" O ARG D 836 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 876 Processing helix chain 'D' and resid 884 through 888 Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.792A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 930 Processing helix chain 'D' and resid 1137 through 1147 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1243 removed outlier: 4.210A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR D1241 " --> pdb=" O VAL D1237 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.431A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1294 Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1326 Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 4.027A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1359 through 1361 No H-bonds generated for 'chain 'D' and resid 1359 through 1361' Processing helix chain 'D' and resid 1362 through 1373 Processing helix chain 'E' and resid 6 through 14 Processing helix chain 'E' and resid 15 through 33 Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.510A pdb=" N GLU E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 78 Processing helix chain 'F' and resid 96 through 107 removed outlier: 4.169A pdb=" N THR F 107 " --> pdb=" O ARG F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 137 removed outlier: 3.508A pdb=" N TYR F 137 " --> pdb=" O SER F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 152 removed outlier: 3.741A pdb=" N ILE F 141 " --> pdb=" O TYR F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 237 removed outlier: 4.299A pdb=" N GLU F 223 " --> pdb=" O GLU F 219 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR F 234 " --> pdb=" O VAL F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 258 removed outlier: 3.666A pdb=" N GLN F 258 " --> pdb=" O GLU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 294 removed outlier: 3.962A pdb=" N MET F 276 " --> pdb=" O SER F 272 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU F 286 " --> pdb=" O THR F 282 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ILE F 287 " --> pdb=" O GLN F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 352 removed outlier: 4.465A pdb=" N LYS F 343 " --> pdb=" O ARG F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 383 removed outlier: 4.019A pdb=" N GLU F 378 " --> pdb=" O ARG F 374 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N MET F 379 " --> pdb=" O ALA F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 393 Processing helix chain 'F' and resid 400 through 419 Processing helix chain 'F' and resid 420 through 424 removed outlier: 3.551A pdb=" N ARG F 423 " --> pdb=" O GLU F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 446 removed outlier: 3.875A pdb=" N TYR F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 475 removed outlier: 3.697A pdb=" N GLN F 469 " --> pdb=" O ARG F 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 488 Processing helix chain 'F' and resid 490 through 501 Processing helix chain 'F' and resid 518 through 523 removed outlier: 3.560A pdb=" N ILE F 523 " --> pdb=" O GLY F 520 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 551 removed outlier: 3.643A pdb=" N LEU F 551 " --> pdb=" O VAL F 547 " (cutoff:3.500A) Processing helix chain 'F' and resid 552 through 564 Processing helix chain 'F' and resid 572 through 580 Processing helix chain 'F' and resid 583 through 600 removed outlier: 3.914A pdb=" N ILE F 587 " --> pdb=" O THR F 583 " (cutoff:3.500A) Processing helix chain 'F' and resid 606 through 611 Processing helix chain 'G' and resid 152 through 156 Processing helix chain 'G' and resid 157 through 169 Processing helix chain 'G' and resid 172 through 181 Processing helix chain 'G' and resid 183 through 199 removed outlier: 3.701A pdb=" N VAL G 187 " --> pdb=" O THR G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 213 removed outlier: 3.977A pdb=" N ALA G 206 " --> pdb=" O SER G 202 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU G 213 " --> pdb=" O TRP G 209 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 156 removed outlier: 3.796A pdb=" N GLN H 155 " --> pdb=" O ASP H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 157 through 169 Processing helix chain 'H' and resid 172 through 181 Processing helix chain 'H' and resid 183 through 198 Processing helix chain 'H' and resid 202 through 214 removed outlier: 3.999A pdb=" N ALA H 206 " --> pdb=" O SER H 202 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU H 213 " --> pdb=" O TRP H 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 17 removed outlier: 4.868A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 105 removed outlier: 7.656A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'B' and resid 12 through 15 removed outlier: 5.481A pdb=" N LEU B 13 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU B 29 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 105 removed outlier: 3.893A pdb=" N GLU B 58 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 111 removed outlier: 3.707A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.656A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.751A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP C 116 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AB5, first strand: chain 'C' and resid 451 through 454 Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 160 removed outlier: 3.660A pdb=" N LEU C 171 " --> pdb=" O ASP C 160 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N TYR C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 284 through 286 removed outlier: 5.172A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 255 through 256 removed outlier: 3.558A pdb=" N VAL C 263 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 301 through 302 Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 removed outlier: 7.270A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N LYS C 593 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC3, first strand: chain 'C' and resid 616 through 617 Processing sheet with id=AC4, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.438A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.739A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 755 through 758 Processing sheet with id=AC7, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.434A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 846 through 847 removed outlier: 6.613A pdb=" N ASP C 842 " --> pdb=" O VAL C1046 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL C1046 " --> pdb=" O ASP C 842 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N LEU C1047 " --> pdb=" O THR C 935 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N THR C 935 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE C1049 " --> pdb=" O VAL C 933 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N VAL C 933 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LYS C1051 " --> pdb=" O VAL C 931 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL C 931 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N TYR C1053 " --> pdb=" O ILE C 929 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AD1, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.752A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 7.790A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1269 through 1270 Processing sheet with id=AD4, first strand: chain 'C' and resid 1335 through 1341 removed outlier: 3.525A pdb=" N ALA D 19 " --> pdb=" O GLU C1340 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.691A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 10.128A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.410A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 159 through 160 removed outlier: 7.100A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 252 through 254 removed outlier: 6.399A pdb=" N PHE D 260 " --> pdb=" O ILE F 505 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AD9, first strand: chain 'D' and resid 706 through 708 Processing sheet with id=AE1, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AE2, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE3, first strand: chain 'D' and resid 949 through 951 removed outlier: 6.818A pdb=" N ILE D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 956 through 957 removed outlier: 3.696A pdb=" N GLY D 956 " --> pdb=" O VAL D1011 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AE6, first strand: chain 'D' and resid 980 through 985 removed outlier: 4.268A pdb=" N THR D 980 " --> pdb=" O VAL D 997 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1025 through 1028 removed outlier: 6.217A pdb=" N MET D1025 " --> pdb=" O ARG D1123 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ARG D1123 " --> pdb=" O MET D1025 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL D1027 " --> pdb=" O LEU D1121 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1034 through 1038 Processing sheet with id=AE9, first strand: chain 'D' and resid 1046 through 1047 removed outlier: 3.617A pdb=" N THR D1047 " --> pdb=" O VAL D1060 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N VAL D1060 " --> pdb=" O THR D1047 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'D' and resid 1156 through 1157 Processing sheet with id=AF2, first strand: chain 'D' and resid 1162 through 1165 Processing sheet with id=AF3, first strand: chain 'D' and resid 1279 through 1281 1412 hydrogen bonds defined for protein. 3989 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 38 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 58 stacking parallelities Total time for adding SS restraints: 7.20 Time building geometry restraints manager: 3.65 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: 8127 1.33 - 1.45: 6509 1.45 - 1.57: 18909 1.57 - 1.69: 281 1.69 - 1.81: 240 Bond restraints: 34066 Sorted by residual: bond pdb=" C5 GTP 3 1 " pdb=" C6 GTP 3 1 " ideal model delta sigma weight residual 1.390 1.474 -0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" C3' DC 1 54 " pdb=" O3' DC 1 54 " ideal model delta sigma weight residual 1.435 1.387 0.048 1.30e-02 5.92e+03 1.39e+01 bond pdb=" C3' DG 2 25 " pdb=" C2' DG 2 25 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.27e+01 bond pdb=" C4 GTP 3 1 " pdb=" C5 GTP 3 1 " ideal model delta sigma weight residual 1.390 1.459 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C1' DT 2 48 " pdb=" N1 DT 2 48 " ideal model delta sigma weight residual 1.468 1.515 -0.047 1.40e-02 5.10e+03 1.12e+01 ... (remaining 34061 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 45698 2.89 - 5.78: 811 5.78 - 8.67: 63 8.67 - 11.56: 9 11.56 - 14.45: 2 Bond angle restraints: 46583 Sorted by residual: angle pdb=" O4' DT 2 48 " pdb=" C4' DT 2 48 " pdb=" C3' DT 2 48 " ideal model delta sigma weight residual 106.00 102.52 3.48 6.00e-01 2.78e+00 3.37e+01 angle pdb=" N ILE C1109 " pdb=" CA ILE C1109 " pdb=" C ILE C1109 " ideal model delta sigma weight residual 112.83 107.31 5.52 9.90e-01 1.02e+00 3.11e+01 angle pdb=" O3' DG 2 34 " pdb=" C3' DG 2 34 " pdb=" C2' DG 2 34 " ideal model delta sigma weight residual 109.40 96.03 13.37 2.50e+00 1.60e-01 2.86e+01 angle pdb=" N GLN C1135 " pdb=" CA GLN C1135 " pdb=" CB GLN C1135 " ideal model delta sigma weight residual 114.17 108.15 6.02 1.14e+00 7.69e-01 2.79e+01 angle pdb=" N SER D 353 " pdb=" CA SER D 353 " pdb=" C SER D 353 " ideal model delta sigma weight residual 107.88 115.19 -7.31 1.41e+00 5.03e-01 2.69e+01 ... (remaining 46578 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 19898 35.63 - 71.25: 721 71.25 - 106.88: 37 106.88 - 142.51: 1 142.51 - 178.14: 4 Dihedral angle restraints: 20661 sinusoidal: 9542 harmonic: 11119 Sorted by residual: dihedral pdb=" CA ASP C 340 " pdb=" C ASP C 340 " pdb=" N LEU C 341 " pdb=" CA LEU C 341 " ideal model delta harmonic sigma weight residual -180.00 -136.61 -43.39 0 5.00e+00 4.00e-02 7.53e+01 dihedral pdb=" CA GLN C1135 " pdb=" C GLN C1135 " pdb=" N GLN C1136 " pdb=" CA GLN C1136 " ideal model delta harmonic sigma weight residual 180.00 136.84 43.16 0 5.00e+00 4.00e-02 7.45e+01 dihedral pdb=" C5' GTP 3 1 " pdb=" O5' GTP 3 1 " pdb=" PA GTP 3 1 " pdb=" O3A GTP 3 1 " ideal model delta sinusoidal sigma weight residual 69.27 -108.87 178.14 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 20658 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 4340 0.072 - 0.144: 909 0.144 - 0.216: 57 0.216 - 0.287: 7 0.287 - 0.359: 1 Chirality restraints: 5314 Sorted by residual: chirality pdb=" C3' DT 1 41 " pdb=" C4' DT 1 41 " pdb=" O3' DT 1 41 " pdb=" C2' DT 1 41 " both_signs ideal model delta sigma weight residual False -2.73 -2.37 -0.36 2.00e-01 2.50e+01 3.23e+00 chirality pdb=" CB THR C1184 " pdb=" CA THR C1184 " pdb=" OG1 THR C1184 " pdb=" CG2 THR C1184 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C3' DG 2 34 " pdb=" C4' DG 2 34 " pdb=" O3' DG 2 34 " pdb=" C2' DG 2 34 " both_signs ideal model delta sigma weight residual False -2.73 -2.99 0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 5311 not shown) Planarity restraints: 5582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 178 " 0.049 5.00e-02 4.00e+02 7.25e-02 8.40e+00 pdb=" N PRO B 179 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO B 179 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 179 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 166 " -0.044 5.00e-02 4.00e+02 6.55e-02 6.87e+00 pdb=" N PRO B 167 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 167 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 167 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN C1135 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.79e+00 pdb=" C GLN C1135 " -0.045 2.00e-02 2.50e+03 pdb=" O GLN C1135 " 0.016 2.00e-02 2.50e+03 pdb=" N GLN C1136 " 0.016 2.00e-02 2.50e+03 ... (remaining 5579 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 252 2.57 - 3.16: 27791 3.16 - 3.74: 48876 3.74 - 4.32: 67304 4.32 - 4.90: 112183 Nonbonded interactions: 256406 Sorted by model distance: nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1503 " model vdw 1.992 2.170 nonbonded pdb=" O3' A 3 3 " pdb="MG MG D1503 " model vdw 2.046 2.170 nonbonded pdb=" NH2 ARG A 265 " pdb=" O ASN A 294 " model vdw 2.122 3.120 nonbonded pdb=" O GLU C 44 " pdb=" NE2 GLN C 46 " model vdw 2.123 3.120 nonbonded pdb=" NH1 ARG H 203 " pdb=" OP2 DA 1 19 " model vdw 2.127 3.120 ... (remaining 256401 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'H' } 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=0.25 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: 3.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.720 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 33.450 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 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 : 0.012 0.871 34076 Z= 0.707 Angle : 0.992 16.352 46595 Z= 0.609 Chirality : 0.055 0.359 5314 Planarity : 0.005 0.072 5582 Dihedral : 16.994 178.135 13485 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.33 % Favored : 94.54 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.98 (0.13), residues: 3831 helix: 0.42 (0.13), residues: 1568 sheet: -0.79 (0.22), residues: 463 loop : -1.58 (0.13), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 744 TYR 0.029 0.003 TYR C1285 PHE 0.038 0.003 PHE B 8 TRP 0.022 0.002 TRP F 433 HIS 0.012 0.002 HIS D 469 Details of bonding type rmsd/Z covalent geometry : bond 0.01155 / 0.53 (34066) covalent geometry : angle 0.98594 / 0.61 (46583) hydrogen bonds : bond 0.16289 / 11.44 ( 1448) hydrogen bonds : angle 6.52298 / 4.49 ( 4061) metal coordination : bond 0.02204 / 1.23 ( 8) metal coordination : angle 6.99630 / 4.11 ( 12) Misc. bond : bond 0.61654 / 32.44 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 160 ASP cc_start: 0.7893 (t70) cc_final: 0.7536 (p0) REVERT: C 337 PHE cc_start: 0.8203 (t80) cc_final: 0.7651 (t80) REVERT: C 339 ASN cc_start: 0.7266 (m110) cc_final: 0.7001 (t0) REVERT: C 1135 GLN cc_start: 0.8298 (tp-100) cc_final: 0.7926 (tp-100) REVERT: D 709 ARG cc_start: 0.6863 (pmt-80) cc_final: 0.5814 (pmt-80) REVERT: E 68 GLU cc_start: 0.8772 (tm-30) cc_final: 0.8341 (tm-30) REVERT: E 69 ARG cc_start: 0.8631 (ttm-80) cc_final: 0.8333 (tpp80) REVERT: F 242 HIS cc_start: 0.7600 (t-90) cc_final: 0.7224 (t-90) REVERT: F 561 MET cc_start: 0.8613 (tpp) cc_final: 0.8395 (tpp) REVERT: H 188 LYS cc_start: 0.8265 (ttpt) cc_final: 0.7653 (pptt) REVERT: H 194 MET cc_start: 0.9311 (mmt) cc_final: 0.8799 (mmm) REVERT: H 196 LYS cc_start: 0.8761 (mppt) cc_final: 0.8451 (mptt) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.1984 time to fit residues: 85.5865 Evaluate side-chains 222 residues out of total 3310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 40.0000 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN B 66 HIS D 232 ASN D 739 GLN D1126 GLN D1350 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.121284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.066344 restraints weight = 97398.577| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 3.40 r_work: 0.2673 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9009 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34076 Z= 0.164 Angle : 0.684 13.983 46595 Z= 0.366 Chirality : 0.046 0.340 5314 Planarity : 0.005 0.057 5582 Dihedral : 17.247 173.525 5789 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.10 % Favored : 95.85 % Rotamer: Outliers : 0.42 % Allowed : 5.16 % Favored : 94.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.41 (0.13), residues: 3831 helix: 0.91 (0.13), residues: 1598 sheet: -0.32 (0.24), residues: 426 loop : -1.34 (0.14), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 285 TYR 0.025 0.001 TYR C1018 PHE 0.023 0.001 PHE C 405 TRP 0.020 0.001 TRP D1193 HIS 0.010 0.001 HIS G 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (34066) covalent geometry : angle 0.67833 / 0.37 (46583) hydrogen bonds : bond 0.05973 / 4.22 ( 1448) hydrogen bonds : angle 4.91365 / 3.36 ( 4061) metal coordination : bond 0.00821 / 0.41 ( 8) metal coordination : angle 5.37350 / 3.22 ( 12) Misc. bond : bond 0.01944 / 1.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 252 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.4008 (mtt) cc_final: 0.3310 (mpp) REVERT: B 67 GLU cc_start: 0.8496 (pm20) cc_final: 0.8275 (pm20) REVERT: C 160 ASP cc_start: 0.8215 (t70) cc_final: 0.7694 (p0) REVERT: C 239 MET cc_start: 0.6479 (tmm) cc_final: 0.6275 (tmm) REVERT: C 479 LEU cc_start: 0.9200 (tp) cc_final: 0.8957 (tp) REVERT: C 912 ASP cc_start: 0.8601 (p0) cc_final: 0.8399 (p0) REVERT: C 1016 GLU cc_start: 0.8717 (mp0) cc_final: 0.8385 (mp0) REVERT: D 715 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8581 (mmmt) REVERT: D 1189 MET cc_start: 0.8712 (tmm) cc_final: 0.8435 (tmm) REVERT: E 68 GLU cc_start: 0.8999 (tm-30) cc_final: 0.8480 (tm-30) REVERT: E 69 ARG cc_start: 0.8797 (ttm-80) cc_final: 0.8439 (tpp80) REVERT: E 71 GLU cc_start: 0.8460 (tp30) cc_final: 0.8190 (tp30) REVERT: F 242 HIS cc_start: 0.7949 (t-90) cc_final: 0.7660 (t70) REVERT: F 561 MET cc_start: 0.8784 (tpp) cc_final: 0.8545 (tpp) REVERT: H 188 LYS cc_start: 0.8029 (ttpt) cc_final: 0.7498 (pptt) REVERT: H 194 MET cc_start: 0.9168 (mmt) cc_final: 0.8876 (mmt) outliers start: 14 outliers final: 8 residues processed: 258 average time/residue: 0.1913 time to fit residues: 81.2458 Evaluate side-chains 234 residues out of total 3310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 225 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 715 LYS Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain G residue 187 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 315 optimal weight: 0.6980 chunk 278 optimal weight: 6.9990 chunk 163 optimal weight: 0.9990 chunk 320 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 chunk 229 optimal weight: 4.9990 chunk 370 optimal weight: 9.9990 chunk 292 optimal weight: 30.0000 chunk 323 optimal weight: 0.0670 chunk 224 optimal weight: 2.9990 chunk 388 optimal weight: 40.0000 overall best weight: 1.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 84 ASN D 669 GLN D1252 HIS E 31 GLN E 62 GLN ** F 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.121243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.066291 restraints weight = 101417.406| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 3.43 r_work: 0.2673 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34076 Z= 0.145 Angle : 0.601 11.142 46595 Z= 0.323 Chirality : 0.043 0.243 5314 Planarity : 0.004 0.048 5582 Dihedral : 17.161 174.783 5789 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.28 % Favored : 95.69 % Rotamer: Outliers : 0.88 % Allowed : 7.19 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.13 (0.13), residues: 3831 helix: 1.19 (0.13), residues: 1599 sheet: -0.20 (0.24), residues: 430 loop : -1.24 (0.14), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D1373 TYR 0.017 0.001 TYR C1018 PHE 0.026 0.001 PHE D 172 TRP 0.023 0.001 TRP D1193 HIS 0.010 0.001 HIS G 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (34066) covalent geometry : angle 0.59675 / 0.32 (46583) hydrogen bonds : bond 0.05208 / 3.65 ( 1448) hydrogen bonds : angle 4.57770 / 3.13 ( 4061) metal coordination : bond 0.00787 / 0.43 ( 8) metal coordination : angle 4.36348 / 2.62 ( 12) Misc. bond : bond 0.00332 / 0.17 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 244 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.4080 (mtt) cc_final: 0.3204 (mpp) REVERT: B 67 GLU cc_start: 0.8625 (pm20) cc_final: 0.8398 (pm20) REVERT: C 160 ASP cc_start: 0.8112 (t70) cc_final: 0.7782 (t0) REVERT: C 239 MET cc_start: 0.6412 (tmm) cc_final: 0.6171 (tmm) REVERT: D 153 ASN cc_start: 0.8064 (m110) cc_final: 0.7828 (t0) REVERT: D 715 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8358 (mmmt) REVERT: D 1189 MET cc_start: 0.8754 (tmm) cc_final: 0.8450 (tmm) REVERT: D 1196 LEU cc_start: 0.9118 (tt) cc_final: 0.8748 (mp) REVERT: E 68 GLU cc_start: 0.9000 (tm-30) cc_final: 0.8413 (tm-30) REVERT: E 69 ARG cc_start: 0.8801 (ttm-80) cc_final: 0.8506 (tpp80) REVERT: E 73 GLN cc_start: 0.8714 (tt0) cc_final: 0.8359 (pp30) REVERT: F 242 HIS cc_start: 0.7808 (t-90) cc_final: 0.7506 (t70) REVERT: F 561 MET cc_start: 0.8790 (tpp) cc_final: 0.8453 (tpp) REVERT: F 600 HIS cc_start: 0.8679 (t-170) cc_final: 0.8453 (t-170) REVERT: H 188 LYS cc_start: 0.7815 (ttpt) cc_final: 0.7303 (pptt) outliers start: 29 outliers final: 9 residues processed: 262 average time/residue: 0.2028 time to fit residues: 87.6639 Evaluate side-chains 233 residues out of total 3310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 223 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 715 LYS Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 872 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 138 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 286 optimal weight: 30.0000 chunk 275 optimal weight: 9.9990 chunk 54 optimal weight: 0.0570 chunk 259 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 chunk 294 optimal weight: 2.9990 chunk 205 optimal weight: 9.9990 chunk 101 optimal weight: 7.9990 chunk 266 optimal weight: 8.9990 overall best weight: 1.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 103 ASN C1080 ASN D 865 HIS E 62 GLN F 600 HIS H 173 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.121367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.066564 restraints weight = 82800.935| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.86 r_work: 0.2715 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34076 Z= 0.142 Angle : 0.572 10.579 46595 Z= 0.309 Chirality : 0.042 0.266 5314 Planarity : 0.004 0.050 5582 Dihedral : 17.108 172.245 5789 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.13 % Favored : 95.85 % Rotamer: Outliers : 0.94 % Allowed : 8.85 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % 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: 0.07 (0.13), residues: 3831 helix: 1.34 (0.13), residues: 1602 sheet: -0.06 (0.25), residues: 419 loop : -1.12 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1033 TYR 0.040 0.001 TYR F 228 PHE 0.019 0.001 PHE C 405 TRP 0.020 0.001 TRP D1193 HIS 0.009 0.001 HIS G 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (34066) covalent geometry : angle 0.56877 / 0.31 (46583) hydrogen bonds : bond 0.04758 / 3.32 ( 1448) hydrogen bonds : angle 4.38475 / 3.00 ( 4061) metal coordination : bond 0.00723 / 0.41 ( 8) metal coordination : angle 3.91529 / 2.37 ( 12) Misc. bond : bond 0.00217 / 0.11 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 238 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.3921 (mtt) cc_final: 0.3025 (mpp) REVERT: C 160 ASP cc_start: 0.7929 (t70) cc_final: 0.7613 (t0) REVERT: C 239 MET cc_start: 0.6456 (tmm) cc_final: 0.6176 (tmm) REVERT: C 1016 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8542 (mp0) REVERT: D 151 MET cc_start: 0.5984 (ptp) cc_final: 0.5754 (ptp) REVERT: D 153 ASN cc_start: 0.8010 (m110) cc_final: 0.7755 (t0) REVERT: D 1189 MET cc_start: 0.8755 (tmm) cc_final: 0.8448 (tmm) REVERT: E 3 ARG cc_start: 0.8627 (mpt-90) cc_final: 0.8397 (mpt-90) REVERT: E 68 GLU cc_start: 0.8993 (tm-30) cc_final: 0.8410 (tm-30) REVERT: E 69 ARG cc_start: 0.8782 (ttm-80) cc_final: 0.8449 (tpp80) REVERT: E 73 GLN cc_start: 0.8749 (tt0) cc_final: 0.8390 (pp30) REVERT: F 242 HIS cc_start: 0.7622 (t-90) cc_final: 0.7294 (t70) REVERT: F 276 MET cc_start: 0.9449 (pmm) cc_final: 0.9054 (tpt) REVERT: F 397 ARG cc_start: 0.7982 (mtt180) cc_final: 0.7375 (mpp80) REVERT: F 561 MET cc_start: 0.8811 (tpp) cc_final: 0.8603 (tpp) REVERT: H 188 LYS cc_start: 0.7730 (ttpt) cc_final: 0.7204 (pptt) outliers start: 31 outliers final: 14 residues processed: 261 average time/residue: 0.1909 time to fit residues: 82.9224 Evaluate side-chains 243 residues out of total 3310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 228 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 1016 GLU Chi-restraints excluded: chain C residue 1080 ASN Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain G residue 187 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 132 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 290 optimal weight: 50.0000 chunk 179 optimal weight: 2.9990 chunk 294 optimal weight: 30.0000 chunk 84 optimal weight: 9.9990 chunk 238 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 447 HIS E 62 GLN F 600 HIS G 173 ASN H 173 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.120370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.065359 restraints weight = 85790.799| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.89 r_work: 0.2685 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 34076 Z= 0.185 Angle : 0.587 10.050 46595 Z= 0.315 Chirality : 0.043 0.258 5314 Planarity : 0.004 0.048 5582 Dihedral : 17.109 171.265 5789 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.44 % Favored : 95.54 % Rotamer: Outliers : 1.12 % Allowed : 10.18 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % 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: 0.11 (0.13), residues: 3831 helix: 1.37 (0.13), residues: 1606 sheet: -0.04 (0.25), residues: 425 loop : -1.10 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 214 TYR 0.020 0.001 TYR B 68 PHE 0.019 0.001 PHE C 405 TRP 0.020 0.001 TRP D1193 HIS 0.010 0.001 HIS G 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.18 (34066) covalent geometry : angle 0.58380 / 0.31 (46583) hydrogen bonds : bond 0.04939 / 3.42 ( 1448) hydrogen bonds : angle 4.34679 / 2.98 ( 4061) metal coordination : bond 0.00910 / 0.54 ( 8) metal coordination : angle 3.73353 / 2.26 ( 12) Misc. bond : bond 0.00050 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 234 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.3925 (mtt) cc_final: 0.2967 (mpp) REVERT: C 160 ASP cc_start: 0.7945 (t70) cc_final: 0.7634 (t0) REVERT: C 239 MET cc_start: 0.6475 (tmm) cc_final: 0.6197 (tmm) REVERT: C 1016 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8530 (mp0) REVERT: D 140 TYR cc_start: 0.8459 (m-10) cc_final: 0.8107 (m-10) REVERT: D 180 MET cc_start: 0.8990 (ttm) cc_final: 0.8637 (ttm) REVERT: D 736 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8104 (mp10) REVERT: D 1189 MET cc_start: 0.8761 (tmm) cc_final: 0.8451 (tmm) REVERT: E 3 ARG cc_start: 0.8647 (mpt-90) cc_final: 0.8416 (mpt-90) REVERT: E 68 GLU cc_start: 0.9000 (tm-30) cc_final: 0.8677 (tm-30) REVERT: E 69 ARG cc_start: 0.8805 (ttm-80) cc_final: 0.8594 (tpp80) REVERT: F 242 HIS cc_start: 0.7591 (t-90) cc_final: 0.7249 (t70) REVERT: F 397 ARG cc_start: 0.8093 (mtt180) cc_final: 0.7566 (mpp80) REVERT: F 561 MET cc_start: 0.8836 (tpp) cc_final: 0.8596 (tpp) REVERT: H 188 LYS cc_start: 0.7729 (ttpt) cc_final: 0.7127 (pptt) REVERT: H 193 HIS cc_start: 0.9330 (m170) cc_final: 0.9125 (m170) outliers start: 37 outliers final: 22 residues processed: 257 average time/residue: 0.1954 time to fit residues: 84.2422 Evaluate side-chains 253 residues out of total 3310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 229 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 1016 GLU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain F residue 470 MET Chi-restraints excluded: chain G residue 187 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 162 optimal weight: 0.0970 chunk 159 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 54 optimal weight: 0.1980 chunk 165 optimal weight: 3.9990 chunk 240 optimal weight: 2.9990 chunk 239 optimal weight: 0.9980 overall best weight: 1.0380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 62 GLN H 173 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.121612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.067418 restraints weight = 72449.199| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.66 r_work: 0.2740 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2745 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2745 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 34076 Z= 0.125 Angle : 0.552 10.452 46595 Z= 0.297 Chirality : 0.041 0.242 5314 Planarity : 0.004 0.049 5582 Dihedral : 17.059 169.435 5789 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.13 % Favored : 95.85 % Rotamer: Outliers : 1.30 % Allowed : 10.45 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % 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: 0.27 (0.14), residues: 3831 helix: 1.48 (0.13), residues: 1607 sheet: 0.07 (0.25), residues: 427 loop : -1.02 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1211 TYR 0.024 0.001 TYR B 68 PHE 0.017 0.001 PHE C 405 TRP 0.022 0.001 TRP D1193 HIS 0.010 0.001 HIS G 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (34066) covalent geometry : angle 0.54936 / 0.30 (46583) hydrogen bonds : bond 0.04378 / 3.05 ( 1448) hydrogen bonds : angle 4.20723 / 2.88 ( 4061) metal coordination : bond 0.00610 / 0.35 ( 8) metal coordination : angle 3.48695 / 2.12 ( 12) Misc. bond : bond 0.00033 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 236 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.3899 (mtt) cc_final: 0.3140 (mpp) REVERT: C 160 ASP cc_start: 0.7844 (t70) cc_final: 0.7534 (t0) REVERT: C 239 MET cc_start: 0.6516 (tmm) cc_final: 0.6255 (tmm) REVERT: C 1016 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8550 (mp0) REVERT: C 1212 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8966 (mp) REVERT: D 140 TYR cc_start: 0.8379 (m-10) cc_final: 0.7973 (m-10) REVERT: D 180 MET cc_start: 0.8935 (ttm) cc_final: 0.8724 (ttm) REVERT: D 736 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8041 (mp10) REVERT: E 3 ARG cc_start: 0.8640 (mpt-90) cc_final: 0.8410 (mpt-90) REVERT: E 68 GLU cc_start: 0.8980 (tm-30) cc_final: 0.8674 (tm-30) REVERT: E 69 ARG cc_start: 0.8804 (ttm-80) cc_final: 0.8601 (tpp80) REVERT: E 73 GLN cc_start: 0.8807 (tt0) cc_final: 0.8380 (pp30) REVERT: F 242 HIS cc_start: 0.7531 (t-90) cc_final: 0.7173 (t70) REVERT: F 561 MET cc_start: 0.8810 (tpp) cc_final: 0.8542 (tpp) REVERT: H 188 LYS cc_start: 0.7656 (ttpt) cc_final: 0.7037 (pptt) outliers start: 43 outliers final: 20 residues processed: 267 average time/residue: 0.2029 time to fit residues: 90.5950 Evaluate side-chains 247 residues out of total 3310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 224 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 1016 GLU Chi-restraints excluded: chain C residue 1137 GLU Chi-restraints excluded: chain C residue 1212 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain G residue 187 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 279 optimal weight: 20.0000 chunk 363 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 337 optimal weight: 5.9990 chunk 382 optimal weight: 50.0000 chunk 13 optimal weight: 0.1980 chunk 83 optimal weight: 9.9990 chunk 266 optimal weight: 10.0000 chunk 269 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.118506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.062450 restraints weight = 108716.877| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 3.74 r_work: 0.2607 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2613 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2613 r_free = 0.2613 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2613 r_free = 0.2613 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2613 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 34076 Z= 0.234 Angle : 0.627 11.344 46595 Z= 0.333 Chirality : 0.044 0.260 5314 Planarity : 0.004 0.044 5582 Dihedral : 17.110 168.084 5789 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.83 % Favored : 95.14 % Rotamer: Outliers : 1.24 % Allowed : 10.87 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % 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: 0.19 (0.14), residues: 3831 helix: 1.39 (0.13), residues: 1609 sheet: 0.10 (0.25), residues: 418 loop : -1.05 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 44 TYR 0.029 0.001 TYR B 68 PHE 0.019 0.001 PHE C 405 TRP 0.021 0.001 TRP D1193 HIS 0.014 0.001 HIS H 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.23 (34066) covalent geometry : angle 0.62463 / 0.33 (46583) hydrogen bonds : bond 0.05193 / 3.58 ( 1448) hydrogen bonds : angle 4.29385 / 2.94 ( 4061) metal coordination : bond 0.01113 / 0.68 ( 8) metal coordination : angle 3.49334 / 2.12 ( 12) Misc. bond : bond 0.00113 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 225 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.4059 (mtt) cc_final: 0.3292 (mpp) REVERT: C 160 ASP cc_start: 0.7886 (t70) cc_final: 0.7500 (t0) REVERT: C 239 MET cc_start: 0.6452 (tmm) cc_final: 0.6186 (tmm) REVERT: C 1212 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.8970 (mp) REVERT: D 140 TYR cc_start: 0.8548 (m-10) cc_final: 0.8188 (m-10) REVERT: D 736 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8020 (mp10) REVERT: D 1174 ARG cc_start: 0.7271 (tpp-160) cc_final: 0.6952 (mmm160) REVERT: E 3 ARG cc_start: 0.8686 (mpt-90) cc_final: 0.8441 (mpt-90) REVERT: E 68 GLU cc_start: 0.8996 (tm-30) cc_final: 0.8679 (tm-30) REVERT: E 69 ARG cc_start: 0.8839 (ttm-80) cc_final: 0.8591 (tpp80) REVERT: F 242 HIS cc_start: 0.7668 (t-90) cc_final: 0.7320 (t70) REVERT: F 561 MET cc_start: 0.8776 (tpp) cc_final: 0.8504 (tpp) REVERT: H 188 LYS cc_start: 0.7514 (ttpt) cc_final: 0.6938 (pptt) REVERT: H 194 MET cc_start: 0.9283 (mmt) cc_final: 0.9075 (mmt) outliers start: 41 outliers final: 27 residues processed: 252 average time/residue: 0.1884 time to fit residues: 79.6811 Evaluate side-chains 247 residues out of total 3310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 218 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 1137 GLU Chi-restraints excluded: chain C residue 1212 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 73 GLN Chi-restraints excluded: chain F residue 470 MET Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 195 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 269 optimal weight: 9.9990 chunk 140 optimal weight: 4.9990 chunk 265 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 392 optimal weight: 40.0000 chunk 313 optimal weight: 5.9990 chunk 204 optimal weight: 5.9990 chunk 373 optimal weight: 20.0000 chunk 156 optimal weight: 0.9990 chunk 304 optimal weight: 5.9990 chunk 170 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 103 ASN F 600 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.119916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.065178 restraints weight = 76424.568| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.75 r_work: 0.2681 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 34076 Z= 0.185 Angle : 0.595 15.369 46595 Z= 0.316 Chirality : 0.043 0.251 5314 Planarity : 0.004 0.045 5582 Dihedral : 17.095 167.685 5789 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.52 % Favored : 95.46 % Rotamer: Outliers : 1.15 % Allowed : 11.42 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % 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: 0.23 (0.14), residues: 3831 helix: 1.42 (0.13), residues: 1611 sheet: 0.16 (0.25), residues: 411 loop : -1.03 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 44 TYR 0.016 0.001 TYR C1018 PHE 0.019 0.001 PHE C 405 TRP 0.021 0.001 TRP D1193 HIS 0.010 0.001 HIS G 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (34066) covalent geometry : angle 0.59273 / 0.32 (46583) hydrogen bonds : bond 0.04882 / 3.38 ( 1448) hydrogen bonds : angle 4.23666 / 2.90 ( 4061) metal coordination : bond 0.00914 / 0.56 ( 8) metal coordination : angle 3.48684 / 2.11 ( 12) Misc. bond : bond 0.00077 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 224 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.4090 (mtt) cc_final: 0.3326 (mpp) REVERT: C 160 ASP cc_start: 0.7824 (t70) cc_final: 0.7448 (t0) REVERT: C 239 MET cc_start: 0.6548 (tmm) cc_final: 0.6247 (tmm) REVERT: C 1212 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8987 (mp) REVERT: D 140 TYR cc_start: 0.8388 (m-10) cc_final: 0.7990 (m-10) REVERT: D 736 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8086 (mp10) REVERT: E 3 ARG cc_start: 0.8675 (mpt-90) cc_final: 0.8438 (mpt-90) REVERT: E 68 GLU cc_start: 0.8991 (tm-30) cc_final: 0.8675 (tm-30) REVERT: E 69 ARG cc_start: 0.8832 (ttm-80) cc_final: 0.8613 (tpp80) REVERT: F 242 HIS cc_start: 0.7555 (t-90) cc_final: 0.7182 (t70) REVERT: H 188 LYS cc_start: 0.7581 (ttpt) cc_final: 0.6970 (pptt) outliers start: 38 outliers final: 26 residues processed: 252 average time/residue: 0.2080 time to fit residues: 87.6652 Evaluate side-chains 247 residues out of total 3310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 219 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 1137 GLU Chi-restraints excluded: chain C residue 1212 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 195 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 276 optimal weight: 1.9990 chunk 382 optimal weight: 50.0000 chunk 307 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 375 optimal weight: 2.9990 chunk 288 optimal weight: 4.9990 chunk 274 optimal weight: 2.9990 chunk 54 optimal weight: 0.4980 chunk 294 optimal weight: 20.0000 chunk 14 optimal weight: 0.6980 chunk 246 optimal weight: 0.6980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 258 GLN F 600 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.120253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.064829 restraints weight = 76255.040| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.82 r_work: 0.2709 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 34076 Z= 0.131 Angle : 0.569 13.328 46595 Z= 0.302 Chirality : 0.042 0.236 5314 Planarity : 0.004 0.044 5582 Dihedral : 17.026 166.123 5789 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.39 % Favored : 95.59 % Rotamer: Outliers : 0.91 % Allowed : 11.87 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % 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: 0.37 (0.14), residues: 3831 helix: 1.54 (0.13), residues: 1609 sheet: 0.31 (0.26), residues: 401 loop : -0.96 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1033 TYR 0.017 0.001 TYR C1018 PHE 0.018 0.001 PHE C 405 TRP 0.024 0.001 TRP D1193 HIS 0.011 0.001 HIS G 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (34066) covalent geometry : angle 0.56632 / 0.30 (46583) hydrogen bonds : bond 0.04419 / 3.07 ( 1448) hydrogen bonds : angle 4.13629 / 2.83 ( 4061) metal coordination : bond 0.00616 / 0.37 ( 8) metal coordination : angle 3.25439 / 1.98 ( 12) Misc. bond : bond 0.00047 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 224 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.4105 (mtt) cc_final: 0.3365 (mpp) REVERT: C 160 ASP cc_start: 0.7712 (t70) cc_final: 0.7321 (t0) REVERT: C 239 MET cc_start: 0.6517 (tmm) cc_final: 0.6225 (tmm) REVERT: C 959 ASP cc_start: 0.8687 (m-30) cc_final: 0.8301 (m-30) REVERT: C 1016 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8265 (mp0) REVERT: C 1212 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.9022 (mp) REVERT: D 29 MET cc_start: 0.8825 (tpp) cc_final: 0.8486 (ttp) REVERT: D 140 TYR cc_start: 0.8363 (m-10) cc_final: 0.7900 (m-10) REVERT: D 736 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.7997 (mp10) REVERT: E 3 ARG cc_start: 0.8658 (mpt-90) cc_final: 0.8409 (mpt-90) REVERT: E 68 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8654 (tm-30) REVERT: E 69 ARG cc_start: 0.8813 (ttm-80) cc_final: 0.8591 (tpp80) REVERT: E 73 GLN cc_start: 0.8764 (tt0) cc_final: 0.8342 (pp30) REVERT: F 242 HIS cc_start: 0.7603 (t-90) cc_final: 0.7225 (t70) REVERT: H 188 LYS cc_start: 0.7595 (ttpt) cc_final: 0.6999 (pptt) outliers start: 30 outliers final: 21 residues processed: 245 average time/residue: 0.2006 time to fit residues: 81.7042 Evaluate side-chains 242 residues out of total 3310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 218 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 1016 GLU Chi-restraints excluded: chain C residue 1137 GLU Chi-restraints excluded: chain C residue 1212 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain H residue 195 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 29 optimal weight: 6.9990 chunk 340 optimal weight: 20.0000 chunk 277 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 91 optimal weight: 0.0050 chunk 206 optimal weight: 4.9990 chunk 208 optimal weight: 0.0570 chunk 307 optimal weight: 2.9990 chunk 312 optimal weight: 0.0000 chunk 9 optimal weight: 0.8980 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D1326 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.121829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.066921 restraints weight = 100043.653| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 3.63 r_work: 0.2706 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 34076 Z= 0.108 Angle : 0.552 13.504 46595 Z= 0.294 Chirality : 0.041 0.223 5314 Planarity : 0.004 0.045 5582 Dihedral : 16.955 162.288 5789 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.92 % Favored : 96.06 % Rotamer: Outliers : 0.69 % Allowed : 12.14 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.66 % 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: 0.55 (0.14), residues: 3831 helix: 1.66 (0.13), residues: 1613 sheet: 0.43 (0.26), residues: 401 loop : -0.85 (0.14), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1033 TYR 0.017 0.001 TYR C1018 PHE 0.014 0.001 PHE C 405 TRP 0.026 0.001 TRP D1193 HIS 0.012 0.001 HIS G 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.11 (34066) covalent geometry : angle 0.55040 / 0.29 (46583) hydrogen bonds : bond 0.03877 / 2.72 ( 1448) hydrogen bonds : angle 4.01337 / 2.74 ( 4061) metal coordination : bond 0.00405 / 0.24 ( 8) metal coordination : angle 3.04828 / 1.87 ( 12) Misc. bond : bond 0.00035 / 0.02 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 238 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.4096 (mtt) cc_final: 0.3366 (mpp) REVERT: C 160 ASP cc_start: 0.7628 (t70) cc_final: 0.7259 (t0) REVERT: C 239 MET cc_start: 0.6464 (tmm) cc_final: 0.6187 (tmm) REVERT: C 959 ASP cc_start: 0.8723 (m-30) cc_final: 0.8428 (m-30) REVERT: C 1016 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8297 (mp0) REVERT: D 29 MET cc_start: 0.8788 (tpp) cc_final: 0.8485 (ttp) REVERT: D 140 TYR cc_start: 0.8333 (m-10) cc_final: 0.8052 (m-10) REVERT: D 321 LYS cc_start: 0.8683 (ptmm) cc_final: 0.8377 (ptmm) REVERT: D 736 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8037 (mp10) REVERT: D 1189 MET cc_start: 0.8746 (tmm) cc_final: 0.8493 (tmm) REVERT: E 3 ARG cc_start: 0.8653 (mpt-90) cc_final: 0.8381 (mpt-90) REVERT: E 44 ASP cc_start: 0.9013 (m-30) cc_final: 0.8804 (m-30) REVERT: E 68 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8592 (tm-30) REVERT: E 69 ARG cc_start: 0.8831 (ttm-80) cc_final: 0.8588 (tpp80) REVERT: E 73 GLN cc_start: 0.8694 (tt0) cc_final: 0.8295 (pp30) REVERT: F 242 HIS cc_start: 0.7806 (t-90) cc_final: 0.7457 (t70) REVERT: F 397 ARG cc_start: 0.8040 (mtt180) cc_final: 0.7340 (mpp80) REVERT: H 188 LYS cc_start: 0.7558 (ttpt) cc_final: 0.6944 (pptt) outliers start: 23 outliers final: 16 residues processed: 253 average time/residue: 0.2107 time to fit residues: 89.4662 Evaluate side-chains 241 residues out of total 3310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 223 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 1016 GLU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 195 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 173 optimal weight: 2.9990 chunk 243 optimal weight: 2.9990 chunk 297 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 110 optimal weight: 0.5980 chunk 125 optimal weight: 1.9990 chunk 324 optimal weight: 3.9990 chunk 223 optimal weight: 0.7980 chunk 283 optimal weight: 0.0270 chunk 361 optimal weight: 3.9990 chunk 76 optimal weight: 0.0370 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 62 GLN F 600 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.122444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.068112 restraints weight = 86271.573| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.91 r_work: 0.2745 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2751 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2751 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 34076 Z= 0.111 Angle : 0.559 17.440 46595 Z= 0.293 Chirality : 0.041 0.224 5314 Planarity : 0.004 0.046 5582 Dihedral : 16.923 157.611 5789 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.02 % Favored : 95.95 % Rotamer: Outliers : 0.69 % Allowed : 12.47 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % 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: 0.60 (0.14), residues: 3831 helix: 1.68 (0.13), residues: 1615 sheet: 0.50 (0.26), residues: 401 loop : -0.82 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1033 TYR 0.019 0.001 TYR C1018 PHE 0.015 0.001 PHE C 405 TRP 0.025 0.001 TRP D1193 HIS 0.017 0.001 HIS H 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (34066) covalent geometry : angle 0.55666 / 0.29 (46583) hydrogen bonds : bond 0.03909 / 2.73 ( 1448) hydrogen bonds : angle 3.97865 / 2.72 ( 4061) metal coordination : bond 0.00433 / 0.26 ( 8) metal coordination : angle 2.91022 / 1.79 ( 12) Misc. bond : bond 0.00046 / 0.02 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10682.43 seconds wall clock time: 182 minutes 19.77 seconds (10939.77 seconds total)