Starting phenix.real_space_refine on Fri May 30 10:40:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u3b_41856/05_2025/8u3b_41856.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u3b_41856/05_2025/8u3b_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8u3b_41856/05_2025/8u3b_41856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u3b_41856/05_2025/8u3b_41856.map" model { file = "/net/cci-nas-00/data/ceres_data/8u3b_41856/05_2025/8u3b_41856.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u3b_41856/05_2025/8u3b_41856.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'RNA': 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: 19.25, per 1000 atoms: 0.58 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: 8.60 Conformation dependent library (CDL) restraints added in 4.3 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: 12.06 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: 15.78 Time building geometry restraints manager: 10.02 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=" 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=" CA ASP D 54 " pdb=" C ASP D 54 " ideal model delta sigma weight residual 1.524 1.490 0.034 1.29e-02 6.01e+03 6.97e+00 bond pdb=" C MET C1180 " pdb=" N PRO C1181 " ideal model delta sigma weight residual 1.334 1.306 0.028 1.11e-02 8.12e+03 6.33e+00 bond pdb=" CA ALA C 795 " pdb=" CB ALA C 795 " ideal model delta sigma weight residual 1.524 1.484 0.040 1.62e-02 3.81e+03 6.10e+00 ... (remaining 34061 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 45878 3.09 - 6.19: 653 6.19 - 9.28: 42 9.28 - 12.37: 8 12.37 - 15.47: 2 Bond angle restraints: 46583 Sorted by residual: angle pdb=" O3' DG 2 34 " pdb=" C3' DG 2 34 " pdb=" C2' DG 2 34 " ideal model delta sigma weight residual 111.50 96.03 15.47 1.50e+00 4.44e-01 1.06e+02 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=" 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 angle pdb=" C LYS D 39 " pdb=" N LYS D 40 " pdb=" CA LYS D 40 " ideal model delta sigma weight residual 122.38 107.93 14.45 2.90e+00 1.19e-01 2.48e+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 - 0.067: 4289 0.067 - 0.133: 936 0.133 - 0.200: 75 0.200 - 0.267: 12 0.267 - 0.333: 2 Chirality restraints: 5314 Sorted by residual: 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 -2.66 -2.99 0.33 2.00e-01 2.50e+01 2.78e+00 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 -2.66 -2.37 -0.29 2.00e-01 2.50e+01 2.08e+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 ... (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: 3.290 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: 1.460 Check model and map are aligned: 0.260 Set scattering table: 0.320 Process input model: 90.690 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 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= 0.671 Angle : 0.970 16.352 46595 Z= 0.553 Chirality : 0.053 0.333 5314 Planarity : 0.005 0.072 5582 Dihedral : 16.987 178.135 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (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 TRP 0.022 0.002 TRP F 433 HIS 0.012 0.002 HIS D 469 PHE 0.038 0.003 PHE B 8 TYR 0.029 0.003 TYR C1285 ARG 0.014 0.001 ARG D 744 Details of bonding type rmsd hydrogen bonds : bond 0.16289 ( 1448) hydrogen bonds : angle 6.52298 ( 4061) metal coordination : bond 0.02204 ( 8) metal coordination : angle 6.99630 ( 12) covalent geometry : bond 0.01143 (34066) covalent geometry : angle 0.96337 (46583) Misc. bond : bond 0.61654 ( 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 : 3.351 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: 0.4570 time to fit residues: 195.2667 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 : 3.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 332 optimal weight: 20.0000 chunk 298 optimal weight: 8.9990 chunk 165 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 201 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 308 optimal weight: 0.8980 chunk 119 optimal weight: 0.8980 chunk 187 optimal weight: 0.8980 chunk 229 optimal weight: 0.8980 chunk 357 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN D 669 GLN 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 = 0.3907 r_free = 0.3907 target = 0.121826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.066954 restraints weight = 86854.671| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.93 r_work: 0.2720 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2726 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2726 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34076 Z= 0.151 Angle : 0.628 12.224 46595 Z= 0.335 Chirality : 0.043 0.189 5314 Planarity : 0.005 0.053 5582 Dihedral : 17.212 170.144 5789 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.15 % Favored : 95.80 % Rotamer: Outliers : 0.42 % Allowed : 5.07 % Favored : 94.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.13), residues: 3831 helix: 1.04 (0.13), residues: 1594 sheet: -0.31 (0.24), residues: 421 loop : -1.31 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D1193 HIS 0.005 0.001 HIS C1116 PHE 0.021 0.001 PHE C 405 TYR 0.022 0.001 TYR C1018 ARG 0.009 0.001 ARG D 214 Details of bonding type rmsd hydrogen bonds : bond 0.05311 ( 1448) hydrogen bonds : angle 4.75273 ( 4061) metal coordination : bond 0.00817 ( 8) metal coordination : angle 5.01531 ( 12) covalent geometry : bond 0.00319 (34066) covalent geometry : angle 0.62282 (46583) Misc. bond : bond 0.00176 ( 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 272 residues out of total 3310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 258 time to evaluate : 3.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.4060 (mtt) cc_final: 0.3318 (mpp) REVERT: B 66 HIS cc_start: 0.7567 (p-80) cc_final: 0.7195 (p-80) REVERT: C 160 ASP cc_start: 0.8157 (t70) cc_final: 0.7578 (p0) REVERT: C 1304 MET cc_start: 0.9065 (tpp) cc_final: 0.8700 (tpp) REVERT: C 1315 MET cc_start: 0.9128 (tpp) cc_final: 0.8803 (ttt) REVERT: D 715 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8595 (mmmt) REVERT: D 1189 MET cc_start: 0.8709 (tmm) cc_final: 0.8432 (tmm) REVERT: E 68 GLU cc_start: 0.8973 (tm-30) cc_final: 0.8456 (tm-30) REVERT: E 69 ARG cc_start: 0.8784 (ttm-80) cc_final: 0.8447 (tpp80) REVERT: E 71 GLU cc_start: 0.8457 (tp30) cc_final: 0.8224 (tp30) REVERT: F 242 HIS cc_start: 0.7707 (t-90) cc_final: 0.7421 (t70) REVERT: F 273 MET cc_start: 0.9157 (mtp) cc_final: 0.8853 (mtp) REVERT: F 561 MET cc_start: 0.8793 (tpp) cc_final: 0.8529 (tpp) REVERT: H 188 LYS cc_start: 0.7894 (ttpt) cc_final: 0.7357 (pptt) outliers start: 14 outliers final: 5 residues processed: 265 average time/residue: 0.4653 time to fit residues: 202.6249 Evaluate side-chains 234 residues out of total 3310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 228 time to evaluate : 3.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 628 HIS 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 G residue 187 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 385 optimal weight: 10.0000 chunk 342 optimal weight: 20.0000 chunk 132 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 chunk 54 optimal weight: 0.0770 chunk 347 optimal weight: 7.9990 chunk 265 optimal weight: 4.9990 chunk 255 optimal weight: 0.2980 overall best weight: 1.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS C 273 HIS D 865 HIS D1350 ASN E 31 GLN E 62 GLN G 190 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.121232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.066633 restraints weight = 95352.312| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 3.38 r_work: 0.2677 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2685 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 34076 Z= 0.152 Angle : 0.579 11.111 46595 Z= 0.309 Chirality : 0.042 0.172 5314 Planarity : 0.004 0.049 5582 Dihedral : 17.056 165.630 5789 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.36 % Favored : 95.61 % Rotamer: Outliers : 0.69 % Allowed : 7.85 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.13), residues: 3831 helix: 1.31 (0.13), residues: 1599 sheet: -0.19 (0.24), residues: 427 loop : -1.20 (0.14), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D1193 HIS 0.007 0.001 HIS G 193 PHE 0.023 0.001 PHE D 172 TYR 0.017 0.001 TYR F 228 ARG 0.004 0.000 ARG D1373 Details of bonding type rmsd hydrogen bonds : bond 0.04894 ( 1448) hydrogen bonds : angle 4.43427 ( 4061) metal coordination : bond 0.00783 ( 8) metal coordination : angle 3.96302 ( 12) covalent geometry : bond 0.00356 (34066) covalent geometry : angle 0.57603 (46583) Misc. bond : bond 0.00107 ( 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 274 residues out of total 3310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 251 time to evaluate : 3.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.3875 (mtt) cc_final: 0.2881 (mpp) REVERT: C 160 ASP cc_start: 0.7967 (t70) cc_final: 0.7668 (t0) REVERT: D 151 MET cc_start: 0.6176 (ptp) cc_final: 0.5839 (ptp) REVERT: D 153 ASN cc_start: 0.8084 (m110) cc_final: 0.7760 (t160) REVERT: D 330 MET cc_start: 0.9023 (mtm) cc_final: 0.8820 (mtm) REVERT: D 1189 MET cc_start: 0.8771 (tmm) cc_final: 0.8466 (tmm) REVERT: D 1196 LEU cc_start: 0.9047 (tt) cc_final: 0.8665 (mp) REVERT: E 68 GLU cc_start: 0.8987 (tm-30) cc_final: 0.8418 (tm-30) REVERT: E 69 ARG cc_start: 0.8800 (ttm-80) cc_final: 0.8456 (tpp80) REVERT: F 242 HIS cc_start: 0.7763 (t-90) cc_final: 0.7459 (t70) REVERT: H 188 LYS cc_start: 0.7712 (ttpt) cc_final: 0.7201 (pptt) REVERT: H 194 MET cc_start: 0.9238 (mmt) cc_final: 0.8937 (mmt) outliers start: 23 outliers final: 7 residues processed: 266 average time/residue: 0.4361 time to fit residues: 192.0481 Evaluate side-chains 234 residues out of total 3310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 227 time to evaluate : 4.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain D residue 705 THR 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 141 optimal weight: 0.8980 chunk 74 optimal weight: 8.9990 chunk 44 optimal weight: 9.9990 chunk 234 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 186 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 373 optimal weight: 40.0000 chunk 9 optimal weight: 0.7980 chunk 275 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 339 ASN C 447 HIS C1111 GLN D1252 HIS E 62 GLN ** G 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.120062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.064209 restraints weight = 82551.208| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.88 r_work: 0.2700 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2704 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2704 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 34076 Z= 0.159 Angle : 0.567 10.475 46595 Z= 0.302 Chirality : 0.041 0.221 5314 Planarity : 0.004 0.050 5582 Dihedral : 17.034 161.173 5789 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.33 % Favored : 95.64 % Rotamer: Outliers : 1.18 % Allowed : 9.48 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.13), residues: 3831 helix: 1.42 (0.13), residues: 1603 sheet: -0.02 (0.25), residues: 415 loop : -1.12 (0.14), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D1193 HIS 0.007 0.001 HIS G 193 PHE 0.021 0.001 PHE C 337 TYR 0.017 0.001 TYR C1018 ARG 0.004 0.000 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.04668 ( 1448) hydrogen bonds : angle 4.29319 ( 4061) metal coordination : bond 0.00806 ( 8) metal coordination : angle 3.63901 ( 12) covalent geometry : bond 0.00379 (34066) covalent geometry : angle 0.56411 (46583) Misc. bond : bond 0.00083 ( 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 277 residues out of total 3310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 238 time to evaluate : 3.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.3788 (mtt) cc_final: 0.2775 (mpp) REVERT: C 160 ASP cc_start: 0.7870 (t70) cc_final: 0.7552 (t0) REVERT: C 337 PHE cc_start: 0.8577 (t80) cc_final: 0.8314 (t80) REVERT: C 1016 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8531 (mp0) REVERT: D 715 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8530 (mmmt) REVERT: D 960 LEU cc_start: 0.8237 (mm) cc_final: 0.7959 (mt) REVERT: D 1040 MET cc_start: 0.4386 (tmm) cc_final: 0.4186 (tmm) REVERT: E 68 GLU cc_start: 0.8997 (tm-30) cc_final: 0.8673 (tm-30) REVERT: E 69 ARG cc_start: 0.8816 (ttm-80) cc_final: 0.8607 (tpp80) REVERT: E 73 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8452 (pp30) REVERT: F 242 HIS cc_start: 0.7576 (t-90) cc_final: 0.7229 (t70) REVERT: F 561 MET cc_start: 0.8782 (tpp) cc_final: 0.8485 (tpp) REVERT: H 188 LYS cc_start: 0.7608 (ttpt) cc_final: 0.6993 (pptt) REVERT: H 194 MET cc_start: 0.9244 (mmt) cc_final: 0.8952 (mmt) outliers start: 39 outliers final: 18 residues processed: 266 average time/residue: 0.4356 time to fit residues: 191.3812 Evaluate side-chains 244 residues out of total 3310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 223 time to evaluate : 3.351 ------------------------------------------------------------------------------- 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 339 ASN Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 628 HIS 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 1255 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 715 LYS 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 73 GLN 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 293 optimal weight: 50.0000 chunk 142 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 328 optimal weight: 5.9990 chunk 320 optimal weight: 0.2980 chunk 369 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 87 optimal weight: 8.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 ASN C 339 ASN C1080 ASN D 153 ASN E 62 GLN ** G 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.119738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.064094 restraints weight = 97577.429| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 3.67 r_work: 0.2644 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2648 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2648 r_free = 0.2648 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2648 r_free = 0.2648 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2648 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 34076 Z= 0.166 Angle : 0.570 10.863 46595 Z= 0.302 Chirality : 0.041 0.234 5314 Planarity : 0.004 0.048 5582 Dihedral : 17.010 159.572 5789 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.33 % Favored : 95.64 % Rotamer: Outliers : 1.39 % Allowed : 10.27 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.14), residues: 3831 helix: 1.47 (0.13), residues: 1605 sheet: 0.03 (0.25), residues: 425 loop : -1.06 (0.14), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D1193 HIS 0.012 0.001 HIS H 193 PHE 0.019 0.001 PHE C 405 TYR 0.020 0.001 TYR C1018 ARG 0.005 0.000 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.04659 ( 1448) hydrogen bonds : angle 4.22682 ( 4061) metal coordination : bond 0.00805 ( 8) metal coordination : angle 3.37055 ( 12) covalent geometry : bond 0.00398 (34066) covalent geometry : angle 0.56749 (46583) Misc. bond : bond 0.00082 ( 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 275 residues out of total 3310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 229 time to evaluate : 3.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.3833 (mtt) cc_final: 0.2836 (mpp) REVERT: C 160 ASP cc_start: 0.7831 (t70) cc_final: 0.7460 (t0) REVERT: C 337 PHE cc_start: 0.8499 (t80) cc_final: 0.8191 (t80) REVERT: C 1212 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9036 (mp) REVERT: D 321 LYS cc_start: 0.8749 (ptmm) cc_final: 0.8437 (ptmm) REVERT: D 715 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8487 (mmmt) REVERT: D 736 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.7968 (mp10) REVERT: D 865 HIS cc_start: 0.7388 (OUTLIER) cc_final: 0.7164 (m90) REVERT: E 68 GLU cc_start: 0.8984 (tm-30) cc_final: 0.8641 (tm-30) REVERT: E 69 ARG cc_start: 0.8839 (ttm-80) cc_final: 0.8599 (tpp80) REVERT: E 73 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8409 (pp30) REVERT: F 242 HIS cc_start: 0.7709 (t-90) cc_final: 0.7361 (t70) REVERT: H 188 LYS cc_start: 0.7572 (ttpt) cc_final: 0.7231 (pttt) REVERT: H 194 MET cc_start: 0.9249 (mmt) cc_final: 0.9031 (mmt) outliers start: 46 outliers final: 23 residues processed: 258 average time/residue: 0.4306 time to fit residues: 186.2094 Evaluate side-chains 248 residues out of total 3310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 220 time to evaluate : 3.427 ------------------------------------------------------------------------------- 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 339 ASN Chi-restraints excluded: chain C residue 360 LEU 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 1080 ASN Chi-restraints excluded: chain C residue 1212 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 198 CYS 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 715 LYS Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 865 HIS 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 E residue 73 GLN Chi-restraints excluded: chain H residue 166 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 71 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 303 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 221 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 357 optimal weight: 6.9990 chunk 317 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 258 GLN ** G 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.118415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.062641 restraints weight = 77024.049| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 2.76 r_work: 0.2665 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2672 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2672 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 34076 Z= 0.227 Angle : 0.607 11.781 46595 Z= 0.320 Chirality : 0.043 0.231 5314 Planarity : 0.004 0.044 5582 Dihedral : 17.035 159.862 5789 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.60 % Favored : 95.38 % Rotamer: Outliers : 1.33 % Allowed : 10.96 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.14), residues: 3831 helix: 1.40 (0.13), residues: 1611 sheet: 0.03 (0.25), residues: 419 loop : -1.06 (0.14), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D1193 HIS 0.008 0.001 HIS G 193 PHE 0.019 0.001 PHE C 405 TYR 0.017 0.001 TYR C1087 ARG 0.007 0.000 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.05084 ( 1448) hydrogen bonds : angle 4.28177 ( 4061) metal coordination : bond 0.01072 ( 8) metal coordination : angle 3.48575 ( 12) covalent geometry : bond 0.00555 (34066) covalent geometry : angle 0.60427 (46583) Misc. bond : bond 0.00119 ( 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 265 residues out of total 3310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 221 time to evaluate : 3.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 160 ASP cc_start: 0.7807 (t70) cc_final: 0.7458 (t0) REVERT: C 1016 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8274 (mp0) REVERT: C 1212 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8955 (mp) REVERT: D 715 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8518 (mmmt) REVERT: D 736 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.7982 (mp10) REVERT: D 865 HIS cc_start: 0.7420 (OUTLIER) cc_final: 0.7149 (m90) REVERT: E 68 GLU cc_start: 0.9013 (tm-30) cc_final: 0.8685 (tm-30) REVERT: E 69 ARG cc_start: 0.8835 (ttm-80) cc_final: 0.8629 (tpp80) REVERT: E 73 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8480 (pp30) REVERT: F 242 HIS cc_start: 0.7479 (t-90) cc_final: 0.7115 (t70) REVERT: F 561 MET cc_start: 0.8752 (tpp) cc_final: 0.8479 (tpp) REVERT: H 188 LYS cc_start: 0.7618 (ttpt) cc_final: 0.6921 (pptt) REVERT: H 194 MET cc_start: 0.9249 (mmt) cc_final: 0.9045 (mmt) outliers start: 44 outliers final: 25 residues processed: 250 average time/residue: 0.4310 time to fit residues: 179.7844 Evaluate side-chains 249 residues out of total 3310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 218 time to evaluate : 3.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 273 HIS 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 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 192 MET Chi-restraints excluded: chain D residue 198 CYS 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 715 LYS Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 865 HIS 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 E residue 73 GLN Chi-restraints excluded: chain H residue 166 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 160 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 chunk 389 optimal weight: 10.0000 chunk 246 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 344 optimal weight: 30.0000 chunk 203 optimal weight: 2.9990 chunk 169 optimal weight: 0.8980 chunk 297 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1080 ASN ** G 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.120668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.065404 restraints weight = 98179.966| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 3.11 r_work: 0.2678 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2685 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34076 Z= 0.139 Angle : 0.554 12.793 46595 Z= 0.293 Chirality : 0.040 0.244 5314 Planarity : 0.004 0.047 5582 Dihedral : 16.945 158.764 5789 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.18 % Favored : 95.80 % Rotamer: Outliers : 1.42 % Allowed : 11.57 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.14), residues: 3831 helix: 1.56 (0.13), residues: 1610 sheet: 0.28 (0.26), residues: 399 loop : -0.98 (0.14), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D1193 HIS 0.012 0.001 HIS G 193 PHE 0.018 0.001 PHE C 405 TYR 0.015 0.001 TYR C1018 ARG 0.007 0.000 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.04403 ( 1448) hydrogen bonds : angle 4.12737 ( 4061) metal coordination : bond 0.00673 ( 8) metal coordination : angle 3.22016 ( 12) covalent geometry : bond 0.00325 (34066) covalent geometry : angle 0.55136 (46583) Misc. bond : bond 0.00065 ( 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 281 residues out of total 3310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 234 time to evaluate : 3.603 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: 0.3888 (mtt) cc_final: 0.3021 (mpp) REVERT: C 160 ASP cc_start: 0.7744 (t70) cc_final: 0.7419 (t0) REVERT: C 1016 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8289 (mp0) REVERT: C 1212 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.9030 (mp) REVERT: D 140 TYR cc_start: 0.8495 (m-10) cc_final: 0.8219 (m-10) REVERT: D 715 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8529 (mmmt) REVERT: D 736 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8023 (mp10) REVERT: E 68 GLU cc_start: 0.9023 (tm-30) cc_final: 0.8694 (tm-30) REVERT: E 69 ARG cc_start: 0.8854 (ttm-80) cc_final: 0.8636 (tpp80) REVERT: E 73 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8440 (pp30) REVERT: F 242 HIS cc_start: 0.7631 (t-90) cc_final: 0.7268 (t70) REVERT: F 561 MET cc_start: 0.8760 (tpp) cc_final: 0.8449 (tpp) REVERT: G 194 MET cc_start: 0.3128 (mmp) cc_final: 0.2641 (mmt) REVERT: H 188 LYS cc_start: 0.7648 (ttpt) cc_final: 0.6942 (pptt) outliers start: 47 outliers final: 27 residues processed: 266 average time/residue: 0.4352 time to fit residues: 192.3171 Evaluate side-chains 253 residues out of total 3310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 221 time to evaluate : 3.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 273 HIS Chi-restraints excluded: chain C residue 321 LEU 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 456 VAL Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 538 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 C residue 1016 GLU Chi-restraints excluded: chain C residue 1080 ASN Chi-restraints excluded: chain C residue 1137 GLU Chi-restraints excluded: chain C residue 1212 LEU 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 715 LYS Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 743 MET 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 D residue 1209 VAL Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 73 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 58 optimal weight: 10.0000 chunk 227 optimal weight: 2.9990 chunk 219 optimal weight: 0.8980 chunk 231 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 300 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 377 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 283 optimal weight: 7.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1080 ASN ** G 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.119684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.063935 restraints weight = 91987.087| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 3.48 r_work: 0.2655 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 34076 Z= 0.149 Angle : 0.567 14.534 46595 Z= 0.297 Chirality : 0.041 0.229 5314 Planarity : 0.004 0.045 5582 Dihedral : 16.881 157.794 5789 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.28 % Favored : 95.69 % Rotamer: Outliers : 1.24 % Allowed : 12.11 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.14), residues: 3831 helix: 1.58 (0.13), residues: 1611 sheet: 0.33 (0.26), residues: 409 loop : -0.93 (0.14), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D1193 HIS 0.016 0.001 HIS H 193 PHE 0.017 0.001 PHE C 405 TYR 0.013 0.001 TYR C1087 ARG 0.006 0.000 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.04430 ( 1448) hydrogen bonds : angle 4.08661 ( 4061) metal coordination : bond 0.00688 ( 8) metal coordination : angle 3.02746 ( 12) covalent geometry : bond 0.00352 (34066) covalent geometry : angle 0.56510 (46583) Misc. bond : bond 0.00082 ( 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 264 residues out of total 3310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 223 time to evaluate : 3.611 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: 0.3951 (mtt) cc_final: 0.3091 (mpp) REVERT: B 75 GLN cc_start: 0.8698 (pt0) cc_final: 0.8459 (pt0) REVERT: C 160 ASP cc_start: 0.7692 (t70) cc_final: 0.7327 (t0) REVERT: C 959 ASP cc_start: 0.8731 (m-30) cc_final: 0.8346 (m-30) REVERT: C 1016 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8337 (mp0) REVERT: C 1027 LYS cc_start: 0.9031 (mmtp) cc_final: 0.8457 (pttm) REVERT: C 1212 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9061 (mp) REVERT: D 140 TYR cc_start: 0.8418 (m-10) cc_final: 0.8077 (m-10) REVERT: D 736 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.7875 (mp10) REVERT: D 865 HIS cc_start: 0.7350 (OUTLIER) cc_final: 0.7116 (m90) REVERT: E 68 GLU cc_start: 0.8992 (tm-30) cc_final: 0.8674 (tm-30) REVERT: E 69 ARG cc_start: 0.8853 (ttm-80) cc_final: 0.8618 (tpp80) REVERT: E 73 GLN cc_start: 0.8823 (tt0) cc_final: 0.8434 (pp30) REVERT: F 242 HIS cc_start: 0.7803 (t-90) cc_final: 0.7466 (t70) REVERT: F 561 MET cc_start: 0.8743 (tpp) cc_final: 0.8422 (tpp) REVERT: G 194 MET cc_start: 0.2807 (mmp) cc_final: 0.2606 (mmt) REVERT: H 188 LYS cc_start: 0.7589 (ttpt) cc_final: 0.7142 (pttt) outliers start: 41 outliers final: 30 residues processed: 253 average time/residue: 0.4422 time to fit residues: 186.5834 Evaluate side-chains 253 residues out of total 3310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 219 time to evaluate : 3.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 273 HIS 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 456 VAL Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 538 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 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 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 743 MET Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 865 HIS 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 F residue 364 ARG Chi-restraints excluded: chain F residue 470 MET Chi-restraints excluded: chain H residue 194 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 200 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 177 optimal weight: 0.5980 chunk 314 optimal weight: 0.6980 chunk 216 optimal weight: 0.6980 chunk 37 optimal weight: 6.9990 chunk 278 optimal weight: 0.9980 chunk 8 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1080 ASN D1326 GLN F 600 HIS G 173 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.121063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.065791 restraints weight = 82504.795| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 3.29 r_work: 0.2709 rms_B_bonded: 3.76 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 | |-----------------------------------------------------------------------------| r_final: 0.2715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34076 Z= 0.112 Angle : 0.541 13.776 46595 Z= 0.283 Chirality : 0.040 0.213 5314 Planarity : 0.004 0.046 5582 Dihedral : 16.773 155.868 5789 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.89 % Favored : 96.08 % Rotamer: Outliers : 1.00 % Allowed : 12.26 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.14), residues: 3831 helix: 1.70 (0.13), residues: 1615 sheet: 0.49 (0.26), residues: 394 loop : -0.87 (0.14), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D1193 HIS 0.012 0.001 HIS H 193 PHE 0.015 0.001 PHE C 405 TYR 0.018 0.001 TYR C1018 ARG 0.005 0.000 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.03910 ( 1448) hydrogen bonds : angle 3.97998 ( 4061) metal coordination : bond 0.00466 ( 8) metal coordination : angle 2.83601 ( 12) covalent geometry : bond 0.00252 (34066) covalent geometry : angle 0.53927 (46583) Misc. bond : bond 0.00059 ( 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 264 residues out of total 3310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 231 time to evaluate : 3.359 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: 0.3927 (mtt) cc_final: 0.3062 (mpp) REVERT: B 66 HIS cc_start: 0.7715 (p90) cc_final: 0.7461 (p90) REVERT: C 160 ASP cc_start: 0.7614 (t70) cc_final: 0.7259 (t0) REVERT: C 959 ASP cc_start: 0.8717 (m-30) cc_final: 0.8312 (m-30) REVERT: C 1016 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8390 (mp0) REVERT: D 29 MET cc_start: 0.8800 (tpp) cc_final: 0.8474 (ttp) REVERT: D 865 HIS cc_start: 0.7307 (OUTLIER) cc_final: 0.7062 (m90) REVERT: E 68 GLU cc_start: 0.8959 (tm-30) cc_final: 0.8645 (tm-30) REVERT: E 69 ARG cc_start: 0.8840 (ttm-80) cc_final: 0.8610 (tpp80) REVERT: E 73 GLN cc_start: 0.8838 (tt0) cc_final: 0.8457 (pp30) REVERT: F 242 HIS cc_start: 0.7704 (t-90) cc_final: 0.7361 (t70) REVERT: F 276 MET cc_start: 0.9300 (pmm) cc_final: 0.9074 (pmm) REVERT: F 561 MET cc_start: 0.8760 (tpp) cc_final: 0.8422 (tpp) REVERT: H 188 LYS cc_start: 0.7629 (ttpt) cc_final: 0.7240 (pttt) outliers start: 33 outliers final: 23 residues processed: 256 average time/residue: 0.4426 time to fit residues: 188.6336 Evaluate side-chains 250 residues out of total 3310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 225 time to evaluate : 3.462 ------------------------------------------------------------------------------- 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 456 VAL Chi-restraints excluded: chain C residue 538 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 C residue 1016 GLU Chi-restraints excluded: chain C residue 1080 ASN Chi-restraints excluded: chain C residue 1255 THR 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 743 MET Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 865 HIS 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 F residue 470 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 364 optimal weight: 20.0000 chunk 202 optimal weight: 6.9990 chunk 360 optimal weight: 9.9990 chunk 322 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 140 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 223 optimal weight: 0.0370 chunk 113 optimal weight: 5.9990 chunk 265 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 overall best weight: 3.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN E 62 GLN F 600 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.117290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.061196 restraints weight = 78442.897| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 2.84 r_work: 0.2633 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2636 r_free = 0.2636 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2636 r_free = 0.2636 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2636 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 34076 Z= 0.285 Angle : 0.679 15.700 46595 Z= 0.353 Chirality : 0.044 0.208 5314 Planarity : 0.005 0.057 5582 Dihedral : 16.921 156.302 5789 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.04 % Favored : 94.93 % Rotamer: Outliers : 0.97 % Allowed : 12.59 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.14), residues: 3831 helix: 1.37 (0.13), residues: 1620 sheet: 0.26 (0.26), residues: 417 loop : -1.01 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D1193 HIS 0.011 0.001 HIS H 193 PHE 0.020 0.002 PHE C 405 TYR 0.022 0.002 TYR C1087 ARG 0.007 0.001 ARG D 905 Details of bonding type rmsd hydrogen bonds : bond 0.05555 ( 1448) hydrogen bonds : angle 4.29474 ( 4061) metal coordination : bond 0.01264 ( 8) metal coordination : angle 3.19612 ( 12) covalent geometry : bond 0.00696 (34066) covalent geometry : angle 0.67687 (46583) Misc. bond : bond 0.00172 ( 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 252 residues out of total 3310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 220 time to evaluate : 3.728 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: 0.4086 (mtt) cc_final: 0.3192 (mpp) REVERT: B 66 HIS cc_start: 0.7812 (p90) cc_final: 0.7514 (p90) REVERT: C 160 ASP cc_start: 0.7745 (t70) cc_final: 0.7426 (t0) REVERT: C 959 ASP cc_start: 0.8721 (m-30) cc_final: 0.8330 (m-30) REVERT: C 1016 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8363 (mp0) REVERT: C 1027 LYS cc_start: 0.9090 (mmtp) cc_final: 0.8511 (pttm) REVERT: D 140 TYR cc_start: 0.8457 (m-10) cc_final: 0.8027 (m-10) REVERT: D 736 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.7921 (mp10) REVERT: D 865 HIS cc_start: 0.7482 (OUTLIER) cc_final: 0.7244 (m90) REVERT: E 68 GLU cc_start: 0.8989 (tm-30) cc_final: 0.8630 (tm-30) REVERT: E 69 ARG cc_start: 0.8864 (ttm-80) cc_final: 0.8648 (tpp80) REVERT: F 242 HIS cc_start: 0.7701 (t-90) cc_final: 0.7351 (t70) REVERT: F 276 MET cc_start: 0.9277 (pmm) cc_final: 0.9038 (pmm) REVERT: H 188 LYS cc_start: 0.7767 (ttpt) cc_final: 0.7358 (pttt) outliers start: 32 outliers final: 24 residues processed: 240 average time/residue: 0.4453 time to fit residues: 177.6401 Evaluate side-chains 241 residues out of total 3310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 214 time to evaluate : 3.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 273 HIS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 538 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 C residue 1016 GLU Chi-restraints excluded: chain C residue 1255 THR 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 743 MET Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 865 HIS 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 F residue 470 MET Chi-restraints excluded: chain F residue 600 HIS Chi-restraints excluded: chain H residue 194 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 243 optimal weight: 0.4980 chunk 227 optimal weight: 0.4980 chunk 8 optimal weight: 0.7980 chunk 226 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 76 optimal weight: 20.0000 chunk 41 optimal weight: 0.9990 chunk 317 optimal weight: 0.9980 chunk 271 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1080 ASN C1135 GLN E 62 GLN F 600 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.121091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.066645 restraints weight = 92466.294| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 3.30 r_work: 0.2678 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34076 Z= 0.117 Angle : 0.576 13.531 46595 Z= 0.301 Chirality : 0.040 0.212 5314 Planarity : 0.004 0.047 5582 Dihedral : 16.842 155.241 5789 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.07 % Favored : 95.90 % Rotamer: Outliers : 0.85 % Allowed : 12.84 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.95 % Cis-general : 0.00 % Twisted Proline : 0.66 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.14), residues: 3831 helix: 1.59 (0.13), residues: 1612 sheet: 0.46 (0.26), residues: 390 loop : -0.88 (0.14), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D1193 HIS 0.015 0.001 HIS F 600 PHE 0.017 0.001 PHE C 405 TYR 0.019 0.001 TYR C1018 ARG 0.010 0.000 ARG F 599 Details of bonding type rmsd hydrogen bonds : bond 0.04243 ( 1448) hydrogen bonds : angle 4.08294 ( 4061) metal coordination : bond 0.00499 ( 8) metal coordination : angle 3.04765 ( 12) covalent geometry : bond 0.00257 (34066) covalent geometry : angle 0.57426 (46583) Misc. bond : bond 0.00050 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22738.16 seconds wall clock time: 392 minutes 46.40 seconds (23566.40 seconds total)