Starting phenix.real_space_refine on Sat Jul 4 09:41:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d9d_27258/07_2026/8d9d_27258.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d9d_27258/07_2026/8d9d_27258.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8d9d_27258/07_2026/8d9d_27258.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d9d_27258/07_2026/8d9d_27258.cif" model { file = "/net/cci-nas-00/data/ceres_data/8d9d_27258/07_2026/8d9d_27258.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d9d_27258/07_2026/8d9d_27258.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d9d_27258/07_2026/8d9d_27258.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d9d_27258/07_2026/8d9d_27258.map" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.023 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: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 3 6.06 5 P 35 5.49 5 Mg 2 5.21 5 S 102 5.16 5 C 12303 2.51 5 N 3299 2.21 5 O 3661 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19409 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3253 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 16, 'TRANS': 371} Chain breaks: 2 Chain: "B" Number of atoms: 3473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3473 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 20, 'TRANS': 401} Chain breaks: 1 Chain: "C" Number of atoms: 8538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8538 Classifications: {'peptide': 1058} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1004} Chain breaks: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3451 Classifications: {'peptide': 444} Modifications used: {'COO': 1} Link IDs: {'PCIS': 5, 'PTRANS': 26, 'TRANS': 412} Chain: "E" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 264 Unusual residues: {'GTP': 1} Classifications: {'DNA': 3, 'RNA': 8, 'undetermined': 1} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 4, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 9, None: 1} Not linked: pdbres="GTP E 1 " pdbres=" G E 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 387 Classifications: {'DNA': 19} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 18} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' MG': 1, ' ZN': 2, 'DTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1040 SG CYS A 121 68.511 23.000 60.725 1.00129.11 S ATOM 1046 SG CYS A 122 65.409 24.701 59.427 1.00129.54 S ATOM 1085 SG CYS A 128 65.092 21.310 60.446 1.00110.57 S ATOM 1107 SG CYS A 131 65.641 23.554 63.296 1.00107.82 S ATOM 6011 SG CYS B 367 88.700 110.815 102.172 1.00 98.20 S ATOM 6139 SG CYS B 384 83.935 109.872 104.603 1.00 92.42 S ATOM 6455 SG CYS B 424 89.606 109.339 108.342 1.00116.93 S ATOM 5340 SG CYS B 287 86.725 104.716 104.511 1.00 82.99 S ATOM 13852 SG CYS C1283 64.110 106.569 150.449 1.00160.09 S ATOM 13872 SG CYS C1286 64.364 110.333 150.063 1.00163.10 S ATOM 14058 SG CYS C1310 66.946 108.040 148.429 1.00163.35 S ATOM 14094 SG CYS C1315 66.926 108.500 152.191 1.00157.55 S ATOM 14372 SG CYS C1348 47.184 100.766 108.238 1.00152.77 S ATOM 14410 SG CYS C1353 44.647 103.544 107.713 1.00157.66 S ATOM 14560 SG CYS C1371 43.506 99.871 108.065 1.00149.46 S ATOM 14578 SG CYS C1374 45.281 101.096 104.933 1.00145.36 S Time building chain proxies: 3.70, per 1000 atoms: 0.19 Number of scatterers: 19409 At special positions: 0 Unit cell: (115.36, 142.24, 174.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 3 29.99 Fe 4 26.01 S 102 16.00 P 35 15.00 Mg 2 11.99 O 3661 8.00 N 3299 7.00 C 12303 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 784.4 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B 601 " pdb="FE2 SF4 B 601 " - pdb=" SG CYS B 384 " pdb="FE1 SF4 B 601 " - pdb=" SG CYS B 367 " pdb="FE4 SF4 B 601 " - pdb=" SG CYS B 287 " pdb="FE3 SF4 B 601 " - pdb=" SG CYS B 424 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 128 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 121 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 122 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 131 " pdb=" ZN C1502 " pdb="ZN ZN C1502 " - pdb=" SG CYS C1310 " pdb="ZN ZN C1502 " - pdb=" SG CYS C1283 " pdb="ZN ZN C1502 " - pdb=" SG CYS C1315 " pdb="ZN ZN C1502 " - pdb=" SG CYS C1286 " pdb=" ZN C1503 " pdb="ZN ZN C1503 " - pdb=" SG CYS C1374 " pdb="ZN ZN C1503 " - pdb=" SG CYS C1353 " pdb="ZN ZN C1503 " - pdb=" SG CYS C1348 " pdb="ZN ZN C1503 " - pdb=" SG CYS C1371 " Number of angles added : 18 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4398 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 19 sheets defined 48.1% alpha, 15.3% beta 2 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'A' and resid 5 through 7 No H-bonds generated for 'chain 'A' and resid 5 through 7' Processing helix chain 'A' and resid 8 through 20 removed outlier: 3.962A pdb=" N LYS A 14 " --> pdb=" O PRO A 10 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU A 15 " --> pdb=" O GLU A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 32 removed outlier: 3.608A pdb=" N LEU A 30 " --> pdb=" O TYR A 26 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR A 32 " --> pdb=" O ARG A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 35 No H-bonds generated for 'chain 'A' and resid 33 through 35' Processing helix chain 'A' and resid 50 through 52 No H-bonds generated for 'chain 'A' and resid 50 through 52' Processing helix chain 'A' and resid 62 through 72 removed outlier: 3.900A pdb=" N MET A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'A' and resid 113 through 116 removed outlier: 3.659A pdb=" N ASP A 116 " --> pdb=" O THR A 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 113 through 116' Processing helix chain 'A' and resid 128 through 146 removed outlier: 4.254A pdb=" N THR A 133 " --> pdb=" O PRO A 129 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU A 134 " --> pdb=" O LYS A 130 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N MET A 135 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR A 136 " --> pdb=" O TRP A 132 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE A 141 " --> pdb=" O MET A 137 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 177 removed outlier: 3.605A pdb=" N LYS A 176 " --> pdb=" O SER A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 189 removed outlier: 3.627A pdb=" N LEU A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 227 removed outlier: 3.611A pdb=" N SER A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE A 216 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR A 222 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLU A 224 " --> pdb=" O LYS A 220 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N GLU A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 247 removed outlier: 4.474A pdb=" N LYS A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE A 243 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 246 " --> pdb=" O LYS A 242 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 247 " --> pdb=" O ILE A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 250 No H-bonds generated for 'chain 'A' and resid 248 through 250' Processing helix chain 'A' and resid 251 through 261 removed outlier: 3.618A pdb=" N GLN A 257 " --> pdb=" O ASP A 253 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 283 Processing helix chain 'A' and resid 291 through 302 removed outlier: 3.726A pdb=" N ILE A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N MET A 297 " --> pdb=" O GLU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 312 removed outlier: 4.014A pdb=" N SER A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLY A 312 " --> pdb=" O ASN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 342 removed outlier: 4.210A pdb=" N VAL A 339 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ASP A 340 " --> pdb=" O GLN A 337 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 347 Processing helix chain 'A' and resid 349 through 359 Processing helix chain 'A' and resid 388 through 410 removed outlier: 3.894A pdb=" N VAL A 394 " --> pdb=" O PRO A 390 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N PHE A 395 " --> pdb=" O TYR A 391 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 63 removed outlier: 3.511A pdb=" N ALA B 46 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 81 removed outlier: 3.570A pdb=" N GLN B 71 " --> pdb=" O THR B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 108 removed outlier: 3.628A pdb=" N PHE B 104 " --> pdb=" O HIS B 100 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU B 108 " --> pdb=" O PHE B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 134 removed outlier: 3.996A pdb=" N ARG B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N TRP B 119 " --> pdb=" O GLU B 115 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN B 123 " --> pdb=" O TRP B 119 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE B 134 " --> pdb=" O PHE B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 147 removed outlier: 3.501A pdb=" N PHE B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 162 Processing helix chain 'B' and resid 162 through 170 Processing helix chain 'B' and resid 191 through 196 removed outlier: 3.509A pdb=" N ARG B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 236 removed outlier: 3.640A pdb=" N ILE B 217 " --> pdb=" O ASP B 213 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA B 224 " --> pdb=" O ASN B 220 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS B 225 " --> pdb=" O GLU B 221 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG B 235 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER B 236 " --> pdb=" O LEU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 242 removed outlier: 3.846A pdb=" N SER B 242 " --> pdb=" O PRO B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 252 Processing helix chain 'B' and resid 275 through 283 removed outlier: 3.536A pdb=" N THR B 281 " --> pdb=" O ASP B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 299 Processing helix chain 'B' and resid 302 through 317 removed outlier: 3.758A pdb=" N GLY B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 333 removed outlier: 3.665A pdb=" N LYS B 333 " --> pdb=" O GLN B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 345 removed outlier: 3.729A pdb=" N PHE B 341 " --> pdb=" O ASP B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 353 removed outlier: 3.772A pdb=" N PHE B 353 " --> pdb=" O ILE B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 373 Processing helix chain 'B' and resid 384 through 389 Processing helix chain 'B' and resid 390 through 400 removed outlier: 5.121A pdb=" N GLN B 396 " --> pdb=" O GLU B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 417 Processing helix chain 'B' and resid 419 through 433 removed outlier: 3.612A pdb=" N ALA B 423 " --> pdb=" O HIS B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 456 removed outlier: 3.572A pdb=" N ILE B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 420 removed outlier: 3.754A pdb=" N VAL C 413 " --> pdb=" O SER C 409 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP C 418 " --> pdb=" O TYR C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 425 Processing helix chain 'C' and resid 482 through 492 Processing helix chain 'C' and resid 522 through 524 No H-bonds generated for 'chain 'C' and resid 522 through 524' Processing helix chain 'C' and resid 597 through 606 Processing helix chain 'C' and resid 614 through 630 removed outlier: 3.701A pdb=" N HIS C 627 " --> pdb=" O LEU C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 642 through 655 Processing helix chain 'C' and resid 658 through 663 Processing helix chain 'C' and resid 679 through 685 Processing helix chain 'C' and resid 693 through 701 Processing helix chain 'C' and resid 707 through 716 Processing helix chain 'C' and resid 725 through 733 removed outlier: 3.673A pdb=" N GLN C 729 " --> pdb=" O GLU C 726 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER C 733 " --> pdb=" O ASN C 730 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 760 Processing helix chain 'C' and resid 760 through 773 removed outlier: 3.593A pdb=" N LEU C 764 " --> pdb=" O ASN C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 775 through 780 removed outlier: 3.608A pdb=" N THR C 779 " --> pdb=" O ILE C 775 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU C 780 " --> pdb=" O MET C 776 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 775 through 780' Processing helix chain 'C' and resid 784 through 799 removed outlier: 3.647A pdb=" N ASN C 788 " --> pdb=" O ARG C 784 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN C 799 " --> pdb=" O ALA C 795 " (cutoff:3.500A) Processing helix chain 'C' and resid 863 through 873 Processing helix chain 'C' and resid 909 through 931 removed outlier: 3.889A pdb=" N ARG C 913 " --> pdb=" O GLY C 909 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS C 917 " --> pdb=" O ARG C 913 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU C 918 " --> pdb=" O GLU C 914 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN C 931 " --> pdb=" O GLN C 927 " (cutoff:3.500A) Processing helix chain 'C' and resid 935 through 959 removed outlier: 3.582A pdb=" N LEU C 940 " --> pdb=" O PRO C 936 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET C 956 " --> pdb=" O THR C 952 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N TYR C 957 " --> pdb=" O ALA C 953 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY C 958 " --> pdb=" O ASN C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 960 through 962 No H-bonds generated for 'chain 'C' and resid 960 through 962' Processing helix chain 'C' and resid 969 through 994 removed outlier: 3.879A pdb=" N ALA C 973 " --> pdb=" O ALA C 969 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET C 994 " --> pdb=" O MET C 990 " (cutoff:3.500A) Processing helix chain 'C' and resid 1014 through 1033 removed outlier: 3.525A pdb=" N VAL C1018 " --> pdb=" O ASN C1014 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU C1032 " --> pdb=" O GLU C1028 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N TYR C1033 " --> pdb=" O VAL C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1077 through 1081 removed outlier: 3.513A pdb=" N VAL C1080 " --> pdb=" O LEU C1077 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG C1081 " --> pdb=" O ASP C1078 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1077 through 1081' Processing helix chain 'C' and resid 1085 through 1100 Processing helix chain 'C' and resid 1104 through 1126 removed outlier: 3.698A pdb=" N ILE C1108 " --> pdb=" O SER C1104 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL C1109 " --> pdb=" O ARG C1105 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU C1110 " --> pdb=" O ASP C1106 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C1124 " --> pdb=" O GLY C1120 " (cutoff:3.500A) Processing helix chain 'C' and resid 1129 through 1134 removed outlier: 3.518A pdb=" N GLN C1132 " --> pdb=" O PRO C1129 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU C1134 " --> pdb=" O SER C1131 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1146 removed outlier: 3.544A pdb=" N TYR C1146 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 1148 through 1151 Processing helix chain 'C' and resid 1152 through 1164 Processing helix chain 'C' and resid 1187 through 1190 Processing helix chain 'C' and resid 1194 through 1198 removed outlier: 3.736A pdb=" N LEU C1198 " --> pdb=" O PRO C1195 " (cutoff:3.500A) Processing helix chain 'C' and resid 1207 through 1214 removed outlier: 3.618A pdb=" N TYR C1211 " --> pdb=" O ASP C1207 " (cutoff:3.500A) Processing helix chain 'C' and resid 1215 through 1224 removed outlier: 4.190A pdb=" N VAL C1219 " --> pdb=" O GLN C1215 " (cutoff:3.500A) Processing helix chain 'C' and resid 1231 through 1240 Processing helix chain 'C' and resid 1269 through 1273 Processing helix chain 'C' and resid 1299 through 1303 removed outlier: 3.674A pdb=" N ASP C1302 " --> pdb=" O SER C1299 " (cutoff:3.500A) Processing helix chain 'C' and resid 1322 through 1343 Processing helix chain 'C' and resid 1384 through 1399 removed outlier: 3.900A pdb=" N PHE C1399 " --> pdb=" O TYR C1395 " (cutoff:3.500A) Processing helix chain 'C' and resid 1400 through 1406 removed outlier: 3.697A pdb=" N GLU C1406 " --> pdb=" O GLU C1402 " (cutoff:3.500A) Processing helix chain 'C' and resid 1410 through 1421 removed outlier: 3.642A pdb=" N PHE C1421 " --> pdb=" O LEU C1417 " (cutoff:3.500A) Processing helix chain 'C' and resid 1423 through 1443 removed outlier: 4.001A pdb=" N PHE C1440 " --> pdb=" O THR C1436 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ARG C1443 " --> pdb=" O GLN C1439 " (cutoff:3.500A) Processing helix chain 'C' and resid 1451 through 1456 Processing helix chain 'D' and resid 158 through 164 removed outlier: 3.533A pdb=" N ARG D 164 " --> pdb=" O LYS D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 236 removed outlier: 3.968A pdb=" N ILE D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ARG D 217 " --> pdb=" O LEU D 213 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLU D 218 " --> pdb=" O PRO D 214 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL D 219 " --> pdb=" O ASP D 215 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU D 227 " --> pdb=" O LYS D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 268 No H-bonds generated for 'chain 'D' and resid 266 through 268' Processing helix chain 'D' and resid 333 through 337 removed outlier: 3.861A pdb=" N PHE D 337 " --> pdb=" O ASP D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 371 Processing helix chain 'D' and resid 386 through 391 removed outlier: 3.647A pdb=" N GLU D 390 " --> pdb=" O HIS D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 413 removed outlier: 3.641A pdb=" N ILE D 409 " --> pdb=" O CYS D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 451 removed outlier: 3.631A pdb=" N LYS D 451 " --> pdb=" O ARG D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 482 removed outlier: 3.807A pdb=" N ALA D 482 " --> pdb=" O PHE D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 505 Processing helix chain 'D' and resid 521 through 529 removed outlier: 3.828A pdb=" N TYR D 526 " --> pdb=" O TYR D 522 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N VAL D 527 " --> pdb=" O GLU D 523 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 58 removed outlier: 5.639A pdb=" N ARG A 56 " --> pdb=" O PHE A 47 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N PHE A 47 " --> pdb=" O ARG A 56 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLU A 44 " --> pdb=" O GLY A 81 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS A 77 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU A 103 " --> pdb=" O VAL A 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 58 removed outlier: 5.639A pdb=" N ARG A 56 " --> pdb=" O PHE A 47 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N PHE A 47 " --> pdb=" O ARG A 56 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLU A 44 " --> pdb=" O GLY A 81 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS A 77 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 317 " --> pdb=" O ILE A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 106 through 111 removed outlier: 3.650A pdb=" N ILE A 110 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL A 165 " --> pdb=" O ILE A 110 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 36 through 38 Processing sheet with id=AA5, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.786A pdb=" N TYR B 201 " --> pdb=" O TYR B 208 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 516 through 520 removed outlier: 9.753A pdb=" N VAL C 516 " --> pdb=" O HIS C 373 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N SER C 375 " --> pdb=" O VAL C 516 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N ALA C 518 " --> pdb=" O SER C 375 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N CYS C 377 " --> pdb=" O ALA C 518 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ALA C 520 " --> pdb=" O CYS C 377 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N MET C 379 " --> pdb=" O ALA C 520 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR C 372 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE C 367 " --> pdb=" O THR C 372 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N VAL C 358 " --> pdb=" O GLU C 350 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N GLU C 350 " --> pdb=" O VAL C 358 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N PHE C 360 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ALA C 348 " --> pdb=" O PHE C 360 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N PHE C 362 " --> pdb=" O LEU C 346 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N TRP C 366 " --> pdb=" O HIS C 342 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N HIS C 342 " --> pdb=" O TRP C 366 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TRP C 498 " --> pdb=" O ILE C 529 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 431 through 438 removed outlier: 3.534A pdb=" N VAL C 435 " --> pdb=" O TYR C 452 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N GLU C 451 " --> pdb=" O PRO C 391 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N HIS C 475 " --> pdb=" O LEU C 390 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 609 through 611 removed outlier: 8.769A pdb=" N GLU C 610 " --> pdb=" O HIS C 582 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N CYS C 584 " --> pdb=" O GLU C 610 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE C 557 " --> pdb=" O MET C 547 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N MET C 547 " --> pdb=" O ILE C 557 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA C 559 " --> pdb=" O LYS C 545 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER C 567 " --> pdb=" O LEU C 537 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LEU C 537 " --> pdb=" O SER C 567 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE C 542 " --> pdb=" O VAL C 635 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 850 through 852 removed outlier: 7.254A pdb=" N LEU C 858 " --> pdb=" O ASP C1041 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL C1043 " --> pdb=" O ILE C 856 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE C 856 " --> pdb=" O VAL C1043 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR C1000 " --> pdb=" O MET C1007 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASN C1009 " --> pdb=" O VAL C 998 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL C 998 " --> pdb=" O ASN C1009 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 850 through 852 removed outlier: 20.219A pdb=" N ILE C1040 " --> pdb=" O SER C1064 " (cutoff:3.500A) removed outlier: 16.565A pdb=" N SER C1064 " --> pdb=" O ILE C1040 " (cutoff:3.500A) removed outlier: 12.656A pdb=" N GLY C1042 " --> pdb=" O PRO C1062 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N PHE C1044 " --> pdb=" O VAL C1060 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL C1060 " --> pdb=" O PHE C1044 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N SER C1046 " --> pdb=" O LEU C1058 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LYS C1054 " --> pdb=" O LEU C1050 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASN C1067 " --> pdb=" O THR C1063 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 1135 through 1138 Processing sheet with id=AB3, first strand: chain 'C' and resid 1135 through 1138 removed outlier: 3.591A pdb=" N THR C1205 " --> pdb=" O GLN C1181 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 1296 through 1297 Processing sheet with id=AB5, first strand: chain 'C' and resid 1356 through 1357 Processing sheet with id=AB6, first strand: chain 'D' and resid 170 through 174 removed outlier: 6.710A pdb=" N VAL D 170 " --> pdb=" O ARG D 597 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ARG D 597 " --> pdb=" O VAL D 170 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N CYS D 375 " --> pdb=" O VAL D 421 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL D 423 " --> pdb=" O CYS D 375 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU D 377 " --> pdb=" O VAL D 423 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU D 420 " --> pdb=" O GLN D 454 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 193 through 195 removed outlier: 6.120A pdb=" N LEU D 538 " --> pdb=" O VAL D 557 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 247 through 259 removed outlier: 4.896A pdb=" N VAL D 270 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N LEU D 314 " --> pdb=" O GLN D 283 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ALA D 316 " --> pdb=" O PRO D 285 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ASP D 287 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N LYS D 318 " --> pdb=" O ASP D 287 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N GLU D 305 " --> pdb=" O THR D 317 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LEU D 319 " --> pdb=" O ILE D 303 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ILE D 303 " --> pdb=" O LEU D 319 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL D 302 " --> pdb=" O GLY D 255 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY D 255 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ASN D 308 " --> pdb=" O GLU D 249 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLU D 249 " --> pdb=" O ASN D 308 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 295 through 296 Processing sheet with id=AC1, first strand: chain 'D' and resid 563 through 564 812 hydrogen bonds defined for protein. 2304 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 5 hydrogen bonds 10 hydrogen bond angles 0 basepair planarities 2 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 3.94 Time building geometry restraints manager: 2.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 8166 1.42 - 1.63: 11589 1.63 - 1.85: 141 1.85 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 19908 Sorted by residual: bond pdb=" C3' DC F 16 " pdb=" C2' DC F 16 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" CA SER B 236 " pdb=" CB SER B 236 " ideal model delta sigma weight residual 1.526 1.483 0.043 1.36e-02 5.41e+03 9.78e+00 bond pdb=" C3' DG F 12 " pdb=" C2' DG F 12 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.27e+00 bond pdb=" C PRO B 238 " pdb=" O PRO B 238 " ideal model delta sigma weight residual 1.237 1.199 0.038 1.26e-02 6.30e+03 9.20e+00 bond pdb=" C3' DC F 17 " pdb=" C2' DC F 17 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.73e+00 ... (remaining 19903 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 26567 2.15 - 4.31: 426 4.31 - 6.46: 44 6.46 - 8.62: 9 8.62 - 10.77: 8 Bond angle restraints: 27054 Sorted by residual: angle pdb=" N VAL A 118 " pdb=" CA VAL A 118 " pdb=" C VAL A 118 " ideal model delta sigma weight residual 113.53 107.55 5.98 9.80e-01 1.04e+00 3.73e+01 angle pdb=" C MET C 394 " pdb=" N LYS C 395 " pdb=" CA LYS C 395 " ideal model delta sigma weight residual 122.64 113.80 8.84 1.70e+00 3.46e-01 2.70e+01 angle pdb=" N GLY C 405 " pdb=" CA GLY C 405 " pdb=" C GLY C 405 " ideal model delta sigma weight residual 113.18 123.95 -10.77 2.37e+00 1.78e-01 2.07e+01 angle pdb=" N PRO B 238 " pdb=" CA PRO B 238 " pdb=" C PRO B 238 " ideal model delta sigma weight residual 113.53 107.57 5.96 1.39e+00 5.18e-01 1.84e+01 angle pdb=" N3 DT F 20 " pdb=" C4 DT F 20 " pdb=" O4 DT F 20 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+01 ... (remaining 27049 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.26: 11563 31.26 - 62.51: 401 62.51 - 93.77: 50 93.77 - 125.02: 1 125.02 - 156.28: 3 Dihedral angle restraints: 12018 sinusoidal: 5218 harmonic: 6800 Sorted by residual: dihedral pdb=" C5' GTP E 1 " pdb=" O5' GTP E 1 " pdb=" PA GTP E 1 " pdb=" O3A GTP E 1 " ideal model delta sinusoidal sigma weight residual 69.27 -87.01 156.28 1 2.00e+01 2.50e-03 4.60e+01 dihedral pdb=" O3B GTP E 1 " pdb=" O3A GTP E 1 " pdb=" PB GTP E 1 " pdb=" PA GTP E 1 " ideal model delta sinusoidal sigma weight residual 291.08 154.29 136.78 1 2.00e+01 2.50e-03 4.15e+01 dihedral pdb=" O5' GTP E 1 " pdb=" O3A GTP E 1 " pdb=" PA GTP E 1 " pdb=" PB GTP E 1 " ideal model delta sinusoidal sigma weight residual -85.88 41.39 -127.26 1 2.00e+01 2.50e-03 3.85e+01 ... (remaining 12015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2692 0.073 - 0.145: 274 0.145 - 0.218: 6 0.218 - 0.291: 0 0.291 - 0.364: 1 Chirality restraints: 2973 Sorted by residual: chirality pdb=" P G E 2 " pdb=" OP1 G E 2 " pdb=" OP2 G E 2 " pdb=" O5' G E 2 " both_signs ideal model delta sigma weight residual True 2.41 -2.77 -0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" C3' G E 2 " pdb=" C4' G E 2 " pdb=" O3' G E 2 " pdb=" C2' G E 2 " both_signs ideal model delta sigma weight residual False -2.48 -2.65 0.17 2.00e-01 2.50e+01 7.31e-01 chirality pdb=" C3' GTP E 1 " pdb=" C2' GTP E 1 " pdb=" C4' GTP E 1 " pdb=" O3' GTP E 1 " both_signs ideal model delta sigma weight residual False -2.47 -2.64 0.17 2.00e-01 2.50e+01 7.18e-01 ... (remaining 2970 not shown) Planarity restraints: 3352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 235 " -0.295 9.50e-02 1.11e+02 1.32e-01 1.07e+01 pdb=" NE ARG B 235 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG B 235 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 235 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 235 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 232 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.86e+00 pdb=" C LEU B 232 " 0.049 2.00e-02 2.50e+03 pdb=" O LEU B 232 " -0.018 2.00e-02 2.50e+03 pdb=" N THR B 233 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 240 " 0.015 2.00e-02 2.50e+03 1.73e-02 7.48e+00 pdb=" CG TRP A 240 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP A 240 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP A 240 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 240 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 240 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 240 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 240 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 240 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP A 240 " -0.004 2.00e-02 2.50e+03 ... (remaining 3349 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 232 2.66 - 3.22: 17656 3.22 - 3.78: 28545 3.78 - 4.34: 38592 4.34 - 4.90: 62915 Nonbonded interactions: 147940 Sorted by model distance: nonbonded pdb=" O PRO D 559 " pdb=" OG1 THR D 570 " model vdw 2.101 3.040 nonbonded pdb=" O SER B 236 " pdb=" OG SER B 236 " model vdw 2.139 3.040 nonbonded pdb=" NZ LYS C 395 " pdb=" OG1 THR C 406 " model vdw 2.140 3.120 nonbonded pdb=" O ASN D 166 " pdb=" NH1 ARG D 597 " model vdw 2.177 3.120 nonbonded pdb=" OG SER D 461 " pdb=" OH TYR D 508 " model vdw 2.216 3.040 ... (remaining 147935 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 23.020 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19925 Z= 0.183 Angle : 0.720 22.443 27084 Z= 0.376 Chirality : 0.043 0.364 2973 Planarity : 0.005 0.132 3352 Dihedral : 15.423 156.279 7620 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.58 % Favored : 96.16 % Rotamer: Outliers : 0.19 % Allowed : 0.38 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.18), residues: 2290 helix: 0.76 (0.18), residues: 929 sheet: 0.49 (0.32), residues: 257 loop : -0.48 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 407 TYR 0.019 0.001 TYR A 159 PHE 0.026 0.001 PHE C 622 TRP 0.045 0.001 TRP A 240 HIS 0.015 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.18 (19908) covalent geometry : angle 0.66526 / 0.37 (27054) hydrogen bonds : bond 0.16135 / 10.68 ( 803) hydrogen bonds : angle 5.99467 / 4.31 ( 2314) metal coordination : bond 0.00772 / 0.42 ( 16) metal coordination : angle 8.28673 / 4.50 ( 30) Misc. bond : bond 0.04617 / 2.43 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 130 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 341 MET cc_start: -0.3467 (mtp) cc_final: -0.3690 (ttm) outliers start: 4 outliers final: 3 residues processed: 134 average time/residue: 0.1850 time to fit residues: 35.5079 Evaluate side-chains 68 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 237 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 50.0000 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.4980 chunk 200 optimal weight: 50.0000 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 ASN A 257 GLN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 GLN B 425 GLN C1215 GLN C1359 HIS ** C1391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.072081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.046061 restraints weight = 100545.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.047726 restraints weight = 49889.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.047556 restraints weight = 31360.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.047728 restraints weight = 33628.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.047786 restraints weight = 29601.542| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19925 Z= 0.167 Angle : 0.685 21.242 27084 Z= 0.330 Chirality : 0.043 0.171 2973 Planarity : 0.005 0.054 3352 Dihedral : 10.676 172.801 2869 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.41 % Favored : 96.33 % Rotamer: Outliers : 0.48 % Allowed : 5.63 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.18), residues: 2290 helix: 0.94 (0.17), residues: 948 sheet: 0.54 (0.33), residues: 254 loop : -0.49 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 86 TYR 0.020 0.001 TYR D 206 PHE 0.016 0.001 PHE B 42 TRP 0.027 0.001 TRP A 240 HIS 0.005 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (19908) covalent geometry : angle 0.63269 / 0.33 (27054) hydrogen bonds : bond 0.04873 / 3.16 ( 803) hydrogen bonds : angle 4.91543 / 3.53 ( 2314) metal coordination : bond 0.00616 / 0.32 ( 16) metal coordination : angle 7.93160 / 4.33 ( 30) Misc. bond : bond 0.01295 / 0.68 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8666 (tmm) REVERT: C 394 MET cc_start: 0.8027 (tpt) cc_final: 0.7626 (tpp) REVERT: C 461 MET cc_start: 0.8651 (mpp) cc_final: 0.8244 (mpp) REVERT: C 994 MET cc_start: 0.8704 (mtm) cc_final: 0.7894 (mtm) REVERT: D 498 ILE cc_start: 0.6409 (OUTLIER) cc_final: 0.5876 (tt) outliers start: 10 outliers final: 3 residues processed: 70 average time/residue: 0.1600 time to fit residues: 17.4346 Evaluate side-chains 64 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLN Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain D residue 498 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 50 optimal weight: 0.8980 chunk 26 optimal weight: 20.0000 chunk 38 optimal weight: 3.9990 chunk 228 optimal weight: 10.0000 chunk 161 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 133 optimal weight: 3.9990 chunk 217 optimal weight: 30.0000 chunk 110 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1290 ASN ** C1391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 558 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.070885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.043170 restraints weight = 101542.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.044917 restraints weight = 48987.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.046006 restraints weight = 32365.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.046636 restraints weight = 25637.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.046909 restraints weight = 22472.218| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19925 Z= 0.173 Angle : 0.637 19.091 27084 Z= 0.307 Chirality : 0.042 0.154 2973 Planarity : 0.004 0.053 3352 Dihedral : 10.732 179.666 2867 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.41 % Favored : 96.42 % Rotamer: Outliers : 0.62 % Allowed : 7.02 % Favored : 92.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.18), residues: 2290 helix: 1.09 (0.17), residues: 948 sheet: 0.56 (0.32), residues: 257 loop : -0.47 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 118 TYR 0.026 0.001 TYR C1446 PHE 0.020 0.001 PHE C 622 TRP 0.024 0.001 TRP A 240 HIS 0.008 0.001 HIS C 794 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (19908) covalent geometry : angle 0.59535 / 0.31 (27054) hydrogen bonds : bond 0.04367 / 2.79 ( 803) hydrogen bonds : angle 4.64207 / 3.31 ( 2314) metal coordination : bond 0.00682 / 0.33 ( 16) metal coordination : angle 6.87383 / 3.64 ( 30) Misc. bond : bond 0.00427 / 0.22 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.9084 (mmm) cc_final: 0.8422 (mmm) REVERT: B 307 MET cc_start: 0.8954 (mmm) cc_final: 0.8465 (mmm) REVERT: C 394 MET cc_start: 0.8033 (tpt) cc_final: 0.6853 (tpt) REVERT: C 461 MET cc_start: 0.8761 (mpp) cc_final: 0.8406 (mpp) REVERT: C 519 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.7750 (tmm) REVERT: C 994 MET cc_start: 0.8661 (mtm) cc_final: 0.8121 (mtm) REVERT: D 498 ILE cc_start: 0.6736 (OUTLIER) cc_final: 0.6193 (tt) outliers start: 13 outliers final: 3 residues processed: 73 average time/residue: 0.1454 time to fit residues: 16.8699 Evaluate side-chains 63 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 519 MET Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain D residue 498 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 117 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 215 optimal weight: 40.0000 chunk 229 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 0.0870 chunk 3 optimal weight: 0.4980 chunk 68 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 overall best weight: 1.4762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 ASN ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 HIS ** 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 = 0.3801 r_free = 0.3801 target = 0.071206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.043667 restraints weight = 100943.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.045386 restraints weight = 48353.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.046463 restraints weight = 31899.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.047084 restraints weight = 25146.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.047407 restraints weight = 22031.626| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 19925 Z= 0.116 Angle : 0.593 18.210 27084 Z= 0.282 Chirality : 0.041 0.143 2973 Planarity : 0.004 0.050 3352 Dihedral : 10.478 167.222 2863 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.06 % Favored : 96.77 % Rotamer: Outliers : 0.57 % Allowed : 8.07 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.18), residues: 2290 helix: 1.29 (0.17), residues: 941 sheet: 0.59 (0.33), residues: 245 loop : -0.38 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 118 TYR 0.015 0.001 TYR A 17 PHE 0.015 0.001 PHE B 42 TRP 0.018 0.001 TRP A 240 HIS 0.004 0.001 HIS D 479 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (19908) covalent geometry : angle 0.54874 / 0.28 (27054) hydrogen bonds : bond 0.03801 / 2.41 ( 803) hydrogen bonds : angle 4.47514 / 3.19 ( 2314) metal coordination : bond 0.00885 / 0.45 ( 16) metal coordination : angle 6.77025 / 3.56 ( 30) Misc. bond : bond 0.00126 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.9076 (mmm) cc_final: 0.8392 (mmm) REVERT: B 307 MET cc_start: 0.8938 (mmm) cc_final: 0.8398 (mmm) REVERT: C 394 MET cc_start: 0.8083 (tpt) cc_final: 0.6889 (tpt) REVERT: C 461 MET cc_start: 0.8627 (mpp) cc_final: 0.8336 (mpp) REVERT: C 519 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.7776 (tmm) REVERT: C 994 MET cc_start: 0.8634 (mtm) cc_final: 0.8093 (mtm) REVERT: C 1292 TYR cc_start: 0.7525 (m-80) cc_final: 0.7253 (m-80) REVERT: D 498 ILE cc_start: 0.6716 (OUTLIER) cc_final: 0.6212 (tt) outliers start: 12 outliers final: 5 residues processed: 68 average time/residue: 0.1387 time to fit residues: 15.3060 Evaluate side-chains 64 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 519 MET Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 1375 MET Chi-restraints excluded: chain D residue 498 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 102 optimal weight: 8.9990 chunk 211 optimal weight: 50.0000 chunk 39 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 169 optimal weight: 50.0000 chunk 47 optimal weight: 3.9990 chunk 212 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN ** B 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 794 HIS C1290 ASN ** C1391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 HIS ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.070377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.046488 restraints weight = 100627.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.045671 restraints weight = 55701.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.045855 restraints weight = 42338.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.046020 restraints weight = 37772.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.046210 restraints weight = 33185.794| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19925 Z= 0.124 Angle : 0.586 17.644 27084 Z= 0.281 Chirality : 0.041 0.164 2973 Planarity : 0.004 0.049 3352 Dihedral : 10.202 149.075 2863 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.06 % Favored : 96.77 % Rotamer: Outliers : 0.86 % Allowed : 8.78 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.18), residues: 2290 helix: 1.46 (0.17), residues: 934 sheet: 0.61 (0.34), residues: 238 loop : -0.32 (0.19), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 118 TYR 0.011 0.001 TYR A 17 PHE 0.014 0.001 PHE B 42 TRP 0.016 0.001 TRP A 240 HIS 0.008 0.001 HIS D 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (19908) covalent geometry : angle 0.54746 / 0.28 (27054) hydrogen bonds : bond 0.03669 / 2.32 ( 803) hydrogen bonds : angle 4.39388 / 3.13 ( 2314) metal coordination : bond 0.00493 / 0.23 ( 16) metal coordination : angle 6.32182 / 3.28 ( 30) Misc. bond : bond 0.00079 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 307 MET cc_start: 0.8898 (mmm) cc_final: 0.8393 (mmm) REVERT: B 430 MET cc_start: 0.9047 (mpp) cc_final: 0.8692 (mpp) REVERT: C 394 MET cc_start: 0.8345 (tpt) cc_final: 0.7143 (tpt) REVERT: C 461 MET cc_start: 0.8532 (mpp) cc_final: 0.8296 (mpp) REVERT: C 519 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.7767 (tmm) REVERT: C 547 MET cc_start: 0.8592 (tmm) cc_final: 0.8309 (tmm) REVERT: C 994 MET cc_start: 0.8649 (mtm) cc_final: 0.8150 (mtm) REVERT: C 1292 TYR cc_start: 0.7185 (m-80) cc_final: 0.6933 (m-80) REVERT: D 498 ILE cc_start: 0.6367 (OUTLIER) cc_final: 0.5825 (tt) REVERT: D 518 MET cc_start: 0.7432 (ppp) cc_final: 0.6928 (ptm) outliers start: 18 outliers final: 9 residues processed: 72 average time/residue: 0.1163 time to fit residues: 13.8739 Evaluate side-chains 69 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 519 MET Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 1290 ASN Chi-restraints excluded: chain C residue 1375 MET Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 498 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 130 optimal weight: 0.7980 chunk 202 optimal weight: 7.9990 chunk 135 optimal weight: 0.0470 chunk 95 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 177 optimal weight: 30.0000 chunk 106 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 78 optimal weight: 0.2980 chunk 52 optimal weight: 4.9990 overall best weight: 1.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 GLN ** C1391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 HIS ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.070879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.043365 restraints weight = 100858.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.045079 restraints weight = 48727.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.046115 restraints weight = 32281.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.046799 restraints weight = 25642.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.047108 restraints weight = 22404.005| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19925 Z= 0.116 Angle : 0.570 17.361 27084 Z= 0.275 Chirality : 0.041 0.178 2973 Planarity : 0.004 0.047 3352 Dihedral : 10.057 136.637 2863 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.97 % Favored : 96.86 % Rotamer: Outliers : 0.81 % Allowed : 9.31 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.18), residues: 2290 helix: 1.52 (0.17), residues: 933 sheet: 0.62 (0.33), residues: 238 loop : -0.24 (0.19), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1443 TYR 0.009 0.001 TYR B 85 PHE 0.014 0.001 PHE B 42 TRP 0.014 0.001 TRP A 240 HIS 0.006 0.001 HIS A 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (19908) covalent geometry : angle 0.53084 / 0.27 (27054) hydrogen bonds : bond 0.03550 / 2.25 ( 803) hydrogen bonds : angle 4.34408 / 3.10 ( 2314) metal coordination : bond 0.00405 / 0.20 ( 16) metal coordination : angle 6.22420 / 3.22 ( 30) Misc. bond : bond 0.00020 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 307 MET cc_start: 0.8964 (mmm) cc_final: 0.8417 (mmm) REVERT: B 430 MET cc_start: 0.9021 (mpp) cc_final: 0.8614 (mpp) REVERT: C 394 MET cc_start: 0.8225 (tpt) cc_final: 0.7113 (tpt) REVERT: C 994 MET cc_start: 0.8620 (mtm) cc_final: 0.8099 (mtm) REVERT: C 1292 TYR cc_start: 0.7233 (m-80) cc_final: 0.6746 (m-80) REVERT: C 1375 MET cc_start: 0.5528 (OUTLIER) cc_final: 0.4934 (tpp) REVERT: D 498 ILE cc_start: 0.6575 (OUTLIER) cc_final: 0.6003 (tt) REVERT: D 518 MET cc_start: 0.7448 (ppp) cc_final: 0.7155 (ptm) outliers start: 17 outliers final: 8 residues processed: 71 average time/residue: 0.1307 time to fit residues: 15.1983 Evaluate side-chains 66 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 1375 MET Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 498 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 0.0170 chunk 128 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 200 optimal weight: 50.0000 chunk 188 optimal weight: 0.2980 chunk 100 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 chunk 110 optimal weight: 0.6980 overall best weight: 0.8022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1290 ASN ** C1391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 HIS ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.071220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.043738 restraints weight = 101423.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.045469 restraints weight = 48623.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.046549 restraints weight = 32137.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.047232 restraints weight = 25379.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.047538 restraints weight = 22185.890| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19925 Z= 0.097 Angle : 0.562 16.856 27084 Z= 0.269 Chirality : 0.041 0.164 2973 Planarity : 0.004 0.047 3352 Dihedral : 9.873 118.224 2862 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.93 % Favored : 96.90 % Rotamer: Outliers : 0.67 % Allowed : 10.17 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.18), residues: 2290 helix: 1.59 (0.18), residues: 933 sheet: 0.65 (0.33), residues: 238 loop : -0.19 (0.19), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 118 TYR 0.011 0.001 TYR B 85 PHE 0.014 0.001 PHE B 42 TRP 0.013 0.001 TRP A 240 HIS 0.006 0.001 HIS D 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.10 (19908) covalent geometry : angle 0.52323 / 0.27 (27054) hydrogen bonds : bond 0.03367 / 2.12 ( 803) hydrogen bonds : angle 4.28242 / 3.05 ( 2314) metal coordination : bond 0.00315 / 0.16 ( 16) metal coordination : angle 6.16353 / 3.18 ( 30) Misc. bond : bond 0.00030 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.9118 (mmm) cc_final: 0.8276 (mmm) REVERT: B 288 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8239 (mmt) REVERT: B 307 MET cc_start: 0.8937 (mmm) cc_final: 0.8379 (mmm) REVERT: B 430 MET cc_start: 0.8993 (mpp) cc_final: 0.8716 (mpp) REVERT: C 394 MET cc_start: 0.8235 (tpt) cc_final: 0.7696 (tpp) REVERT: C 547 MET cc_start: 0.8496 (tmm) cc_final: 0.8253 (tmm) REVERT: C 994 MET cc_start: 0.8596 (mtm) cc_final: 0.8084 (mtm) REVERT: C 1292 TYR cc_start: 0.7515 (m-80) cc_final: 0.6964 (m-80) REVERT: C 1375 MET cc_start: 0.5524 (OUTLIER) cc_final: 0.4945 (tpp) REVERT: D 498 ILE cc_start: 0.6576 (OUTLIER) cc_final: 0.5989 (tt) REVERT: D 518 MET cc_start: 0.7444 (ppp) cc_final: 0.7120 (ptm) outliers start: 14 outliers final: 6 residues processed: 64 average time/residue: 0.1248 time to fit residues: 13.9331 Evaluate side-chains 64 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 1375 MET Chi-restraints excluded: chain D residue 498 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 222 optimal weight: 2.9990 chunk 195 optimal weight: 8.9990 chunk 13 optimal weight: 0.0770 chunk 171 optimal weight: 9.9990 chunk 88 optimal weight: 0.0980 chunk 91 optimal weight: 0.5980 chunk 37 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 chunk 148 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 overall best weight: 1.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 794 HIS ** C1391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 HIS ** 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 = 0.3793 r_free = 0.3793 target = 0.070789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.043256 restraints weight = 100778.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.044957 restraints weight = 48581.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.045973 restraints weight = 32269.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.046475 restraints weight = 25658.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.046978 restraints weight = 22721.527| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 19925 Z= 0.126 Angle : 0.567 16.831 27084 Z= 0.273 Chirality : 0.041 0.184 2973 Planarity : 0.004 0.046 3352 Dihedral : 9.679 112.545 2862 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.10 % Favored : 96.72 % Rotamer: Outliers : 0.72 % Allowed : 10.50 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.18), residues: 2290 helix: 1.67 (0.18), residues: 928 sheet: 0.50 (0.31), residues: 267 loop : -0.20 (0.20), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1443 TYR 0.009 0.001 TYR C1446 PHE 0.014 0.001 PHE B 42 TRP 0.014 0.001 TRP A 240 HIS 0.007 0.001 HIS D 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (19908) covalent geometry : angle 0.53072 / 0.27 (27054) hydrogen bonds : bond 0.03426 / 2.16 ( 803) hydrogen bonds : angle 4.26904 / 3.03 ( 2314) metal coordination : bond 0.00426 / 0.21 ( 16) metal coordination : angle 6.04839 / 3.13 ( 30) Misc. bond : bond 0.00034 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.9164 (mmm) cc_final: 0.8333 (mmm) REVERT: B 288 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8295 (mmt) REVERT: B 307 MET cc_start: 0.8953 (mmm) cc_final: 0.8400 (mmm) REVERT: B 430 MET cc_start: 0.8987 (mpp) cc_final: 0.8689 (mpp) REVERT: C 394 MET cc_start: 0.8224 (tpt) cc_final: 0.7618 (tpp) REVERT: C 547 MET cc_start: 0.8535 (tmm) cc_final: 0.8276 (tmm) REVERT: C 994 MET cc_start: 0.8658 (mtm) cc_final: 0.8116 (mtm) REVERT: C 1292 TYR cc_start: 0.7464 (m-80) cc_final: 0.6987 (m-80) REVERT: C 1375 MET cc_start: 0.5538 (OUTLIER) cc_final: 0.4955 (tpp) REVERT: D 498 ILE cc_start: 0.6591 (OUTLIER) cc_final: 0.6000 (tt) REVERT: D 518 MET cc_start: 0.7469 (ppp) cc_final: 0.7151 (ptm) outliers start: 15 outliers final: 9 residues processed: 65 average time/residue: 0.1396 time to fit residues: 15.3331 Evaluate side-chains 66 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 1375 MET Chi-restraints excluded: chain D residue 498 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 213 optimal weight: 30.0000 chunk 105 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 125 optimal weight: 0.8980 chunk 144 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 chunk 95 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 chunk 218 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.070012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.046445 restraints weight = 100369.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.045481 restraints weight = 50867.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.045646 restraints weight = 45142.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.045844 restraints weight = 36894.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.046097 restraints weight = 32447.935| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19925 Z= 0.124 Angle : 0.577 16.604 27084 Z= 0.276 Chirality : 0.041 0.188 2973 Planarity : 0.004 0.046 3352 Dihedral : 9.557 108.189 2862 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.19 % Favored : 96.64 % Rotamer: Outliers : 0.72 % Allowed : 10.60 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.18), residues: 2290 helix: 1.71 (0.18), residues: 923 sheet: 0.52 (0.32), residues: 265 loop : -0.19 (0.20), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 276 TYR 0.009 0.001 TYR B 85 PHE 0.015 0.001 PHE B 42 TRP 0.015 0.001 TRP A 240 HIS 0.005 0.001 HIS A 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (19908) covalent geometry : angle 0.54087 / 0.28 (27054) hydrogen bonds : bond 0.03448 / 2.17 ( 803) hydrogen bonds : angle 4.24147 / 3.01 ( 2314) metal coordination : bond 0.00687 / 0.35 ( 16) metal coordination : angle 6.06312 / 3.16 ( 30) Misc. bond : bond 0.00034 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.9492 (mmp) cc_final: 0.9265 (mmp) REVERT: B 288 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.8289 (mmt) REVERT: B 307 MET cc_start: 0.8879 (mmm) cc_final: 0.8370 (mmm) REVERT: B 430 MET cc_start: 0.8944 (mpp) cc_final: 0.8619 (mpp) REVERT: C 394 MET cc_start: 0.8444 (tpt) cc_final: 0.7253 (tpt) REVERT: C 547 MET cc_start: 0.8801 (tmm) cc_final: 0.8523 (tmm) REVERT: C 994 MET cc_start: 0.8614 (mtm) cc_final: 0.8112 (mtm) REVERT: C 1292 TYR cc_start: 0.7020 (m-80) cc_final: 0.6808 (m-80) REVERT: C 1375 MET cc_start: 0.5435 (OUTLIER) cc_final: 0.4750 (tpp) REVERT: D 341 MET cc_start: -0.5612 (ttm) cc_final: -0.5944 (ttp) outliers start: 15 outliers final: 10 residues processed: 66 average time/residue: 0.1260 time to fit residues: 14.0113 Evaluate side-chains 65 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 1375 MET Chi-restraints excluded: chain D residue 403 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 142 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 172 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 133 optimal weight: 0.9980 chunk 212 optimal weight: 0.8980 chunk 102 optimal weight: 9.9990 chunk 168 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1439 GLN ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 479 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.070743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.046190 restraints weight = 100644.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.045254 restraints weight = 50779.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.045883 restraints weight = 38020.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.046021 restraints weight = 30311.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.046043 restraints weight = 29581.118| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19925 Z= 0.111 Angle : 0.575 16.410 27084 Z= 0.273 Chirality : 0.041 0.180 2973 Planarity : 0.004 0.046 3352 Dihedral : 9.543 107.364 2862 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.06 % Favored : 96.77 % Rotamer: Outliers : 0.57 % Allowed : 10.79 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.18), residues: 2290 helix: 1.75 (0.18), residues: 922 sheet: 0.49 (0.31), residues: 265 loop : -0.17 (0.20), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 385 TYR 0.010 0.001 TYR B 85 PHE 0.014 0.001 PHE B 42 TRP 0.014 0.001 TRP A 240 HIS 0.004 0.001 HIS A 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (19908) covalent geometry : angle 0.53901 / 0.27 (27054) hydrogen bonds : bond 0.03343 / 2.10 ( 803) hydrogen bonds : angle 4.21106 / 2.98 ( 2314) metal coordination : bond 0.00482 / 0.24 ( 16) metal coordination : angle 6.04472 / 3.14 ( 30) Misc. bond : bond 0.00029 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 288 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8302 (mmt) REVERT: B 307 MET cc_start: 0.8882 (mmm) cc_final: 0.8364 (mmm) REVERT: B 430 MET cc_start: 0.8966 (mpp) cc_final: 0.8625 (mpp) REVERT: C 394 MET cc_start: 0.8477 (tpt) cc_final: 0.7263 (tpt) REVERT: C 547 MET cc_start: 0.8819 (tmm) cc_final: 0.8522 (tmm) REVERT: C 994 MET cc_start: 0.8606 (mtm) cc_final: 0.8095 (mtm) REVERT: C 1292 TYR cc_start: 0.7109 (m-80) cc_final: 0.6846 (m-80) REVERT: C 1375 MET cc_start: 0.5448 (OUTLIER) cc_final: 0.4790 (tpp) outliers start: 12 outliers final: 10 residues processed: 61 average time/residue: 0.1179 time to fit residues: 12.2838 Evaluate side-chains 66 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 1375 MET Chi-restraints excluded: chain D residue 403 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 85 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 193 optimal weight: 9.9990 chunk 159 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 224 optimal weight: 8.9990 chunk 200 optimal weight: 0.0770 chunk 60 optimal weight: 0.9980 chunk 165 optimal weight: 3.9990 chunk 204 optimal weight: 40.0000 chunk 33 optimal weight: 1.9990 overall best weight: 2.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.069827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.042647 restraints weight = 101107.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.044320 restraints weight = 48832.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.045363 restraints weight = 32435.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.045950 restraints weight = 25728.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.046358 restraints weight = 22607.017| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19925 Z= 0.128 Angle : 0.576 16.585 27084 Z= 0.276 Chirality : 0.041 0.183 2973 Planarity : 0.004 0.046 3352 Dihedral : 9.550 106.150 2862 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.19 % Favored : 96.64 % Rotamer: Outliers : 0.53 % Allowed : 10.93 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.18), residues: 2290 helix: 1.77 (0.18), residues: 923 sheet: 0.48 (0.31), residues: 265 loop : -0.16 (0.20), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 453 TYR 0.008 0.001 TYR B 85 PHE 0.015 0.001 PHE B 42 TRP 0.014 0.001 TRP A 240 HIS 0.005 0.001 HIS A 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (19908) covalent geometry : angle 0.54112 / 0.28 (27054) hydrogen bonds : bond 0.03415 / 2.15 ( 803) hydrogen bonds : angle 4.21468 / 2.98 ( 2314) metal coordination : bond 0.00514 / 0.26 ( 16) metal coordination : angle 5.99915 / 3.11 ( 30) Misc. bond : bond 0.00030 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3717.59 seconds wall clock time: 64 minutes 48.31 seconds (3888.31 seconds total)