Starting phenix.real_space_refine on Tue Jun 17 13:02:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d9d_27258/06_2025/8d9d_27258.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d9d_27258/06_2025/8d9d_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8d9d_27258/06_2025/8d9d_27258.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d9d_27258/06_2025/8d9d_27258.map" model { file = "/net/cci-nas-00/data/ceres_data/8d9d_27258/06_2025/8d9d_27258.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d9d_27258/06_2025/8d9d_27258.cif" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.48, per 1000 atoms: 0.59 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: 5.27 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 5.87 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: 11.63 Time building geometry restraints manager: 6.04 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=" 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=" 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=" C2 GTP E 1 " pdb=" N3 GTP E 1 " ideal model delta sigma weight residual 1.380 1.329 0.051 2.00e-02 2.50e+03 6.43e+00 bond pdb=" N PRO B 238 " pdb=" CA PRO B 238 " ideal model delta sigma weight residual 1.472 1.444 0.028 1.32e-02 5.74e+03 4.38e+00 bond pdb=" C SER B 236 " pdb=" O SER B 236 " ideal model delta sigma weight residual 1.232 1.205 0.027 1.36e-02 5.41e+03 4.03e+00 ... (remaining 19903 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 26575 2.15 - 4.31: 418 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=" N ASP B 91 " pdb=" CA ASP B 91 " pdb=" C ASP B 91 " ideal model delta sigma weight residual 109.39 115.87 -6.48 1.59e+00 3.96e-01 1.66e+01 ... (remaining 27049 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.26: 11599 31.26 - 62.51: 415 62.51 - 93.77: 63 93.77 - 125.02: 1 125.02 - 156.28: 3 Dihedral angle restraints: 12081 sinusoidal: 5281 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 12078 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2707 0.073 - 0.145: 259 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: 11.120 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: 0.020 Extract box with map and model: 0.800 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 62.710 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 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= 0.149 Angle : 0.712 22.443 27084 Z= 0.355 Chirality : 0.042 0.364 2973 Planarity : 0.005 0.132 3352 Dihedral : 15.760 156.279 7683 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (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 TRP 0.045 0.001 TRP A 240 HIS 0.015 0.001 HIS A 315 PHE 0.026 0.001 PHE C 622 TYR 0.019 0.001 TYR A 159 ARG 0.009 0.001 ARG D 407 Details of bonding type rmsd hydrogen bonds : bond 0.16135 ( 803) hydrogen bonds : angle 5.99467 ( 2314) metal coordination : bond 0.00772 ( 16) metal coordination : angle 8.28673 ( 30) covalent geometry : bond 0.00275 (19908) covalent geometry : angle 0.65722 (27054) Misc. bond : bond 0.04617 ( 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 : 3.096 Fit side-chains 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: -0.3691 (ttm) outliers start: 4 outliers final: 3 residues processed: 134 average time/residue: 0.5649 time to fit residues: 113.3547 Evaluate side-chains 67 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 2.655 ------------------------------------------------------------------------------- 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 195 optimal weight: 3.9990 chunk 175 optimal weight: 50.0000 chunk 97 optimal weight: 9.9990 chunk 59 optimal weight: 8.9990 chunk 118 optimal weight: 0.0050 chunk 93 optimal weight: 10.0000 chunk 181 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 209 optimal weight: 6.9990 overall best weight: 3.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 ASN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN B 308 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.070678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.043464 restraints weight = 100919.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.045100 restraints weight = 49164.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.046077 restraints weight = 32787.085| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 19925 Z= 0.217 Angle : 0.708 20.692 27084 Z= 0.339 Chirality : 0.044 0.154 2973 Planarity : 0.005 0.054 3352 Dihedral : 12.124 171.952 2932 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.49 % Favored : 96.24 % Rotamer: Outliers : 0.43 % Allowed : 6.54 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.18), residues: 2290 helix: 0.89 (0.17), residues: 949 sheet: 0.45 (0.31), residues: 262 loop : -0.51 (0.19), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 240 HIS 0.007 0.001 HIS D 369 PHE 0.018 0.002 PHE B 42 TYR 0.014 0.001 TYR B 427 ARG 0.011 0.001 ARG C1247 Details of bonding type rmsd hydrogen bonds : bond 0.04686 ( 803) hydrogen bonds : angle 4.83840 ( 2314) metal coordination : bond 0.00938 ( 16) metal coordination : angle 7.65844 ( 30) covalent geometry : bond 0.00492 (19908) covalent geometry : angle 0.66142 (27054) Misc. bond : bond 0.00043 ( 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: 9 poor density : 65 time to evaluate : 2.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8365 (tmm) REVERT: C 394 MET cc_start: 0.8189 (tpt) cc_final: 0.7364 (tpt) REVERT: C 461 MET cc_start: 0.8717 (mpp) cc_final: 0.8288 (mpp) REVERT: C 994 MET cc_start: 0.8727 (mtm) cc_final: 0.8015 (mtm) REVERT: C 1292 TYR cc_start: 0.7238 (m-80) cc_final: 0.6995 (m-80) REVERT: D 498 ILE cc_start: 0.6464 (OUTLIER) cc_final: 0.6043 (tt) outliers start: 9 outliers final: 2 residues processed: 70 average time/residue: 0.4233 time to fit residues: 50.6526 Evaluate side-chains 60 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 2.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 170 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 208 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 60 optimal weight: 0.2980 chunk 3 optimal weight: 2.9990 chunk 184 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 203 optimal weight: 20.0000 chunk 198 optimal weight: 20.0000 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** B 374 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 = 0.3797 r_free = 0.3797 target = 0.070783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.043701 restraints weight = 98941.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.045330 restraints weight = 47671.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.046392 restraints weight = 31673.707| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19925 Z= 0.131 Angle : 0.597 17.707 27084 Z= 0.285 Chirality : 0.041 0.142 2973 Planarity : 0.004 0.053 3352 Dihedral : 11.884 173.909 2930 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.14 % Favored : 96.64 % Rotamer: Outliers : 0.62 % Allowed : 7.45 % Favored : 91.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.18), residues: 2290 helix: 1.14 (0.17), residues: 944 sheet: 0.56 (0.32), residues: 257 loop : -0.37 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 240 HIS 0.004 0.001 HIS A 42 PHE 0.015 0.001 PHE B 42 TYR 0.013 0.001 TYR D 206 ARG 0.016 0.001 ARG C 682 Details of bonding type rmsd hydrogen bonds : bond 0.03986 ( 803) hydrogen bonds : angle 4.55330 ( 2314) metal coordination : bond 0.00460 ( 16) metal coordination : angle 6.70933 ( 30) covalent geometry : bond 0.00293 (19908) covalent geometry : angle 0.55378 (27054) Misc. bond : bond 0.00041 ( 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 76 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 2.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.8708 (ppp) cc_final: 0.8403 (tmm) REVERT: A 73 MET cc_start: 0.9366 (OUTLIER) cc_final: 0.9075 (mpp) REVERT: A 137 MET cc_start: 0.9102 (mmm) cc_final: 0.8869 (mmm) REVERT: C 394 MET cc_start: 0.8184 (tpt) cc_final: 0.7210 (tpt) REVERT: C 461 MET cc_start: 0.8777 (mpp) cc_final: 0.8390 (mpp) REVERT: C 519 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.7671 (tmm) REVERT: C 994 MET cc_start: 0.8667 (mtm) cc_final: 0.8135 (mtm) REVERT: C 1292 TYR cc_start: 0.7211 (m-80) cc_final: 0.6540 (m-80) REVERT: C 1375 MET cc_start: 0.5263 (OUTLIER) cc_final: 0.4636 (tpp) REVERT: D 498 ILE cc_start: 0.6707 (OUTLIER) cc_final: 0.6205 (tt) outliers start: 13 outliers final: 4 residues processed: 69 average time/residue: 0.3181 time to fit residues: 36.3440 Evaluate side-chains 64 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 2.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 336 MET 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 C residue 1375 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 149 optimal weight: 0.2980 chunk 119 optimal weight: 10.0000 chunk 163 optimal weight: 4.9990 chunk 173 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 147 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 19 optimal weight: 8.9990 chunk 80 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3805 r_free = 0.3805 target = 0.071221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.043790 restraints weight = 101011.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.045545 restraints weight = 48378.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.046643 restraints weight = 31946.870| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19925 Z= 0.100 Angle : 0.564 16.634 27084 Z= 0.268 Chirality : 0.040 0.138 2973 Planarity : 0.004 0.050 3352 Dihedral : 11.455 149.681 2926 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.06 % Favored : 96.77 % Rotamer: Outliers : 0.95 % Allowed : 8.59 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.18), residues: 2290 helix: 1.39 (0.17), residues: 931 sheet: 0.65 (0.33), residues: 238 loop : -0.29 (0.19), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 240 HIS 0.006 0.001 HIS D 278 PHE 0.014 0.001 PHE B 42 TYR 0.012 0.001 TYR B 427 ARG 0.004 0.000 ARG B 118 Details of bonding type rmsd hydrogen bonds : bond 0.03439 ( 803) hydrogen bonds : angle 4.35414 ( 2314) metal coordination : bond 0.00316 ( 16) metal coordination : angle 6.41746 ( 30) covalent geometry : bond 0.00212 (19908) covalent geometry : angle 0.52276 (27054) Misc. bond : bond 0.00025 ( 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 78 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 2.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 394 MET cc_start: 0.8222 (tpt) cc_final: 0.7167 (tpt) REVERT: C 461 MET cc_start: 0.8601 (mpp) cc_final: 0.8304 (mpp) REVERT: C 519 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.7692 (tmm) REVERT: C 670 MET cc_start: 0.8959 (pmm) cc_final: 0.8521 (ptp) REVERT: C 994 MET cc_start: 0.8673 (mtm) cc_final: 0.8135 (mtm) REVERT: C 1292 TYR cc_start: 0.7226 (m-80) cc_final: 0.6432 (m-80) REVERT: C 1375 MET cc_start: 0.5553 (OUTLIER) cc_final: 0.4971 (tpp) REVERT: D 498 ILE cc_start: 0.6688 (OUTLIER) cc_final: 0.6138 (tt) outliers start: 20 outliers final: 8 residues processed: 72 average time/residue: 0.3338 time to fit residues: 41.8534 Evaluate side-chains 66 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 2.361 ------------------------------------------------------------------------------- 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 1272 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 150 optimal weight: 3.9990 chunk 225 optimal weight: 20.0000 chunk 151 optimal weight: 0.6980 chunk 36 optimal weight: 6.9990 chunk 80 optimal weight: 0.7980 chunk 169 optimal weight: 30.0000 chunk 62 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 HIS ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.070816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.043263 restraints weight = 102072.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.045008 restraints weight = 49001.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.046092 restraints weight = 32416.218| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2256 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= 0.117 Angle : 0.566 16.533 27084 Z= 0.270 Chirality : 0.041 0.142 2973 Planarity : 0.004 0.049 3352 Dihedral : 11.290 130.120 2926 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.06 % Favored : 96.77 % Rotamer: Outliers : 0.81 % Allowed : 9.36 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.18), residues: 2290 helix: 1.46 (0.17), residues: 937 sheet: 0.54 (0.32), residues: 257 loop : -0.25 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 240 HIS 0.004 0.001 HIS A 154 PHE 0.014 0.001 PHE B 42 TYR 0.014 0.001 TYR A 17 ARG 0.002 0.000 ARG B 118 Details of bonding type rmsd hydrogen bonds : bond 0.03465 ( 803) hydrogen bonds : angle 4.32379 ( 2314) metal coordination : bond 0.00598 ( 16) metal coordination : angle 6.20185 ( 30) covalent geometry : bond 0.00263 (19908) covalent geometry : angle 0.52773 (27054) Misc. bond : bond 0.00013 ( 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: 17 poor density : 60 time to evaluate : 2.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.9158 (mmm) cc_final: 0.8338 (mmm) REVERT: B 430 MET cc_start: 0.9025 (mpp) cc_final: 0.8671 (mpp) REVERT: C 394 MET cc_start: 0.8285 (tpt) cc_final: 0.7205 (tpt) REVERT: C 461 MET cc_start: 0.8474 (mpp) cc_final: 0.8238 (mpp) REVERT: C 519 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.7643 (tmm) REVERT: C 994 MET cc_start: 0.8685 (mtm) cc_final: 0.8157 (mtm) REVERT: C 1292 TYR cc_start: 0.7213 (m-80) cc_final: 0.6474 (m-80) REVERT: C 1375 MET cc_start: 0.5486 (OUTLIER) cc_final: 0.4897 (tpp) REVERT: D 498 ILE cc_start: 0.6656 (OUTLIER) cc_final: 0.6087 (tt) outliers start: 17 outliers final: 9 residues processed: 71 average time/residue: 0.3071 time to fit residues: 36.7340 Evaluate side-chains 67 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 2.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain B residue 336 MET 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 1272 LYS 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 53 optimal weight: 0.0060 chunk 121 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 227 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 106 optimal weight: 0.9980 chunk 229 optimal weight: 8.9990 chunk 170 optimal weight: 0.0970 chunk 60 optimal weight: 0.0070 chunk 202 optimal weight: 10.0000 overall best weight: 1.0214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3802 r_free = 0.3802 target = 0.071099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.043595 restraints weight = 101689.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.045321 restraints weight = 48879.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.046398 restraints weight = 32264.813| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19925 Z= 0.097 Angle : 0.556 16.127 27084 Z= 0.265 Chirality : 0.040 0.157 2973 Planarity : 0.004 0.048 3352 Dihedral : 11.030 112.679 2925 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.93 % Favored : 96.90 % Rotamer: Outliers : 0.86 % Allowed : 9.50 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.18), residues: 2290 helix: 1.60 (0.18), residues: 928 sheet: 0.49 (0.31), residues: 267 loop : -0.20 (0.20), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 240 HIS 0.015 0.001 HIS D 278 PHE 0.014 0.001 PHE B 42 TYR 0.010 0.001 TYR B 85 ARG 0.004 0.000 ARG B 118 Details of bonding type rmsd hydrogen bonds : bond 0.03231 ( 803) hydrogen bonds : angle 4.23942 ( 2314) metal coordination : bond 0.00374 ( 16) metal coordination : angle 6.03962 ( 30) covalent geometry : bond 0.00212 (19908) covalent geometry : angle 0.51904 (27054) Misc. bond : bond 0.00025 ( 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 75 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 2.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 288 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.8266 (mmt) REVERT: B 430 MET cc_start: 0.8969 (mpp) cc_final: 0.8506 (mpp) REVERT: C 394 MET cc_start: 0.8243 (tpt) cc_final: 0.7704 (tpp) REVERT: C 519 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.7628 (tmm) REVERT: C 547 MET cc_start: 0.8562 (tmm) cc_final: 0.8286 (tmm) REVERT: C 994 MET cc_start: 0.8657 (mtm) cc_final: 0.8116 (mtm) REVERT: C 1292 TYR cc_start: 0.7175 (m-80) cc_final: 0.6592 (m-80) REVERT: C 1375 MET cc_start: 0.5661 (OUTLIER) cc_final: 0.5143 (tpp) REVERT: C 1443 ARG cc_start: 0.8857 (mtm-85) cc_final: 0.8564 (ptt-90) outliers start: 18 outliers final: 9 residues processed: 69 average time/residue: 0.3060 time to fit residues: 36.2390 Evaluate side-chains 68 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 2.250 ------------------------------------------------------------------------------- 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 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 1272 LYS Chi-restraints excluded: chain C residue 1375 MET Chi-restraints excluded: chain D residue 403 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 2 optimal weight: 1.9990 chunk 142 optimal weight: 8.9990 chunk 217 optimal weight: 20.0000 chunk 41 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 163 optimal weight: 0.6980 chunk 11 optimal weight: 8.9990 chunk 230 optimal weight: 4.9990 chunk 165 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 188 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 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 = 0.3805 r_free = 0.3805 target = 0.071236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.045218 restraints weight = 100368.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.046230 restraints weight = 53791.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.045996 restraints weight = 33640.990| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 19925 Z= 0.097 Angle : 0.547 15.824 27084 Z= 0.260 Chirality : 0.040 0.155 2973 Planarity : 0.004 0.047 3352 Dihedral : 10.871 108.597 2925 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.06 % Favored : 96.77 % Rotamer: Outliers : 0.48 % Allowed : 10.60 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.18), residues: 2290 helix: 1.65 (0.18), residues: 937 sheet: 0.51 (0.31), residues: 265 loop : -0.19 (0.20), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 240 HIS 0.003 0.001 HIS B 443 PHE 0.014 0.001 PHE B 42 TYR 0.010 0.001 TYR A 17 ARG 0.003 0.000 ARG B 118 Details of bonding type rmsd hydrogen bonds : bond 0.03081 ( 803) hydrogen bonds : angle 4.15982 ( 2314) metal coordination : bond 0.00340 ( 16) metal coordination : angle 5.90893 ( 30) covalent geometry : bond 0.00212 (19908) covalent geometry : angle 0.51076 (27054) Misc. bond : bond 0.00024 ( 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 67 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 2.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 288 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8313 (mmt) REVERT: B 430 MET cc_start: 0.8887 (mpp) cc_final: 0.8574 (mpp) REVERT: C 394 MET cc_start: 0.8372 (tpt) cc_final: 0.7616 (tpp) REVERT: C 994 MET cc_start: 0.8594 (mtm) cc_final: 0.8085 (mtm) REVERT: C 1292 TYR cc_start: 0.7126 (m-80) cc_final: 0.6610 (m-80) REVERT: C 1375 MET cc_start: 0.5597 (OUTLIER) cc_final: 0.5054 (tpp) REVERT: D 341 MET cc_start: -0.5586 (ttm) cc_final: -0.5890 (ttp) outliers start: 10 outliers final: 8 residues processed: 62 average time/residue: 0.3001 time to fit residues: 32.3726 Evaluate side-chains 64 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 2.267 ------------------------------------------------------------------------------- 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 635 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 1272 LYS Chi-restraints excluded: chain C residue 1375 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 177 optimal weight: 20.0000 chunk 39 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 162 optimal weight: 5.9990 chunk 143 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 191 optimal weight: 0.9990 chunk 207 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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 = 0.3788 r_free = 0.3788 target = 0.070534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.044568 restraints weight = 101225.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.045355 restraints weight = 53019.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.045299 restraints weight = 34698.637| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19925 Z= 0.128 Angle : 0.564 16.053 27084 Z= 0.268 Chirality : 0.040 0.156 2973 Planarity : 0.004 0.047 3352 Dihedral : 10.871 107.110 2925 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.19 % Favored : 96.64 % Rotamer: Outliers : 0.53 % Allowed : 11.03 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.18), residues: 2290 helix: 1.71 (0.18), residues: 937 sheet: 0.48 (0.31), residues: 265 loop : -0.14 (0.20), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 240 HIS 0.004 0.001 HIS B 103 PHE 0.014 0.001 PHE B 42 TYR 0.010 0.001 TYR C1446 ARG 0.003 0.000 ARG B 453 Details of bonding type rmsd hydrogen bonds : bond 0.03324 ( 803) hydrogen bonds : angle 4.17387 ( 2314) metal coordination : bond 0.00447 ( 16) metal coordination : angle 5.80022 ( 30) covalent geometry : bond 0.00291 (19908) covalent geometry : angle 0.52970 (27054) Misc. bond : bond 0.00019 ( 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 69 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 2.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.9117 (mmm) cc_final: 0.8880 (mmm) REVERT: B 288 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8367 (mmt) REVERT: B 430 MET cc_start: 0.8897 (mpp) cc_final: 0.8566 (mpp) REVERT: C 394 MET cc_start: 0.8491 (tpt) cc_final: 0.7293 (tpt) REVERT: C 725 MET cc_start: 0.8599 (ppp) cc_final: 0.8205 (ppp) REVERT: C 994 MET cc_start: 0.8600 (mtm) cc_final: 0.8100 (mtm) REVERT: C 1292 TYR cc_start: 0.7153 (m-80) cc_final: 0.6593 (m-80) REVERT: C 1375 MET cc_start: 0.5495 (OUTLIER) cc_final: 0.4907 (tpp) REVERT: D 341 MET cc_start: -0.5297 (ttm) cc_final: -0.5621 (ttp) outliers start: 11 outliers final: 8 residues processed: 64 average time/residue: 0.3103 time to fit residues: 34.2917 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 : 2.327 ------------------------------------------------------------------------------- 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 635 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 1272 LYS Chi-restraints excluded: chain C residue 1375 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 99 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 132 optimal weight: 0.6980 chunk 213 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 51 optimal weight: 0.0470 chunk 218 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 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 = 0.3802 r_free = 0.3802 target = 0.071136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.043848 restraints weight = 100711.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.045590 restraints weight = 48135.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.046655 restraints weight = 31857.605| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 19925 Z= 0.094 Angle : 0.560 15.388 27084 Z= 0.265 Chirality : 0.040 0.182 2973 Planarity : 0.004 0.047 3352 Dihedral : 10.810 105.144 2925 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.93 % Favored : 96.90 % Rotamer: Outliers : 0.67 % Allowed : 11.17 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.18), residues: 2290 helix: 1.71 (0.18), residues: 937 sheet: 0.54 (0.31), residues: 265 loop : -0.13 (0.20), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 240 HIS 0.005 0.001 HIS D 369 PHE 0.013 0.001 PHE B 42 TYR 0.010 0.001 TYR B 85 ARG 0.006 0.000 ARG B 118 Details of bonding type rmsd hydrogen bonds : bond 0.02978 ( 803) hydrogen bonds : angle 4.12945 ( 2314) metal coordination : bond 0.00308 ( 16) metal coordination : angle 5.85278 ( 30) covalent geometry : bond 0.00204 (19908) covalent geometry : angle 0.52564 (27054) Misc. bond : bond 0.00020 ( 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 70 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 2.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.9083 (mmm) cc_final: 0.8824 (mmm) REVERT: B 288 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8286 (mmt) REVERT: B 430 MET cc_start: 0.8974 (mpp) cc_final: 0.8664 (mpp) REVERT: C 394 MET cc_start: 0.8380 (tpt) cc_final: 0.7265 (tpt) REVERT: C 994 MET cc_start: 0.8666 (mtm) cc_final: 0.8097 (mtm) REVERT: C 1292 TYR cc_start: 0.7199 (m-80) cc_final: 0.6610 (m-80) REVERT: C 1375 MET cc_start: 0.5709 (OUTLIER) cc_final: 0.5225 (tpp) outliers start: 14 outliers final: 7 residues processed: 65 average time/residue: 0.3487 time to fit residues: 42.5723 Evaluate side-chains 63 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 2.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain B residue 288 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 1272 LYS 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 122 optimal weight: 0.6980 chunk 190 optimal weight: 0.0050 chunk 181 optimal weight: 40.0000 chunk 169 optimal weight: 3.9990 chunk 208 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 85 optimal weight: 9.9990 chunk 167 optimal weight: 6.9990 chunk 223 optimal weight: 6.9990 overall best weight: 2.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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 = 0.3782 r_free = 0.3782 target = 0.070301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.042753 restraints weight = 101537.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.044453 restraints weight = 49401.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.045504 restraints weight = 33022.561| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2875 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= 0.135 Angle : 0.578 16.099 27084 Z= 0.275 Chirality : 0.041 0.185 2973 Planarity : 0.004 0.046 3352 Dihedral : 10.868 104.410 2925 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.23 % Favored : 96.59 % Rotamer: Outliers : 0.48 % Allowed : 11.41 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.18), residues: 2290 helix: 1.73 (0.18), residues: 935 sheet: 0.54 (0.31), residues: 270 loop : -0.16 (0.20), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 240 HIS 0.006 0.001 HIS D 369 PHE 0.015 0.001 PHE B 42 TYR 0.010 0.001 TYR C1446 ARG 0.005 0.000 ARG C1443 Details of bonding type rmsd hydrogen bonds : bond 0.03401 ( 803) hydrogen bonds : angle 4.16514 ( 2314) metal coordination : bond 0.00491 ( 16) metal coordination : angle 5.68621 ( 30) covalent geometry : bond 0.00307 (19908) covalent geometry : angle 0.54641 (27054) Misc. bond : bond 0.00013 ( 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 65 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 3.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.9092 (mmm) cc_final: 0.8835 (mmm) REVERT: B 288 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8361 (mmt) REVERT: B 430 MET cc_start: 0.8970 (mpp) cc_final: 0.8633 (mpp) REVERT: C 394 MET cc_start: 0.8555 (tpt) cc_final: 0.7498 (tpt) REVERT: C 994 MET cc_start: 0.8690 (mtm) cc_final: 0.8410 (mtm) REVERT: C 1292 TYR cc_start: 0.7249 (m-80) cc_final: 0.6629 (m-80) REVERT: C 1375 MET cc_start: 0.5547 (OUTLIER) cc_final: 0.4978 (tpp) outliers start: 10 outliers final: 7 residues processed: 61 average time/residue: 0.4408 time to fit residues: 47.9120 Evaluate side-chains 63 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 3.228 ------------------------------------------------------------------------------- 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 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 1272 LYS Chi-restraints excluded: chain C residue 1375 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 131 optimal weight: 0.9990 chunk 220 optimal weight: 20.0000 chunk 25 optimal weight: 6.9990 chunk 196 optimal weight: 5.9990 chunk 152 optimal weight: 9.9990 chunk 213 optimal weight: 1.9990 chunk 176 optimal weight: 30.0000 chunk 192 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 HIS ** B 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 ASN C 582 HIS C1290 ASN ** C1391 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 = 0.3726 r_free = 0.3726 target = 0.067964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.040312 restraints weight = 101796.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.041875 restraints weight = 50395.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.042865 restraints weight = 34066.676| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 19925 Z= 0.222 Angle : 0.657 17.433 27084 Z= 0.317 Chirality : 0.043 0.179 2973 Planarity : 0.004 0.047 3352 Dihedral : 11.086 101.562 2925 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.89 % Favored : 95.94 % Rotamer: Outliers : 0.72 % Allowed : 11.36 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.18), residues: 2290 helix: 1.55 (0.17), residues: 950 sheet: 0.23 (0.29), residues: 298 loop : -0.29 (0.20), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 240 HIS 0.005 0.001 HIS B 443 PHE 0.019 0.002 PHE B 42 TYR 0.012 0.001 TYR D 512 ARG 0.004 0.001 ARG B 453 Details of bonding type rmsd hydrogen bonds : bond 0.04255 ( 803) hydrogen bonds : angle 4.42911 ( 2314) metal coordination : bond 0.00837 ( 16) metal coordination : angle 5.88446 ( 30) covalent geometry : bond 0.00507 (19908) covalent geometry : angle 0.62739 (27054) Misc. bond : bond 0.00024 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8400.93 seconds wall clock time: 151 minutes 45.09 seconds (9105.09 seconds total)