Starting phenix.real_space_refine on Sun Aug 9 21:12:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ffz_29071/08_2026/8ffz_29071.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ffz_29071/08_2026/8ffz_29071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ffz_29071/08_2026/8ffz_29071.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ffz_29071/08_2026/8ffz_29071.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8ffz_29071/08_2026/8ffz_29071.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ffz_29071/08_2026/8ffz_29071.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ffz_29071/08_2026/8ffz_29071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ffz_29071/08_2026/8ffz_29071.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians Zn 9 6.06 5 P 302 5.49 5 S 143 5.16 5 C 23882 2.51 5 N 6695 2.21 5 O 7931 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 209 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 38962 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2597 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 14, 'TRANS': 299} Chain breaks: 1 Chain: "B" Number of atoms: 7330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7330 Classifications: {'peptide': 905} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 884} Chain breaks: 10 Chain: "C" Number of atoms: 6627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 797, 6627 Classifications: {'peptide': 797} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 780} Chain breaks: 4 Chain: "D" Number of atoms: 2070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2070 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 19, 'TRANS': 242} Chain breaks: 1 Chain: "E" Number of atoms: 4097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 4097 Classifications: {'peptide': 518} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 497} Chain: "F" Number of atoms: 4743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4743 Classifications: {'peptide': 585} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 561} Chain breaks: 1 Chain: "G" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2705 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 312} Chain breaks: 3 Chain: "H" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2593 Classifications: {'peptide': 328} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 312} Chain breaks: 2 Chain: "I" Number of atoms: 3090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3090 Classifications: {'DNA': 151} Link IDs: {'rna3p': 150} Chain: "J" Number of atoms: 3101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3101 Classifications: {'DNA': 151} Link IDs: {'rna3p': 150} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Unusual residues: {' ZN': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 71 SG CYS A 51 87.429 188.358 105.624 1.00 27.87 S ATOM 109 SG CYS A 56 86.797 189.564 108.803 1.00 20.37 S ATOM 318 SG CYS A 82 96.600 214.796 101.474 1.00 49.44 S ATOM 341 SG CYS A 85 97.617 214.810 104.633 1.00 55.29 S ATOM 551 SG CYS A 110 76.109 228.679 109.884 1.00 62.54 S ATOM 575 SG CYS A 113 78.360 230.494 111.423 1.00 64.46 S ATOM 760 SG CYS A 136 63.455 223.527 133.606 1.00 80.62 S ATOM 795 SG CYS A 141 60.787 225.486 134.552 1.00 76.77 S ATOM 1001 SG CYS A 165 68.705 227.460 157.221 1.00 70.54 S ATOM 1024 SG CYS A 168 67.926 230.622 157.662 1.00 67.53 S ATOM 1501 SG CYS A 224 106.714 218.181 141.932 1.00 49.13 S ATOM 1522 SG CYS A 227 105.478 217.112 139.122 1.00 45.50 S ATOM 1741 SG CYS A 255 116.037 215.475 122.996 1.00 72.42 S ATOM 1765 SG CYS A 258 116.810 215.505 119.704 1.00 88.46 S ATOM 2339 SG CYS A 367 78.271 220.702 204.798 1.00144.51 S ATOM 2384 SG CYS A 372 81.244 222.045 205.959 1.00139.56 S ATOM 1270 SG CYS A 196 90.724 219.503 158.311 1.00 42.23 S ATOM 1303 SG CYS A 201 92.749 217.017 159.443 1.00 42.83 S Time building chain proxies: 7.33, per 1000 atoms: 0.19 Number of scatterers: 38962 At special positions: 0 Unit cell: (146.784, 267.168, 228.096, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 9 29.99 S 143 16.00 P 302 15.00 O 7931 8.00 N 6695 7.00 C 23882 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.85 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 74 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 69 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 56 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 51 " pdb=" ZN A 502 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 85 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 82 " pdb="ZN ZN A 502 " - pdb=" NE2 HIS A 98 " pdb="ZN ZN A 502 " - pdb=" NE2 HIS A 102 " pdb=" ZN A 503 " pdb="ZN ZN A 503 " - pdb=" NE2 HIS A 126 " pdb="ZN ZN A 503 " - pdb=" SG CYS A 110 " pdb="ZN ZN A 503 " - pdb=" SG CYS A 113 " pdb=" ZN A 504 " pdb="ZN ZN A 504 " - pdb=" SG CYS A 141 " pdb="ZN ZN A 504 " - pdb=" NE2 HIS A 159 " pdb="ZN ZN A 504 " - pdb=" SG CYS A 136 " pdb="ZN ZN A 504 " - pdb=" NE2 HIS A 154 " pdb=" ZN A 505 " pdb="ZN ZN A 505 " - pdb=" SG CYS A 168 " pdb="ZN ZN A 505 " - pdb=" SG CYS A 165 " pdb="ZN ZN A 505 " - pdb=" NE2 HIS A 181 " pdb="ZN ZN A 505 " - pdb=" NE2 HIS A 186 " pdb=" ZN A 506 " pdb="ZN ZN A 506 " - pdb=" NE2 HIS A 244 " pdb="ZN ZN A 506 " - pdb=" SG CYS A 227 " pdb="ZN ZN A 506 " - pdb=" SG CYS A 224 " pdb="ZN ZN A 506 " - pdb=" NE2 HIS A 240 " pdb=" ZN A 507 " pdb="ZN ZN A 507 " - pdb=" NE2 HIS A 272 " pdb="ZN ZN A 507 " - pdb=" SG CYS A 255 " pdb="ZN ZN A 507 " - pdb=" SG CYS A 258 " pdb=" ZN A 508 " pdb="ZN ZN A 508 " - pdb=" SG CYS A 367 " pdb="ZN ZN A 508 " - pdb=" SG CYS A 372 " pdb="ZN ZN A 508 " - pdb=" NE2 HIS A 389 " pdb="ZN ZN A 508 " - pdb=" NE2 HIS A 385 " pdb=" ZN A 509 " pdb="ZN ZN A 509 " - pdb=" NE2 HIS A 219 " pdb="ZN ZN A 509 " - pdb=" SG CYS A 201 " pdb="ZN ZN A 509 " - pdb=" SG CYS A 196 " pdb="ZN ZN A 509 " - pdb=" NE2 HIS A 214 " Number of angles added : 14 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7754 Finding SS restraints... Secondary structure from input PDB file: 155 helices and 41 sheets defined 46.0% alpha, 15.5% beta 111 base pairs and 240 stacking pairs defined. Time for finding SS restraints: 4.02 Creating SS restraints... Processing helix chain 'A' and resid 62 through 74 removed outlier: 3.569A pdb=" N LEU A 66 " --> pdb=" O ARG A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.538A pdb=" N TYR A 100 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR A 101 " --> pdb=" O ARG A 97 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N HIS A 102 " --> pdb=" O HIS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 130 removed outlier: 3.768A pdb=" N HIS A 130 " --> pdb=" O HIS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 159 removed outlier: 3.812A pdb=" N LEU A 151 " --> pdb=" O LYS A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 186 removed outlier: 3.729A pdb=" N HIS A 186 " --> pdb=" O ILE A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 219 removed outlier: 3.550A pdb=" N LEU A 211 " --> pdb=" O ILE A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 245 removed outlier: 3.737A pdb=" N ILE A 242 " --> pdb=" O GLN A 238 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE A 243 " --> pdb=" O MET A 239 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N HIS A 244 " --> pdb=" O HIS A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 274 removed outlier: 3.889A pdb=" N THR A 271 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N HIS A 272 " --> pdb=" O ASP A 268 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 288 Processing helix chain 'A' and resid 332 through 349 Processing helix chain 'A' and resid 353 through 362 Processing helix chain 'A' and resid 378 through 396 Processing helix chain 'B' and resid 8 through 21 removed outlier: 4.024A pdb=" N GLN B 12 " --> pdb=" O ASP B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 36 removed outlier: 3.833A pdb=" N LYS B 36 " --> pdb=" O ASP B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 56 removed outlier: 3.826A pdb=" N LYS B 56 " --> pdb=" O CYS B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 78 Processing helix chain 'B' and resid 88 through 98 Processing helix chain 'B' and resid 107 through 121 Processing helix chain 'B' and resid 127 through 135 Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.613A pdb=" N LYS B 146 " --> pdb=" O THR B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 184 through 199 removed outlier: 4.169A pdb=" N HIS B 188 " --> pdb=" O ASN B 184 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 189 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ALA B 190 " --> pdb=" O ARG B 186 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N THR B 191 " --> pdb=" O ASP B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 213 Processing helix chain 'B' and resid 218 through 235 Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 333 through 345 Processing helix chain 'B' and resid 346 through 349 Processing helix chain 'B' and resid 352 through 360 Processing helix chain 'B' and resid 361 through 363 No H-bonds generated for 'chain 'B' and resid 361 through 363' Processing helix chain 'B' and resid 364 through 373 Processing helix chain 'B' and resid 408 through 417 removed outlier: 4.270A pdb=" N PHE B 412 " --> pdb=" O THR B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 445 Processing helix chain 'B' and resid 549 through 565 removed outlier: 3.568A pdb=" N LEU B 560 " --> pdb=" O GLN B 556 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS B 561 " --> pdb=" O ARG B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 585 Processing helix chain 'B' and resid 591 through 605 removed outlier: 3.603A pdb=" N ASP B 598 " --> pdb=" O THR B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 643 removed outlier: 4.052A pdb=" N ILE B 631 " --> pdb=" O GLY B 627 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS B 643 " --> pdb=" O LYS B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 757 Processing helix chain 'B' and resid 761 through 766 Processing helix chain 'B' and resid 774 through 810 removed outlier: 3.857A pdb=" N VAL B 786 " --> pdb=" O THR B 782 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG B 787 " --> pdb=" O ALA B 783 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET B 788 " --> pdb=" O ARG B 784 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N HIS B 790 " --> pdb=" O VAL B 786 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N SER B 791 " --> pdb=" O ARG B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 820 removed outlier: 3.804A pdb=" N VAL B 818 " --> pdb=" O SER B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 835 removed outlier: 3.560A pdb=" N TRP B 830 " --> pdb=" O LEU B 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 855 removed outlier: 3.738A pdb=" N ASN B 851 " --> pdb=" O ASN B 847 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG B 852 " --> pdb=" O TYR B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 874 through 885 removed outlier: 3.501A pdb=" N LYS B 885 " --> pdb=" O SER B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 916 Processing helix chain 'B' and resid 933 through 947 removed outlier: 4.067A pdb=" N ILE B 937 " --> pdb=" O GLY B 933 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ASP B 938 " --> pdb=" O ASN B 934 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASN B 939 " --> pdb=" O GLU B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 971 Processing helix chain 'B' and resid 972 through 992 Processing helix chain 'B' and resid 1003 through 1016 removed outlier: 3.912A pdb=" N TRP B1008 " --> pdb=" O ASP B1004 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL B1009 " --> pdb=" O ILE B1005 " (cutoff:3.500A) Processing helix chain 'B' and resid 1041 through 1046 Processing helix chain 'B' and resid 1087 through 1105 removed outlier: 4.352A pdb=" N PHE B1104 " --> pdb=" O ASN B1100 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS B1105 " --> pdb=" O GLU B1101 " (cutoff:3.500A) Processing helix chain 'B' and resid 1109 through 1117 removed outlier: 3.529A pdb=" N ARG B1116 " --> pdb=" O ARG B1112 " (cutoff:3.500A) Processing helix chain 'B' and resid 1122 through 1136 Processing helix chain 'B' and resid 1143 through 1145 No H-bonds generated for 'chain 'B' and resid 1143 through 1145' Processing helix chain 'C' and resid 128 through 141 Processing helix chain 'C' and resid 143 through 156 removed outlier: 3.818A pdb=" N VAL C 154 " --> pdb=" O LEU C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 175 removed outlier: 4.974A pdb=" N THR C 167 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ASP C 170 " --> pdb=" O GLU C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 190 removed outlier: 3.830A pdb=" N ALA C 188 " --> pdb=" O SER C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 198 through 209 Processing helix chain 'C' and resid 211 through 226 Processing helix chain 'C' and resid 229 through 244 removed outlier: 3.909A pdb=" N ILE C 233 " --> pdb=" O GLU C 229 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU C 239 " --> pdb=" O ARG C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 260 removed outlier: 4.027A pdb=" N ALA C 249 " --> pdb=" O GLN C 245 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ASP C 251 " --> pdb=" O ALA C 247 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY C 252 " --> pdb=" O ARG C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 277 removed outlier: 3.509A pdb=" N LEU C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 311 removed outlier: 3.538A pdb=" N LYS C 289 " --> pdb=" O GLU C 285 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 338 Processing helix chain 'C' and resid 342 through 350 Processing helix chain 'C' and resid 356 through 371 removed outlier: 4.527A pdb=" N ILE C 362 " --> pdb=" O SER C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 389 removed outlier: 3.588A pdb=" N GLN C 389 " --> pdb=" O ALA C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 399 Processing helix chain 'C' and resid 403 through 412 removed outlier: 6.178A pdb=" N ASN C 408 " --> pdb=" O GLU C 405 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ARG C 409 " --> pdb=" O PHE C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 420 through 426 Processing helix chain 'C' and resid 431 through 445 Processing helix chain 'C' and resid 447 through 456 Processing helix chain 'C' and resid 457 through 460 Processing helix chain 'C' and resid 462 through 465 Processing helix chain 'C' and resid 466 through 480 Processing helix chain 'C' and resid 482 through 491 Processing helix chain 'C' and resid 492 through 496 Processing helix chain 'C' and resid 501 through 516 Proline residue: C 507 - end of helix Processing helix chain 'C' and resid 517 through 532 Processing helix chain 'C' and resid 535 through 549 Processing helix chain 'C' and resid 551 through 576 Processing helix chain 'C' and resid 614 through 639 removed outlier: 4.406A pdb=" N GLU C 619 " --> pdb=" O ARG C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 666 removed outlier: 3.914A pdb=" N GLU C 659 " --> pdb=" O ASN C 655 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C 660 " --> pdb=" O THR C 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 750 Processing helix chain 'C' and resid 751 through 765 Processing helix chain 'C' and resid 765 through 770 Processing helix chain 'C' and resid 771 through 787 Processing helix chain 'C' and resid 791 through 806 Processing helix chain 'C' and resid 809 through 819 Processing helix chain 'C' and resid 822 through 832 removed outlier: 4.127A pdb=" N SER C 826 " --> pdb=" O ARG C 822 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE C 829 " --> pdb=" O SER C 825 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 852 Processing helix chain 'C' and resid 874 through 887 Processing helix chain 'C' and resid 890 through 903 Processing helix chain 'C' and resid 908 through 924 Processing helix chain 'C' and resid 930 through 953 removed outlier: 3.747A pdb=" N TYR C 953 " --> pdb=" O ARG C 949 " (cutoff:3.500A) Processing helix chain 'C' and resid 954 through 973 Processing helix chain 'C' and resid 974 through 988 removed outlier: 4.185A pdb=" N GLU C 980 " --> pdb=" O SER C 976 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR C 981 " --> pdb=" O ILE C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 992 through 1009 removed outlier: 4.227A pdb=" N HIS C 997 " --> pdb=" O LYS C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1011 through 1023 Processing helix chain 'D' and resid 48 through 59 removed outlier: 3.822A pdb=" N CYS D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 69 Processing helix chain 'D' and resid 124 through 129 removed outlier: 3.908A pdb=" N LYS D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 139 Processing helix chain 'D' and resid 173 through 181 Processing helix chain 'D' and resid 187 through 198 Processing helix chain 'D' and resid 208 through 212 Processing helix chain 'D' and resid 612 through 616 Processing helix chain 'D' and resid 617 through 629 removed outlier: 4.262A pdb=" N LEU D 628 " --> pdb=" O LYS D 624 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 640 removed outlier: 3.549A pdb=" N ALA D 633 " --> pdb=" O ASP D 629 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 163 Processing helix chain 'E' and resid 165 through 175 Processing helix chain 'E' and resid 177 through 192 removed outlier: 4.218A pdb=" N LEU E 183 " --> pdb=" O GLU E 179 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU E 184 " --> pdb=" O LYS E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 204 removed outlier: 4.119A pdb=" N ILE E 203 " --> pdb=" O PRO E 199 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN E 204 " --> pdb=" O PHE E 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 199 through 204' Processing helix chain 'E' and resid 215 through 219 Processing helix chain 'E' and resid 222 through 227 Processing helix chain 'E' and resid 228 through 232 removed outlier: 4.031A pdb=" N ARG E 232 " --> pdb=" O ASP E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 247 Processing helix chain 'E' and resid 326 through 330 removed outlier: 3.503A pdb=" N LEU E 329 " --> pdb=" O ASN E 326 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU E 330 " --> pdb=" O GLU E 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 326 through 330' Processing helix chain 'E' and resid 498 through 503 Processing helix chain 'E' and resid 582 through 587 Processing helix chain 'E' and resid 592 through 597 removed outlier: 3.861A pdb=" N GLN E 597 " --> pdb=" O SER E 593 " (cutoff:3.500A) Processing helix chain 'E' and resid 637 through 640 Processing helix chain 'F' and resid 51 through 54 Processing helix chain 'F' and resid 306 through 322 removed outlier: 3.617A pdb=" N LEU F 310 " --> pdb=" O ILE F 306 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE F 320 " --> pdb=" O LYS F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 360 through 363 Processing helix chain 'F' and resid 385 through 395 removed outlier: 4.127A pdb=" N TYR F 389 " --> pdb=" O GLY F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 433 Processing helix chain 'F' and resid 433 through 444 removed outlier: 3.839A pdb=" N MET F 444 " --> pdb=" O MET F 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 451 through 465 removed outlier: 3.750A pdb=" N ALA F 457 " --> pdb=" O SER F 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 466 through 469 Processing helix chain 'F' and resid 471 through 486 Processing helix chain 'F' and resid 510 through 512 No H-bonds generated for 'chain 'F' and resid 510 through 512' Processing helix chain 'F' and resid 564 through 574 Processing helix chain 'G' and resid 14 through 18 removed outlier: 3.616A pdb=" N LEU G 18 " --> pdb=" O SER G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 54 removed outlier: 3.826A pdb=" N LYS G 45 " --> pdb=" O VAL G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 81 Proline residue: G 75 - end of helix Processing helix chain 'G' and resid 88 through 91 Processing helix chain 'G' and resid 107 through 115 removed outlier: 4.254A pdb=" N LYS G 113 " --> pdb=" O GLU G 109 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE G 114 " --> pdb=" O ILE G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 158 removed outlier: 3.521A pdb=" N TRP G 147 " --> pdb=" O PHE G 143 " (cutoff:3.500A) Proline residue: G 148 - end of helix removed outlier: 3.723A pdb=" N GLU G 152 " --> pdb=" O PRO G 148 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS G 156 " --> pdb=" O GLU G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 182 Processing helix chain 'G' and resid 351 through 354 Processing helix chain 'H' and resid 178 through 190 Processing helix chain 'H' and resid 194 through 212 Processing helix chain 'H' and resid 219 through 235 Processing helix chain 'H' and resid 240 through 248 removed outlier: 3.638A pdb=" N ILE H 244 " --> pdb=" O THR H 240 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 265 Processing helix chain 'H' and resid 267 through 272 Processing helix chain 'H' and resid 287 through 297 removed outlier: 4.816A pdb=" N ASN H 293 " --> pdb=" O SER H 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 407 through 413 Processing helix chain 'H' and resid 454 through 472 removed outlier: 3.567A pdb=" N LYS H 459 " --> pdb=" O GLU H 455 " (cutoff:3.500A) Processing helix chain 'H' and resid 497 through 505 Processing helix chain 'H' and resid 545 through 563 removed outlier: 4.034A pdb=" N ILE H 549 " --> pdb=" O GLN H 545 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR H 550 " --> pdb=" O ARG H 546 " (cutoff:3.500A) Proline residue: H 558 - end of helix removed outlier: 3.631A pdb=" N PHE H 563 " --> pdb=" O VAL H 559 " (cutoff:3.500A) Processing helix chain 'H' and resid 587 through 593 Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81 Processing sheet with id=AA2, first strand: chain 'A' and resid 108 through 109 Processing sheet with id=AA3, first strand: chain 'A' and resid 134 through 135 Processing sheet with id=AA4, first strand: chain 'A' and resid 194 through 195 Processing sheet with id=AA5, first strand: chain 'A' and resid 221 through 223 Processing sheet with id=AA6, first strand: chain 'A' and resid 249 through 251 removed outlier: 4.163A pdb=" N PHE D 643 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ASN B 994 " --> pdb=" O ALA B1053 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ALA B1053 " --> pdb=" O ASN B 994 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 365 through 366 Processing sheet with id=AA8, first strand: chain 'B' and resid 24 through 26 Processing sheet with id=AA9, first strand: chain 'B' and resid 125 through 126 removed outlier: 3.584A pdb=" N SER B 155 " --> pdb=" O GLN B 166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 203 through 205 removed outlier: 6.203A pdb=" N ILE B 251 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 350 through 351 removed outlier: 6.473A pdb=" N GLU B 377 " --> pdb=" O ARG B 393 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N TYR B 395 " --> pdb=" O GLU B 377 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 454 through 457 Processing sheet with id=AB4, first strand: chain 'B' and resid 569 through 571 Processing sheet with id=AB5, first strand: chain 'B' and resid 655 through 656 Processing sheet with id=AB6, first strand: chain 'B' and resid 858 through 859 removed outlier: 4.936A pdb=" N LEU G 335 " --> pdb=" O VAL G 432 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG G 334 " --> pdb=" O ILE G 331 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 888 through 892 removed outlier: 6.917A pdb=" N TRP G 340 " --> pdb=" O ILE B 891 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE D 36 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASN D 156 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE D 160 " --> pdb=" O GLU D 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 888 through 892 removed outlier: 6.917A pdb=" N TRP G 340 " --> pdb=" O ILE B 891 " (cutoff:3.500A) removed outlier: 10.835A pdb=" N LEU G 343 " --> pdb=" O ILE G 427 " (cutoff:3.500A) removed outlier: 11.325A pdb=" N ILE G 427 " --> pdb=" O LEU G 343 " (cutoff:3.500A) removed outlier: 10.687A pdb=" N GLY G 345 " --> pdb=" O GLU G 425 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLU G 425 " --> pdb=" O GLY G 345 " (cutoff:3.500A) removed outlier: 18.068A pdb=" N VAL G 291 " --> pdb=" O TYR G 421 " (cutoff:3.500A) removed outlier: 15.160A pdb=" N ILE G 423 " --> pdb=" O VAL G 291 " (cutoff:3.500A) removed outlier: 14.517A pdb=" N THR G 293 " --> pdb=" O ILE G 423 " (cutoff:3.500A) removed outlier: 11.237A pdb=" N GLU G 425 " --> pdb=" O THR G 293 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N TYR G 295 " --> pdb=" O GLU G 425 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N ILE G 427 " --> pdb=" O TYR G 295 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N SER G 297 " --> pdb=" O ILE G 427 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER D 114 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE D 153 " --> pdb=" O SER D 114 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE D 116 " --> pdb=" O VAL D 151 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG D 147 " --> pdb=" O THR D 120 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 950 through 953 Processing sheet with id=AC1, first strand: chain 'B' and resid 1139 through 1142 removed outlier: 3.757A pdb=" N GLY B1146 " --> pdb=" O THR B1142 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 726 through 727 Processing sheet with id=AC3, first strand: chain 'C' and resid 1024 through 1025 Processing sheet with id=AC4, first strand: chain 'E' and resid 234 through 238 removed outlier: 3.609A pdb=" N LYS E 413 " --> pdb=" O VAL E 234 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N HIS E 236 " --> pdb=" O CYS E 411 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N CYS E 411 " --> pdb=" O HIS E 236 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ILE E 238 " --> pdb=" O LYS E 409 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N LYS E 409 " --> pdb=" O ILE E 238 " (cutoff:3.500A) removed outlier: 9.163A pdb=" N VAL E 407 " --> pdb=" O VAL E 354 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL E 356 " --> pdb=" O VAL E 407 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N LYS E 409 " --> pdb=" O VAL E 356 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N THR E 358 " --> pdb=" O LYS E 409 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N CYS E 411 " --> pdb=" O THR E 358 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N VAL E 360 " --> pdb=" O CYS E 411 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N LYS E 413 " --> pdb=" O VAL E 360 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N CYS E 353 " --> pdb=" O ASN E 347 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ASN E 347 " --> pdb=" O CYS E 353 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LYS E 355 " --> pdb=" O LYS E 345 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LYS E 345 " --> pdb=" O LYS E 355 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N TYR E 312 " --> pdb=" O TRP E 297 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N TRP E 297 " --> pdb=" O TYR E 312 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ALA E 314 " --> pdb=" O ILE E 295 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE E 295 " --> pdb=" O ALA E 314 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA E 316 " --> pdb=" O THR E 293 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 261 through 265 removed outlier: 6.621A pdb=" N LYS E 255 " --> pdb=" O TYR E 614 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE E 616 " --> pdb=" O LYS E 255 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU E 257 " --> pdb=" O ILE E 616 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 271 through 272 removed outlier: 3.902A pdb=" N CYS E 644 " --> pdb=" O SER E 660 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 366 through 371 removed outlier: 5.435A pdb=" N ASP E 368 " --> pdb=" O VAL E 387 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N VAL E 387 " --> pdb=" O ASP E 368 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE E 398 " --> pdb=" O VAL E 381 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N CYS E 383 " --> pdb=" O LEU E 396 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU E 396 " --> pdb=" O CYS E 383 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N SER E 385 " --> pdb=" O ASN E 394 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ASN E 394 " --> pdb=" O SER E 385 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 425 through 432 removed outlier: 6.559A pdb=" N GLY E 439 " --> pdb=" O THR E 426 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE E 428 " --> pdb=" O VAL E 437 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL E 437 " --> pdb=" O PHE E 428 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N PHE E 430 " --> pdb=" O THR E 435 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N THR E 435 " --> pdb=" O PHE E 430 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE E 444 " --> pdb=" O PHE E 440 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 467 through 473 removed outlier: 3.585A pdb=" N SER E 469 " --> pdb=" O VAL E 485 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL E 481 " --> pdb=" O ALA E 473 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA E 486 " --> pdb=" O TYR E 490 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N TYR E 490 " --> pdb=" O ALA E 486 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE E 491 " --> pdb=" O VAL E 506 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 517 through 520 removed outlier: 6.680A pdb=" N LEU E 535 " --> pdb=" O LEU E 549 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 556 through 560 removed outlier: 6.883A pdb=" N GLY E 571 " --> pdb=" O THR E 557 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE E 559 " --> pdb=" O LEU E 569 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU E 569 " --> pdb=" O ILE E 559 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER E 576 " --> pdb=" O SER E 572 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TRP E 603 " --> pdb=" O LEU E 577 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE E 579 " --> pdb=" O ARG E 601 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ARG E 601 " --> pdb=" O ILE E 579 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N ASN E 581 " --> pdb=" O SER E 599 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N SER E 599 " --> pdb=" O ASN E 581 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU E 621 " --> pdb=" O ARG E 601 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 7 through 10 removed outlier: 9.143A pdb=" N SER F 365 " --> pdb=" O MET F 351 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N MET F 351 " --> pdb=" O SER F 365 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY F 335 " --> pdb=" O VAL F 348 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ASP F 350 " --> pdb=" O ILE F 333 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ILE F 333 " --> pdb=" O ASP F 350 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLU F 352 " --> pdb=" O LEU F 331 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N LEU F 331 " --> pdb=" O GLU F 352 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 21 through 23 removed outlier: 4.230A pdb=" N ILE F 37 " --> pdb=" O PHE F 61 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 88 through 93 removed outlier: 6.495A pdb=" N LEU F 103 " --> pdb=" O ARG F 89 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N CYS F 91 " --> pdb=" O ALA F 101 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA F 101 " --> pdb=" O CYS F 91 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL F 109 " --> pdb=" O ASN F 120 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ASN F 120 " --> pdb=" O VAL F 109 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL F 111 " --> pdb=" O LEU F 118 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 132 through 137 removed outlier: 3.673A pdb=" N CYS F 134 " --> pdb=" O GLY F 147 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU F 152 " --> pdb=" O ASN F 148 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER F 172 " --> pdb=" O PHE F 155 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N SER F 157 " --> pdb=" O PHE F 170 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N PHE F 170 " --> pdb=" O SER F 157 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ARG F 159 " --> pdb=" O PHE F 168 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N PHE F 168 " --> pdb=" O ARG F 159 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 185 through 191 removed outlier: 6.803A pdb=" N ALA F 198 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE F 188 " --> pdb=" O VAL F 196 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL F 196 " --> pdb=" O ILE F 188 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TRP F 190 " --> pdb=" O VAL F 194 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL F 194 " --> pdb=" O TRP F 190 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL F 204 " --> pdb=" O ILE F 221 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG F 219 " --> pdb=" O SER F 206 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 231 through 235 removed outlier: 3.731A pdb=" N ASP F 231 " --> pdb=" O THR F 242 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 269 through 272 Processing sheet with id=AE1, first strand: chain 'F' and resid 495 through 499 Processing sheet with id=AE2, first strand: chain 'F' and resid 518 through 520 Processing sheet with id=AE3, first strand: chain 'F' and resid 542 through 544 Processing sheet with id=AE4, first strand: chain 'G' and resid 119 through 120 removed outlier: 6.646A pdb=" N VAL G 84 " --> pdb=" O SER G 120 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ALA G 61 " --> pdb=" O TYR G 85 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA G 60 " --> pdb=" O CYS G 163 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU G 204 " --> pdb=" O ASN G 241 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASN G 241 " --> pdb=" O LEU G 204 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LYS G 206 " --> pdb=" O THR G 239 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 419 through 421 removed outlier: 4.768A pdb=" N ASN H 421 " --> pdb=" O ALA H 427 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ALA H 427 " --> pdb=" O ASN H 421 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL H 428 " --> pdb=" O ILE H 441 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE H 441 " --> pdb=" O VAL H 428 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS H 446 " --> pdb=" O PHE H 442 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLY H 451 " --> pdb=" O ILE H 396 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ILE H 396 " --> pdb=" O GLY H 451 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LEU H 393 " --> pdb=" O VAL H 487 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL H 487 " --> pdb=" O LEU H 393 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ASN H 395 " --> pdb=" O ASN H 485 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ASN H 485 " --> pdb=" O ASN H 395 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL H 397 " --> pdb=" O ILE H 483 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ILE H 483 " --> pdb=" O VAL H 397 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR H 399 " --> pdb=" O PHE H 481 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N PHE H 481 " --> pdb=" O THR H 399 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ILE H 486 " --> pdb=" O GLY H 542 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY H 542 " --> pdb=" O ILE H 486 " (cutoff:3.500A) 1503 hydrogen bonds defined for protein. 4251 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 275 hydrogen bonds 542 hydrogen bond angles 0 basepair planarities 111 basepair parallelities 240 stacking parallelities Total time for adding SS restraints: 11.81 Time building geometry restraints manager: 3.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9995 1.34 - 1.46: 9277 1.46 - 1.58: 20287 1.58 - 1.71: 602 1.71 - 1.83: 221 Bond restraints: 40382 Sorted by residual: bond pdb=" C5' DA I 8 " pdb=" C4' DA I 8 " ideal model delta sigma weight residual 1.512 1.549 -0.037 7.00e-03 2.04e+04 2.73e+01 bond pdb=" C5' DT J 144 " pdb=" C4' DT J 144 " ideal model delta sigma weight residual 1.512 1.548 -0.036 7.00e-03 2.04e+04 2.68e+01 bond pdb=" C5 DA I 106 " pdb=" C4 DA I 106 " ideal model delta sigma weight residual 1.383 1.348 0.035 7.00e-03 2.04e+04 2.49e+01 bond pdb=" C5' DA J 32 " pdb=" C4' DA J 32 " ideal model delta sigma weight residual 1.512 1.547 -0.035 7.00e-03 2.04e+04 2.45e+01 bond pdb=" C5' DG J 28 " pdb=" C4' DG J 28 " ideal model delta sigma weight residual 1.512 1.547 -0.035 7.00e-03 2.04e+04 2.43e+01 ... (remaining 40377 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 40490 1.97 - 3.94: 12903 3.94 - 5.91: 2223 5.91 - 7.88: 220 7.88 - 9.85: 41 Bond angle restraints: 55877 Sorted by residual: angle pdb=" O5' DC I 69 " pdb=" C5' DC I 69 " pdb=" C4' DC I 69 " ideal model delta sigma weight residual 109.40 119.01 -9.61 8.00e-01 1.56e+00 1.44e+02 angle pdb=" O5' DA J 32 " pdb=" C5' DA J 32 " pdb=" C4' DA J 32 " ideal model delta sigma weight residual 109.40 118.83 -9.43 8.00e-01 1.56e+00 1.39e+02 angle pdb=" O5' DG J 15 " pdb=" C5' DG J 15 " pdb=" C4' DG J 15 " ideal model delta sigma weight residual 109.40 118.80 -9.40 8.00e-01 1.56e+00 1.38e+02 angle pdb=" N6 DA I 94 " pdb=" C6 DA I 94 " pdb=" N1 DA I 94 " ideal model delta sigma weight residual 118.60 111.69 6.91 6.00e-01 2.78e+00 1.33e+02 angle pdb=" O5' DA I 41 " pdb=" C5' DA I 41 " pdb=" C4' DA I 41 " ideal model delta sigma weight residual 109.40 118.41 -9.01 8.00e-01 1.56e+00 1.27e+02 ... (remaining 55872 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 22345 35.87 - 71.74: 1238 71.74 - 107.60: 44 107.60 - 143.47: 0 143.47 - 179.34: 9 Dihedral angle restraints: 23636 sinusoidal: 11703 harmonic: 11933 Sorted by residual: dihedral pdb=" C ASP A 281 " pdb=" N ASP A 281 " pdb=" CA ASP A 281 " pdb=" CB ASP A 281 " ideal model delta harmonic sigma weight residual -122.60 -138.75 16.15 0 2.50e+00 1.60e-01 4.17e+01 dihedral pdb=" N ASP A 281 " pdb=" C ASP A 281 " pdb=" CA ASP A 281 " pdb=" CB ASP A 281 " ideal model delta harmonic sigma weight residual 122.80 136.92 -14.12 0 2.50e+00 1.60e-01 3.19e+01 dihedral pdb=" C PHE H 275 " pdb=" N PHE H 275 " pdb=" CA PHE H 275 " pdb=" CB PHE H 275 " ideal model delta harmonic sigma weight residual -122.60 -136.51 13.91 0 2.50e+00 1.60e-01 3.10e+01 ... (remaining 23633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 4915 0.116 - 0.232: 1182 0.232 - 0.348: 118 0.348 - 0.463: 31 0.463 - 0.579: 4 Chirality restraints: 6250 Sorted by residual: chirality pdb=" CA ASP A 281 " pdb=" N ASP A 281 " pdb=" C ASP A 281 " pdb=" CB ASP A 281 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.39e+00 chirality pdb=" C3' DT J 102 " pdb=" C4' DT J 102 " pdb=" O3' DT J 102 " pdb=" C2' DT J 102 " both_signs ideal model delta sigma weight residual False -2.73 -2.20 -0.53 2.00e-01 2.50e+01 6.99e+00 chirality pdb=" CA PHE H 275 " pdb=" N PHE H 275 " pdb=" C PHE H 275 " pdb=" CB PHE H 275 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.96e+00 ... (remaining 6247 not shown) Planarity restraints: 6036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 97 " 0.240 2.00e-02 2.50e+03 9.99e-02 2.99e+02 pdb=" N9 DG I 97 " -0.027 2.00e-02 2.50e+03 pdb=" C8 DG I 97 " -0.071 2.00e-02 2.50e+03 pdb=" N7 DG I 97 " -0.076 2.00e-02 2.50e+03 pdb=" C5 DG I 97 " -0.063 2.00e-02 2.50e+03 pdb=" C6 DG I 97 " 0.018 2.00e-02 2.50e+03 pdb=" O6 DG I 97 " 0.174 2.00e-02 2.50e+03 pdb=" N1 DG I 97 " 0.017 2.00e-02 2.50e+03 pdb=" C2 DG I 97 " -0.043 2.00e-02 2.50e+03 pdb=" N2 DG I 97 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG I 97 " -0.081 2.00e-02 2.50e+03 pdb=" C4 DG I 97 " -0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 963 " 0.204 2.00e-02 2.50e+03 1.13e-01 2.53e+02 pdb=" CG TYR C 963 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR C 963 " -0.099 2.00e-02 2.50e+03 pdb=" CD2 TYR C 963 " -0.096 2.00e-02 2.50e+03 pdb=" CE1 TYR C 963 " -0.066 2.00e-02 2.50e+03 pdb=" CE2 TYR C 963 " -0.069 2.00e-02 2.50e+03 pdb=" CZ TYR C 963 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR C 963 " 0.170 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 66 " -0.201 2.00e-02 2.50e+03 1.03e-01 2.38e+02 pdb=" N1 DC I 66 " 0.026 2.00e-02 2.50e+03 pdb=" C2 DC I 66 " 0.054 2.00e-02 2.50e+03 pdb=" O2 DC I 66 " 0.077 2.00e-02 2.50e+03 pdb=" N3 DC I 66 " 0.020 2.00e-02 2.50e+03 pdb=" C4 DC I 66 " 0.003 2.00e-02 2.50e+03 pdb=" N4 DC I 66 " -0.165 2.00e-02 2.50e+03 pdb=" C5 DC I 66 " 0.097 2.00e-02 2.50e+03 pdb=" C6 DC I 66 " 0.091 2.00e-02 2.50e+03 ... (remaining 6033 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 18186 3.00 - 3.48: 40020 3.48 - 3.95: 64574 3.95 - 4.43: 72855 4.43 - 4.90: 113666 Nonbonded interactions: 309301 Sorted by model distance: nonbonded pdb=" OG SER A 111 " pdb=" OE2 GLU A 127 " model vdw 2.526 3.040 nonbonded pdb=" OE1 GLU H 216 " pdb=" OH TYR H 511 " model vdw 2.544 3.040 nonbonded pdb=" OG SER E 318 " pdb=" OE2 GLU E 365 " model vdw 2.545 3.040 nonbonded pdb=" OG SER F 339 " pdb=" OD1 ASP F 341 " model vdw 2.547 3.040 nonbonded pdb=" OG SER F 128 " pdb=" OD1 ASP F 150 " model vdw 2.547 3.040 ... (remaining 309296 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: 3.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.750 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 43.100 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 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 : 0.017 0.940 40416 Z= 1.036 Angle : 1.907 15.173 55891 Z= 1.569 Chirality : 0.101 0.579 6250 Planarity : 0.018 0.211 6036 Dihedral : 18.551 179.340 15882 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 0.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.50 % Favored : 94.38 % Rotamer: Outliers : 0.38 % Allowed : 2.81 % Favored : 96.81 % Cbeta Deviations : 0.44 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.12), residues: 3985 helix: -0.59 (0.11), residues: 1618 sheet: -0.44 (0.22), residues: 504 loop : -0.85 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 552 TYR 0.204 0.023 TYR C 963 PHE 0.094 0.015 PHE F 324 TRP 0.122 0.023 TRP E 603 HIS 0.019 0.004 HIS E 337 Details of bonding type rmsd/Z covalent geometry : bond 0.01294 / 0.99 (40382) covalent geometry : angle 1.90327 / 1.57 (55877) hydrogen bonds : bond 0.17167 / 11.61 ( 1769) hydrogen bonds : angle 7.49415 / 5.32 ( 4793) metal coordination : bond 0.35535 / 23.49 ( 34) metal coordination : angle 7.83726 / 4.48 ( 14) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 502 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 TYR cc_start: 0.3148 (t80) cc_final: 0.2893 (t80) REVERT: B 415 LEU cc_start: 0.7868 (mm) cc_final: 0.7626 (pp) REVERT: C 228 MET cc_start: 0.4886 (tmm) cc_final: 0.4291 (tmm) REVERT: C 265 ASN cc_start: 0.6745 (m-40) cc_final: 0.5982 (t0) REVERT: C 506 LYS cc_start: 0.5321 (mtmt) cc_final: 0.4673 (tptm) REVERT: C 814 GLN cc_start: 0.8333 (mt0) cc_final: 0.8049 (mt0) REVERT: F 270 ILE cc_start: 0.8688 (mt) cc_final: 0.8273 (mt) REVERT: F 343 TYR cc_start: 0.8335 (m-80) cc_final: 0.8106 (m-80) REVERT: G 139 MET cc_start: 0.7688 (ttp) cc_final: 0.7392 (ttp) REVERT: H 234 MET cc_start: 0.2390 (mmm) cc_final: 0.0662 (ppp) outliers start: 14 outliers final: 2 residues processed: 512 average time/residue: 0.2429 time to fit residues: 202.3237 Evaluate side-chains 243 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 241 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain E residue 420 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 5.9990 chunk 424 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 HIS ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 HIS A 359 ASN B 335 GLN B 442 ASN C 161 ASN C 190 HIS C 930 GLN ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 525 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.151380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.126831 restraints weight = 112923.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.128317 restraints weight = 246807.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.129225 restraints weight = 118072.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.129484 restraints weight = 77622.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.130025 restraints weight = 65602.617| |-----------------------------------------------------------------------------| r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 40416 Z= 0.213 Angle : 0.805 12.598 55891 Z= 0.445 Chirality : 0.054 0.444 6250 Planarity : 0.005 0.055 6036 Dihedral : 22.786 177.738 7707 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.45 % Allowed : 6.64 % Favored : 91.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.13), residues: 3985 helix: 0.67 (0.12), residues: 1645 sheet: -0.61 (0.21), residues: 580 loop : -0.70 (0.15), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 748 TYR 0.020 0.002 TYR C 217 PHE 0.039 0.002 PHE E 273 TRP 0.028 0.003 TRP F 184 HIS 0.014 0.002 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.21 (40382) covalent geometry : angle 0.80074 / 0.45 (55877) hydrogen bonds : bond 0.06707 / 4.61 ( 1769) hydrogen bonds : angle 5.03830 / 3.57 ( 4793) metal coordination : bond 0.02806 / 1.57 ( 34) metal coordination : angle 4.97991 / 3.32 ( 14) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 236 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 415 LEU cc_start: 0.7694 (mm) cc_final: 0.7307 (pp) REVERT: B 458 ASP cc_start: 0.6660 (p0) cc_final: 0.6374 (t0) REVERT: B 563 MET cc_start: 0.6352 (ttm) cc_final: 0.6084 (ttt) REVERT: B 584 MET cc_start: 0.3173 (tmm) cc_final: 0.2971 (tmm) REVERT: B 1160 THR cc_start: 0.2786 (OUTLIER) cc_final: 0.2546 (m) REVERT: C 228 MET cc_start: 0.5111 (tmm) cc_final: 0.4391 (tmm) REVERT: C 265 ASN cc_start: 0.6894 (m-40) cc_final: 0.6074 (t0) REVERT: C 387 TRP cc_start: 0.4306 (t-100) cc_final: 0.3981 (t-100) REVERT: F 343 TYR cc_start: 0.8357 (m-80) cc_final: 0.8134 (m-80) REVERT: G 1 MET cc_start: 0.3701 (mtm) cc_final: 0.3329 (mtm) REVERT: H 214 MET cc_start: 0.0095 (OUTLIER) cc_final: -0.0172 (mtt) REVERT: H 234 MET cc_start: 0.1715 (mmm) cc_final: 0.0308 (ppp) outliers start: 53 outliers final: 29 residues processed: 274 average time/residue: 0.2245 time to fit residues: 106.1695 Evaluate side-chains 232 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 201 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 1160 THR Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 994 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 632 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 379 HIS Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 476 ASP Chi-restraints excluded: chain E residue 593 SER Chi-restraints excluded: chain E residue 616 ILE Chi-restraints excluded: chain E residue 640 ILE Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 656 CYS Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 351 MET Chi-restraints excluded: chain F residue 366 PHE Chi-restraints excluded: chain F residue 381 GLU Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 538 LEU Chi-restraints excluded: chain F residue 583 THR Chi-restraints excluded: chain G residue 310 GLU Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain H residue 214 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 207 optimal weight: 1.9990 chunk 290 optimal weight: 4.9990 chunk 404 optimal weight: 40.0000 chunk 325 optimal weight: 0.0170 chunk 205 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 298 optimal weight: 10.0000 chunk 198 optimal weight: 0.7980 chunk 307 optimal weight: 9.9990 overall best weight: 2.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 HIS B 132 GLN B 201 ASN E 513 ASN G 56 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.150967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.128243 restraints weight = 112344.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.129730 restraints weight = 259535.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.130139 restraints weight = 106512.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.130472 restraints weight = 78958.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.130582 restraints weight = 65828.895| |-----------------------------------------------------------------------------| r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 40416 Z= 0.191 Angle : 0.700 12.989 55891 Z= 0.386 Chirality : 0.049 0.410 6250 Planarity : 0.005 0.068 6036 Dihedral : 23.076 177.228 7705 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.47 % Allowed : 8.49 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.13), residues: 3985 helix: 1.00 (0.12), residues: 1660 sheet: -0.66 (0.21), residues: 563 loop : -0.74 (0.15), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG B 748 TYR 0.039 0.002 TYR G 140 PHE 0.025 0.002 PHE F 574 TRP 0.025 0.002 TRP F 184 HIS 0.010 0.001 HIS E 588 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.19 (40382) covalent geometry : angle 0.69760 / 0.39 (55877) hydrogen bonds : bond 0.05450 / 3.75 ( 1769) hydrogen bonds : angle 4.64179 / 3.29 ( 4793) metal coordination : bond 0.01463 / 0.93 ( 34) metal coordination : angle 3.61752 / 2.53 ( 14) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 207 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 329 ASN cc_start: 0.7447 (OUTLIER) cc_final: 0.7037 (t0) REVERT: C 217 TYR cc_start: 0.1418 (OUTLIER) cc_final: 0.0476 (m-80) REVERT: C 253 PHE cc_start: 0.2907 (m-80) cc_final: 0.2702 (m-80) REVERT: C 265 ASN cc_start: 0.6888 (m-40) cc_final: 0.5813 (t0) REVERT: C 558 MET cc_start: -0.1158 (tpp) cc_final: -0.1428 (tpp) REVERT: C 817 MET cc_start: 0.8630 (mmm) cc_final: 0.8411 (tpt) REVERT: H 234 MET cc_start: 0.1537 (mmm) cc_final: 0.0483 (ppp) outliers start: 54 outliers final: 30 residues processed: 246 average time/residue: 0.2134 time to fit residues: 92.2613 Evaluate side-chains 209 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 886 THR Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 965 LEU Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 379 HIS Chi-restraints excluded: chain E residue 467 ILE Chi-restraints excluded: chain E residue 476 ASP Chi-restraints excluded: chain E residue 525 SER Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 616 ILE Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 351 MET Chi-restraints excluded: chain F residue 366 PHE Chi-restraints excluded: chain F residue 381 GLU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 128 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 37 optimal weight: 10.0000 chunk 397 optimal weight: 30.0000 chunk 354 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 chunk 178 optimal weight: 6.9990 chunk 420 optimal weight: 30.0000 chunk 172 optimal weight: 0.9990 chunk 341 optimal weight: 10.0000 chunk 346 optimal weight: 1.9990 chunk 123 optimal weight: 40.0000 chunk 22 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 ASN ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 513 ASN F 364 GLN H 241 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.147950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.124720 restraints weight = 111906.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.126226 restraints weight = 266476.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.126429 restraints weight = 107286.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.126748 restraints weight = 79892.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.126988 restraints weight = 63816.853| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 40416 Z= 0.315 Angle : 0.787 11.848 55891 Z= 0.424 Chirality : 0.052 0.411 6250 Planarity : 0.005 0.066 6036 Dihedral : 23.227 177.494 7704 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.18 % Allowed : 9.75 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.13), residues: 3985 helix: 0.85 (0.12), residues: 1649 sheet: -0.90 (0.21), residues: 538 loop : -0.98 (0.14), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 281 TYR 0.025 0.003 TYR B 389 PHE 0.028 0.003 PHE E 344 TRP 0.029 0.002 TRP F 184 HIS 0.009 0.002 HIS B1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00716 / 0.31 (40382) covalent geometry : angle 0.78172 / 0.42 (55877) hydrogen bonds : bond 0.05985 / 4.13 ( 1769) hydrogen bonds : angle 4.79091 / 3.40 ( 4793) metal coordination : bond 0.02106 / 1.30 ( 34) metal coordination : angle 5.63925 / 3.55 ( 14) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 186 time to evaluate : 1.455 Fit side-chains revert: symmetry clash REVERT: B 302 PHE cc_start: 0.7182 (OUTLIER) cc_final: 0.6765 (p90) REVERT: B 329 ASN cc_start: 0.7650 (OUTLIER) cc_final: 0.7250 (t0) REVERT: B 458 ASP cc_start: 0.6955 (p0) cc_final: 0.6710 (t0) REVERT: B 999 ASN cc_start: 0.7434 (t0) cc_final: 0.7226 (t0) REVERT: C 217 TYR cc_start: 0.1588 (OUTLIER) cc_final: 0.0479 (m-80) REVERT: C 253 PHE cc_start: 0.2946 (m-80) cc_final: 0.2702 (m-80) REVERT: C 265 ASN cc_start: 0.6920 (m-40) cc_final: 0.5791 (t0) REVERT: C 558 MET cc_start: -0.0299 (tpp) cc_final: -0.0662 (tpp) REVERT: E 567 MET cc_start: 0.8464 (mmm) cc_final: 0.8010 (mmm) REVERT: G 169 HIS cc_start: 0.6641 (OUTLIER) cc_final: 0.5311 (m-70) REVERT: H 234 MET cc_start: 0.1638 (mmm) cc_final: 0.0492 (ppp) REVERT: H 563 PHE cc_start: 0.1444 (m-80) cc_final: 0.1201 (m-10) outliers start: 80 outliers final: 53 residues processed: 250 average time/residue: 0.2195 time to fit residues: 95.8143 Evaluate side-chains 227 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 170 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 81 HIS Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 302 PHE Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 886 THR Chi-restraints excluded: chain B residue 1004 ASP Chi-restraints excluded: chain B residue 1101 GLU Chi-restraints excluded: chain B residue 1110 LEU Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 965 LEU Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 379 HIS Chi-restraints excluded: chain E residue 467 ILE Chi-restraints excluded: chain E residue 470 VAL Chi-restraints excluded: chain E residue 476 ASP Chi-restraints excluded: chain E residue 525 SER Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 550 VAL Chi-restraints excluded: chain E residue 578 ILE Chi-restraints excluded: chain E residue 593 SER Chi-restraints excluded: chain E residue 616 ILE Chi-restraints excluded: chain E residue 640 ILE Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 184 TRP Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 351 MET Chi-restraints excluded: chain F residue 353 ARG Chi-restraints excluded: chain F residue 366 PHE Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 169 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 340 optimal weight: 3.9990 chunk 336 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 298 optimal weight: 5.9990 chunk 216 optimal weight: 0.8980 chunk 297 optimal weight: 0.7980 chunk 248 optimal weight: 6.9990 chunk 288 optimal weight: 0.7980 chunk 422 optimal weight: 50.0000 chunk 54 optimal weight: 0.0870 chunk 129 optimal weight: 5.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 758 ASN E 513 ASN G 56 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.150839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.127226 restraints weight = 112280.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.128640 restraints weight = 259897.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.129411 restraints weight = 112780.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.129582 restraints weight = 77428.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.130324 restraints weight = 64097.971| |-----------------------------------------------------------------------------| r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 40416 Z= 0.129 Angle : 0.617 10.987 55891 Z= 0.341 Chirality : 0.046 0.397 6250 Planarity : 0.004 0.057 6036 Dihedral : 23.076 175.960 7704 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.42 % Allowed : 11.17 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.13), residues: 3985 helix: 1.26 (0.13), residues: 1662 sheet: -0.77 (0.21), residues: 573 loop : -0.87 (0.15), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 748 TYR 0.025 0.001 TYR B 332 PHE 0.022 0.002 PHE C 396 TRP 0.024 0.001 TRP F 184 HIS 0.007 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.13 (40382) covalent geometry : angle 0.61388 / 0.34 (55877) hydrogen bonds : bond 0.04713 / 3.25 ( 1769) hydrogen bonds : angle 4.41770 / 3.13 ( 4793) metal coordination : bond 0.00922 / 0.49 ( 34) metal coordination : angle 3.67109 / 2.23 ( 14) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 193 time to evaluate : 1.512 Fit side-chains revert: symmetry clash REVERT: B 10 LEU cc_start: 0.8396 (tt) cc_final: 0.8185 (tt) REVERT: B 329 ASN cc_start: 0.7256 (OUTLIER) cc_final: 0.6819 (t0) REVERT: B 458 ASP cc_start: 0.7057 (p0) cc_final: 0.6709 (t0) REVERT: B 999 ASN cc_start: 0.7336 (t0) cc_final: 0.7124 (t0) REVERT: C 217 TYR cc_start: 0.1410 (OUTLIER) cc_final: 0.0383 (m-80) REVERT: C 265 ASN cc_start: 0.6878 (m-40) cc_final: 0.5833 (t0) REVERT: C 397 TRP cc_start: 0.6228 (m100) cc_final: 0.5954 (m100) REVERT: E 567 MET cc_start: 0.8376 (mmm) cc_final: 0.7963 (mmm) REVERT: H 234 MET cc_start: 0.1647 (mmm) cc_final: 0.0500 (ppp) outliers start: 52 outliers final: 37 residues processed: 232 average time/residue: 0.2195 time to fit residues: 89.2533 Evaluate side-chains 212 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 173 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 649 VAL Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 1101 GLU Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain C residue 198 PHE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 632 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 308 LYS Chi-restraints excluded: chain E residue 379 HIS Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 470 VAL Chi-restraints excluded: chain E residue 550 VAL Chi-restraints excluded: chain E residue 630 VAL Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 184 TRP Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 351 MET Chi-restraints excluded: chain F residue 366 PHE Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 66 PHE Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain H residue 214 MET Chi-restraints excluded: chain H residue 255 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 114 optimal weight: 0.2980 chunk 306 optimal weight: 5.9990 chunk 406 optimal weight: 40.0000 chunk 312 optimal weight: 4.9990 chunk 257 optimal weight: 3.9990 chunk 150 optimal weight: 20.0000 chunk 421 optimal weight: 50.0000 chunk 206 optimal weight: 4.9990 chunk 157 optimal weight: 10.0000 chunk 151 optimal weight: 2.9990 chunk 389 optimal weight: 3.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 HIS C 214 GLN D 130 ASN ** E 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 ASN H 394 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.148833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.126187 restraints weight = 112349.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.127573 restraints weight = 262873.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.127629 restraints weight = 106824.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.127909 restraints weight = 79162.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.128393 restraints weight = 62274.934| |-----------------------------------------------------------------------------| r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 40416 Z= 0.231 Angle : 0.681 10.828 55891 Z= 0.369 Chirality : 0.047 0.394 6250 Planarity : 0.004 0.063 6036 Dihedral : 23.089 175.537 7704 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.08 % Allowed : 11.69 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.13), residues: 3985 helix: 1.20 (0.13), residues: 1665 sheet: -0.94 (0.21), residues: 573 loop : -0.95 (0.15), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 234 TYR 0.017 0.002 TYR B 389 PHE 0.027 0.002 PHE F 574 TRP 0.025 0.002 TRP F 184 HIS 0.007 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.23 (40382) covalent geometry : angle 0.67783 / 0.37 (55877) hydrogen bonds : bond 0.05134 / 3.56 ( 1769) hydrogen bonds : angle 4.48947 / 3.20 ( 4793) metal coordination : bond 0.01296 / 0.84 ( 34) metal coordination : angle 4.18164 / 2.54 ( 14) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 169 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 10 LEU cc_start: 0.8341 (tt) cc_final: 0.8083 (tt) REVERT: B 302 PHE cc_start: 0.7070 (OUTLIER) cc_final: 0.6586 (p90) REVERT: B 458 ASP cc_start: 0.7057 (p0) cc_final: 0.6582 (t0) REVERT: B 999 ASN cc_start: 0.7431 (t0) cc_final: 0.7198 (t0) REVERT: C 217 TYR cc_start: 0.1502 (OUTLIER) cc_final: 0.0450 (m-80) REVERT: E 385 SER cc_start: 0.8185 (OUTLIER) cc_final: 0.7852 (m) REVERT: E 567 MET cc_start: 0.8568 (mmm) cc_final: 0.7996 (mmm) REVERT: G 169 HIS cc_start: 0.6508 (OUTLIER) cc_final: 0.5282 (m-70) REVERT: H 234 MET cc_start: 0.1544 (mmm) cc_final: 0.0408 (ppp) outliers start: 76 outliers final: 60 residues processed: 231 average time/residue: 0.2136 time to fit residues: 87.1114 Evaluate side-chains 228 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 164 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 81 HIS Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 302 PHE Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 649 VAL Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 886 THR Chi-restraints excluded: chain B residue 1101 GLU Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain C residue 198 PHE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 429 ASN Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 624 ILE Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 632 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 308 LYS Chi-restraints excluded: chain E residue 379 HIS Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 467 ILE Chi-restraints excluded: chain E residue 470 VAL Chi-restraints excluded: chain E residue 525 SER Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 550 VAL Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain E residue 616 ILE Chi-restraints excluded: chain E residue 630 VAL Chi-restraints excluded: chain E residue 640 ILE Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 184 TRP Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 351 MET Chi-restraints excluded: chain F residue 366 PHE Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 544 ILE Chi-restraints excluded: chain F residue 577 ILE Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 66 PHE Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain H residue 255 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 258 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 208 optimal weight: 1.9990 chunk 230 optimal weight: 6.9990 chunk 353 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 212 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 417 optimal weight: 20.0000 chunk 166 optimal weight: 0.6980 chunk 193 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 750 GLN E 513 ASN G 56 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.150216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.126505 restraints weight = 112359.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.127926 restraints weight = 258251.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.128620 restraints weight = 104590.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.128968 restraints weight = 75652.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.129085 restraints weight = 63908.849| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 40416 Z= 0.136 Angle : 0.599 12.784 55891 Z= 0.329 Chirality : 0.045 0.390 6250 Planarity : 0.004 0.060 6036 Dihedral : 23.037 174.681 7704 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.80 % Allowed : 12.15 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.13), residues: 3985 helix: 1.41 (0.13), residues: 1664 sheet: -0.85 (0.21), residues: 574 loop : -0.90 (0.15), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 454 TYR 0.020 0.001 TYR B 332 PHE 0.026 0.001 PHE C 396 TRP 0.023 0.001 TRP F 184 HIS 0.005 0.001 HIS G 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.14 (40382) covalent geometry : angle 0.59694 / 0.33 (55877) hydrogen bonds : bond 0.04507 / 3.13 ( 1769) hydrogen bonds : angle 4.32751 / 3.09 ( 4793) metal coordination : bond 0.00717 / 0.42 ( 34) metal coordination : angle 3.01516 / 1.82 ( 14) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 171 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 10 LEU cc_start: 0.8481 (tt) cc_final: 0.8215 (tt) REVERT: B 458 ASP cc_start: 0.7153 (p0) cc_final: 0.6637 (t0) REVERT: B 584 MET cc_start: 0.2968 (tmm) cc_final: 0.2713 (tmm) REVERT: B 999 ASN cc_start: 0.7446 (t0) cc_final: 0.7197 (t0) REVERT: C 287 TYR cc_start: 0.6125 (OUTLIER) cc_final: 0.4510 (m-80) REVERT: E 248 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7487 (mttp) REVERT: E 385 SER cc_start: 0.8057 (OUTLIER) cc_final: 0.7684 (m) REVERT: E 567 MET cc_start: 0.8544 (mmm) cc_final: 0.7979 (mmm) REVERT: G 169 HIS cc_start: 0.6491 (OUTLIER) cc_final: 0.5410 (m-70) REVERT: H 234 MET cc_start: 0.1614 (mmm) cc_final: 0.0485 (ppp) outliers start: 66 outliers final: 49 residues processed: 229 average time/residue: 0.2141 time to fit residues: 86.3422 Evaluate side-chains 216 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 163 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 649 VAL Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 904 ASP Chi-restraints excluded: chain B residue 1101 GLU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain C residue 198 PHE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 287 TYR Chi-restraints excluded: chain C residue 429 ASN Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 632 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 308 LYS Chi-restraints excluded: chain E residue 379 HIS Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 470 VAL Chi-restraints excluded: chain E residue 476 ASP Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 550 VAL Chi-restraints excluded: chain E residue 578 ILE Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain E residue 630 VAL Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 184 TRP Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 351 MET Chi-restraints excluded: chain F residue 366 PHE Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 492 VAL Chi-restraints excluded: chain H residue 548 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 116 optimal weight: 0.9990 chunk 202 optimal weight: 2.9990 chunk 163 optimal weight: 10.0000 chunk 283 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 180 optimal weight: 2.9990 chunk 222 optimal weight: 0.0270 chunk 42 optimal weight: 1.9990 chunk 271 optimal weight: 6.9990 chunk 335 optimal weight: 0.9980 chunk 165 optimal weight: 10.0000 overall best weight: 1.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 GLN C 750 GLN ** E 513 ASN ** 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 = 0.4360 r_free = 0.4360 target = 0.150872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.129216 restraints weight = 112439.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.130105 restraints weight = 256085.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.130383 restraints weight = 103105.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.130627 restraints weight = 79984.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.130669 restraints weight = 63822.370| |-----------------------------------------------------------------------------| r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 40416 Z= 0.127 Angle : 0.587 12.760 55891 Z= 0.322 Chirality : 0.044 0.385 6250 Planarity : 0.004 0.064 6036 Dihedral : 22.999 174.376 7704 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.56 % Allowed : 12.53 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.13), residues: 3985 helix: 1.51 (0.13), residues: 1658 sheet: -0.71 (0.22), residues: 577 loop : -0.81 (0.15), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 454 TYR 0.018 0.001 TYR B 332 PHE 0.025 0.001 PHE F 574 TRP 0.024 0.001 TRP E 603 HIS 0.008 0.001 HIS G 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.13 (40382) covalent geometry : angle 0.58580 / 0.32 (55877) hydrogen bonds : bond 0.04358 / 3.03 ( 1769) hydrogen bonds : angle 4.20911 / 3.00 ( 4793) metal coordination : bond 0.00618 / 0.38 ( 34) metal coordination : angle 2.65032 / 1.62 ( 14) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 174 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 10 LEU cc_start: 0.8450 (tt) cc_final: 0.8183 (tt) REVERT: B 458 ASP cc_start: 0.7084 (p0) cc_final: 0.6541 (t0) REVERT: B 999 ASN cc_start: 0.7427 (t0) cc_final: 0.7167 (t0) REVERT: E 248 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.7326 (mttp) REVERT: E 385 SER cc_start: 0.8031 (OUTLIER) cc_final: 0.7679 (m) REVERT: E 567 MET cc_start: 0.8479 (mmm) cc_final: 0.7958 (mmm) REVERT: F 431 MET cc_start: 0.5979 (mtm) cc_final: 0.5631 (mtm) REVERT: G 169 HIS cc_start: 0.6342 (OUTLIER) cc_final: 0.5344 (m-70) REVERT: H 234 MET cc_start: 0.1414 (mmm) cc_final: 0.0522 (ppp) REVERT: H 527 LYS cc_start: 0.1944 (tttp) cc_final: 0.1726 (ttmm) outliers start: 57 outliers final: 48 residues processed: 222 average time/residue: 0.2175 time to fit residues: 84.8127 Evaluate side-chains 213 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 162 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 649 VAL Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 904 ASP Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain C residue 198 PHE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 429 ASN Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 308 LYS Chi-restraints excluded: chain E residue 379 HIS Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 467 ILE Chi-restraints excluded: chain E residue 470 VAL Chi-restraints excluded: chain E residue 476 ASP Chi-restraints excluded: chain E residue 525 SER Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 550 VAL Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain E residue 630 VAL Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 184 TRP Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 351 MET Chi-restraints excluded: chain F residue 366 PHE Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 492 VAL Chi-restraints excluded: chain H residue 523 MET Chi-restraints excluded: chain H residue 548 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 3 optimal weight: 20.0000 chunk 194 optimal weight: 0.5980 chunk 282 optimal weight: 6.9990 chunk 346 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 191 optimal weight: 0.1980 chunk 248 optimal weight: 0.0970 chunk 108 optimal weight: 3.9990 chunk 204 optimal weight: 5.9990 chunk 161 optimal weight: 0.8980 chunk 299 optimal weight: 9.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 750 GLN ** E 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.151121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.126412 restraints weight = 113083.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.127312 restraints weight = 264951.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.128564 restraints weight = 133920.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.128845 restraints weight = 80024.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.129482 restraints weight = 68413.625| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 40416 Z= 0.123 Angle : 0.574 13.004 55891 Z= 0.315 Chirality : 0.043 0.383 6250 Planarity : 0.004 0.063 6036 Dihedral : 22.975 173.706 7704 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.58 % Allowed : 12.78 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.13), residues: 3985 helix: 1.58 (0.13), residues: 1661 sheet: -0.68 (0.22), residues: 579 loop : -0.76 (0.15), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 573 TYR 0.021 0.001 TYR B 332 PHE 0.027 0.001 PHE C 396 TRP 0.021 0.001 TRP F 184 HIS 0.006 0.001 HIS G 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (40382) covalent geometry : angle 0.57232 / 0.31 (55877) hydrogen bonds : bond 0.04218 / 2.93 ( 1769) hydrogen bonds : angle 4.14149 / 2.95 ( 4793) metal coordination : bond 0.00559 / 0.34 ( 34) metal coordination : angle 2.47614 / 1.52 ( 14) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 171 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 10 LEU cc_start: 0.8463 (tt) cc_final: 0.8181 (tt) REVERT: B 458 ASP cc_start: 0.7178 (p0) cc_final: 0.6597 (t0) REVERT: B 584 MET cc_start: 0.3051 (tmm) cc_final: 0.2789 (tmm) REVERT: B 999 ASN cc_start: 0.7467 (t0) cc_final: 0.7209 (t0) REVERT: C 287 TYR cc_start: 0.6034 (OUTLIER) cc_final: 0.4375 (m-80) REVERT: E 248 LYS cc_start: 0.7470 (OUTLIER) cc_final: 0.7250 (mttp) REVERT: E 385 SER cc_start: 0.7910 (OUTLIER) cc_final: 0.7565 (m) REVERT: E 567 MET cc_start: 0.8360 (mmm) cc_final: 0.7840 (mmm) REVERT: F 469 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.7127 (pp) REVERT: G 169 HIS cc_start: 0.6283 (OUTLIER) cc_final: 0.5315 (m-70) REVERT: H 234 MET cc_start: 0.1570 (mmm) cc_final: 0.0676 (ppp) outliers start: 58 outliers final: 48 residues processed: 218 average time/residue: 0.2160 time to fit residues: 83.5057 Evaluate side-chains 217 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 164 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 81 HIS Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 649 VAL Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 904 ASP Chi-restraints excluded: chain B residue 1101 GLU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain C residue 198 PHE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 287 TYR Chi-restraints excluded: chain C residue 429 ASN Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 308 LYS Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 467 ILE Chi-restraints excluded: chain E residue 470 VAL Chi-restraints excluded: chain E residue 476 ASP Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain E residue 525 SER Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain E residue 630 VAL Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 184 TRP Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 351 MET Chi-restraints excluded: chain F residue 366 PHE Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 520 THR Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain H residue 214 MET Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 548 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 269 optimal weight: 7.9990 chunk 12 optimal weight: 0.0770 chunk 222 optimal weight: 0.2980 chunk 302 optimal weight: 3.9990 chunk 189 optimal weight: 0.7980 chunk 133 optimal weight: 30.0000 chunk 408 optimal weight: 50.0000 chunk 161 optimal weight: 0.0980 chunk 172 optimal weight: 0.6980 chunk 251 optimal weight: 7.9990 chunk 429 optimal weight: 50.0000 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 750 GLN ** E 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.151743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.127514 restraints weight = 112863.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.128894 restraints weight = 254186.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.130056 restraints weight = 118911.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.130140 restraints weight = 76451.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.130927 restraints weight = 63970.784| |-----------------------------------------------------------------------------| r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 40416 Z= 0.112 Angle : 0.568 14.958 55891 Z= 0.310 Chirality : 0.042 0.378 6250 Planarity : 0.004 0.059 6036 Dihedral : 22.918 173.079 7704 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.31 % Allowed : 13.03 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.13), residues: 3985 helix: 1.71 (0.13), residues: 1662 sheet: -0.51 (0.22), residues: 572 loop : -0.68 (0.15), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 615 TYR 0.017 0.001 TYR G 140 PHE 0.020 0.001 PHE F 61 TRP 0.051 0.002 TRP E 603 HIS 0.007 0.001 HIS G 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.11 (40382) covalent geometry : angle 0.56745 / 0.31 (55877) hydrogen bonds : bond 0.04014 / 2.80 ( 1769) hydrogen bonds : angle 4.03589 / 2.87 ( 4793) metal coordination : bond 0.00500 / 0.28 ( 34) metal coordination : angle 2.07232 / 1.35 ( 14) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 180 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 458 ASP cc_start: 0.7181 (p0) cc_final: 0.6578 (t0) REVERT: B 999 ASN cc_start: 0.7429 (t0) cc_final: 0.7177 (t0) REVERT: C 217 TYR cc_start: 0.1300 (OUTLIER) cc_final: 0.0442 (m-80) REVERT: C 287 TYR cc_start: 0.6203 (OUTLIER) cc_final: 0.4369 (m-80) REVERT: E 385 SER cc_start: 0.7838 (OUTLIER) cc_final: 0.7551 (m) REVERT: F 469 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.7143 (pp) REVERT: H 234 MET cc_start: 0.1692 (mmm) cc_final: 0.0726 (ppp) outliers start: 48 outliers final: 37 residues processed: 220 average time/residue: 0.2135 time to fit residues: 82.9066 Evaluate side-chains 208 residues out of total 3662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 167 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 649 VAL Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 904 ASP Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain C residue 198 PHE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 287 TYR Chi-restraints excluded: chain C residue 429 ASN Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 308 LYS Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 467 ILE Chi-restraints excluded: chain E residue 470 VAL Chi-restraints excluded: chain E residue 630 VAL Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 351 MET Chi-restraints excluded: chain F residue 366 PHE Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 520 THR Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 548 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 261 optimal weight: 0.4980 chunk 197 optimal weight: 0.6980 chunk 234 optimal weight: 0.0030 chunk 146 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 323 optimal weight: 9.9990 chunk 180 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 305 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 750 GLN ** E 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 417 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.151782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.127339 restraints weight = 113458.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.128189 restraints weight = 265746.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.129342 restraints weight = 136857.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.129771 restraints weight = 81775.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.130219 restraints weight = 69522.566| |-----------------------------------------------------------------------------| r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 40416 Z= 0.112 Angle : 0.558 13.230 55891 Z= 0.304 Chirality : 0.042 0.374 6250 Planarity : 0.004 0.060 6036 Dihedral : 22.897 172.802 7704 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.20 % Allowed : 13.13 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.14), residues: 3985 helix: 1.79 (0.13), residues: 1661 sheet: -0.46 (0.22), residues: 577 loop : -0.61 (0.15), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 573 TYR 0.025 0.001 TYR B 332 PHE 0.019 0.001 PHE C 555 TRP 0.038 0.001 TRP E 603 HIS 0.008 0.001 HIS F 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.11 (40382) covalent geometry : angle 0.55733 / 0.30 (55877) hydrogen bonds : bond 0.03958 / 2.76 ( 1769) hydrogen bonds : angle 3.98751 / 2.83 ( 4793) metal coordination : bond 0.00534 / 0.34 ( 34) metal coordination : angle 2.04138 / 1.31 ( 14) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5943.38 seconds wall clock time: 104 minutes 10.44 seconds (6250.44 seconds total)