Starting phenix.real_space_refine on Sat Jul 4 14:27:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v0a_64659/07_2026/9v0a_64659.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v0a_64659/07_2026/9v0a_64659.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v0a_64659/07_2026/9v0a_64659.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v0a_64659/07_2026/9v0a_64659.map" model { file = "/net/cci-nas-00/data/ceres_data/9v0a_64659/07_2026/9v0a_64659.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v0a_64659/07_2026/9v0a_64659.cif" } resolution = 3.69 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= 0.004 sd= 0.057 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: 5 Type Number sf(0) Gaussians Zn 6 6.06 5 S 126 5.16 5 C 13211 2.51 5 N 3577 2.21 5 O 3880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20800 Number of models: 1 Model: "" Number of chains: 11 Chain: "C" Number of atoms: 2915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2915 Classifications: {'peptide': 377} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 20, 'TRANS': 356} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 8, 'HIS:plan': 1, 'GLN:plan1': 4, 'ASN:plan1': 2, 'ARG:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 85 Chain: "D" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1138 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 130} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 442 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "N" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 599 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "U" Number of atoms: 593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 593 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 8696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1108, 8696 Classifications: {'peptide': 1108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 1067} Unresolved chain links: 1 Chain breaks: 4 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 5728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 699, 5728 Classifications: {'peptide': 699} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 679} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "R" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 663 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain breaks: 1 Chain: "C" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {' ZN': 1, 'Y70': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2139 SG CYS C 323 41.713 65.705 111.302 1.00145.69 S ATOM 2155 SG CYS C 326 38.855 67.071 109.323 1.00156.32 S ATOM 2653 SG CYS C 391 38.190 65.920 112.984 1.00151.50 S ATOM 2672 SG CYS C 394 38.767 63.445 110.323 1.00158.73 S ATOM 4323 SG CYS I 176 35.415 35.469 99.950 1.00237.20 S ATOM 4347 SG CYS I 179 33.277 36.665 97.021 1.00235.38 S ATOM 4106 SG CYS I 148 35.176 50.067 113.588 1.00156.17 S ATOM 4129 SG CYS I 151 36.309 52.806 116.012 1.00150.55 S ATOM 20317 SG CYS R 42 32.575 34.387 75.320 1.00150.23 S ATOM 20336 SG CYS R 45 36.279 33.424 74.668 1.00149.39 S ATOM 20584 SG CYS R 83 34.559 31.959 77.679 1.00185.97 S ATOM 20513 SG CYS R 75 18.446 33.782 82.146 1.00206.46 S ATOM 20680 SG CYS R 94 22.119 34.039 83.166 1.00186.62 S ATOM 20403 SG CYS R 53 36.016 28.887 74.365 1.00177.28 S ATOM 20426 SG CYS R 56 38.717 26.250 75.184 1.00184.74 S ATOM 20463 SG CYS R 68 36.233 25.626 72.338 1.00183.33 S Time building chain proxies: 4.50, per 1000 atoms: 0.22 Number of scatterers: 20800 At special positions: 0 Unit cell: (160.026, 142.842, 156.804, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 6 29.99 S 126 16.00 O 3880 8.00 N 3577 7.00 C 13211 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: 1.81 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 394 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 326 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 391 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 323 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" NE2 HIS I 192 " pdb="ZN ZN I 201 " - pdb=" NE2 HIS I 196 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 179 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 176 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" NE2 HIS I 164 " pdb="ZN ZN I 202 " - pdb=" ND1 HIS I 168 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 148 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 151 " pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" NE2 HIS R 80 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 45 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 83 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 42 " pdb=" ZN R 202 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 94 " pdb="ZN ZN R 202 " - pdb=" NE2 HIS R 77 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 75 " pdb=" ZN R 203 " pdb="ZN ZN R 203 " - pdb=" ND1 HIS R 82 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 68 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 53 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 56 " Number of angles added : 15 5172 Ramachandran restraints generated. 2586 Oldfield, 0 Emsley, 2586 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4936 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 36 sheets defined 31.0% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'C' and resid 53 through 57 Processing helix chain 'C' and resid 103 through 112 Processing helix chain 'C' and resid 192 through 197 removed outlier: 3.961A pdb=" N ALA C 196 " --> pdb=" O THR C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 232 Processing helix chain 'C' and resid 233 through 238 removed outlier: 3.724A pdb=" N ASN C 236 " --> pdb=" O HIS C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 247 removed outlier: 3.990A pdb=" N TYR C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 265 removed outlier: 3.507A pdb=" N LEU C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 286 Processing helix chain 'C' and resid 291 through 301 removed outlier: 3.559A pdb=" N ILE C 301 " --> pdb=" O GLN C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 317 Processing helix chain 'D' and resid 3 through 16 Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 98 through 112 removed outlier: 3.629A pdb=" N CYS D 111 " --> pdb=" O CYS D 107 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP D 112 " --> pdb=" O SER D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 130 Processing helix chain 'D' and resid 130 through 145 removed outlier: 4.017A pdb=" N TYR D 134 " --> pdb=" O ASP D 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 168 removed outlier: 3.981A pdb=" N LEU I 161 " --> pdb=" O GLN I 157 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 195 Processing helix chain 'N' and resid 22 through 34 removed outlier: 3.719A pdb=" N ILE N 26 " --> pdb=" O LYS N 22 " (cutoff:3.500A) Processing helix chain 'U' and resid 22 through 34 removed outlier: 3.967A pdb=" N VAL U 26 " --> pdb=" O THR U 22 " (cutoff:3.500A) Processing helix chain 'U' and resid 56 through 60 Processing helix chain 'B' and resid 252 through 256 Processing helix chain 'B' and resid 366 through 370 removed outlier: 3.762A pdb=" N ARG B 369 " --> pdb=" O ASP B 366 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN B 370 " --> pdb=" O LEU B 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 366 through 370' Processing helix chain 'B' and resid 986 through 991 removed outlier: 3.727A pdb=" N ARG B 989 " --> pdb=" O ASP B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 1044 through 1062 Processing helix chain 'B' and resid 1069 through 1074 Processing helix chain 'B' and resid 1091 through 1095 Processing helix chain 'B' and resid 1096 through 1100 removed outlier: 3.702A pdb=" N ASP B1099 " --> pdb=" O SER B1096 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE B1100 " --> pdb=" O PHE B1097 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1096 through 1100' Processing helix chain 'B' and resid 1101 through 1108 removed outlier: 4.167A pdb=" N GLU B1107 " --> pdb=" O PRO B1103 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL B1108 " --> pdb=" O LYS B1104 " (cutoff:3.500A) Processing helix chain 'B' and resid 1125 through 1138 removed outlier: 3.722A pdb=" N LYS B1131 " --> pdb=" O ASP B1127 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL B1132 " --> pdb=" O ASP B1128 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL B1133 " --> pdb=" O LEU B1129 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG B1138 " --> pdb=" O GLU B1134 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 75 Processing helix chain 'A' and resid 82 through 95 Processing helix chain 'A' and resid 98 through 115 removed outlier: 3.788A pdb=" N LEU A 102 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N HIS A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 123 removed outlier: 3.662A pdb=" N LEU A 119 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Proline residue: A 120 - end of helix removed outlier: 4.163A pdb=" N GLU A 123 " --> pdb=" O PRO A 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 116 through 123' Processing helix chain 'A' and resid 127 through 153 removed outlier: 3.583A pdb=" N PHE A 131 " --> pdb=" O ASP A 127 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET A 148 " --> pdb=" O ARG A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 164 removed outlier: 3.720A pdb=" N VAL A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N LEU A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLN A 163 " --> pdb=" O THR A 159 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN A 164 " --> pdb=" O TYR A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 182 removed outlier: 3.635A pdb=" N LEU A 175 " --> pdb=" O TRP A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 205 Processing helix chain 'A' and resid 211 through 224 removed outlier: 3.853A pdb=" N LEU A 224 " --> pdb=" O MET A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 231 through 252 removed outlier: 4.294A pdb=" N ALA A 245 " --> pdb=" O CYS A 241 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N GLY A 247 " --> pdb=" O TYR A 243 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLN A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLN A 252 " --> pdb=" O GLN A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 277 removed outlier: 3.563A pdb=" N TYR A 277 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 282 Processing helix chain 'A' and resid 283 through 295 Processing helix chain 'A' and resid 298 through 314 removed outlier: 5.037A pdb=" N ASP A 308 " --> pdb=" O GLN A 304 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N HIS A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASP A 312 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 327 Processing helix chain 'A' and resid 331 through 354 removed outlier: 4.513A pdb=" N ASN A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 359 No H-bonds generated for 'chain 'A' and resid 357 through 359' Processing helix chain 'A' and resid 360 through 379 Processing helix chain 'A' and resid 383 through 399 removed outlier: 4.149A pdb=" N ASN A 399 " --> pdb=" O GLU A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 417 removed outlier: 3.886A pdb=" N GLU A 407 " --> pdb=" O ASN A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 441 removed outlier: 3.530A pdb=" N ARG A 441 " --> pdb=" O MET A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 464 removed outlier: 4.025A pdb=" N LYS A 459 " --> pdb=" O LYS A 455 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG A 460 " --> pdb=" O ASP A 456 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 461 " --> pdb=" O LEU A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 515 removed outlier: 7.100A pdb=" N ALA A 485 " --> pdb=" O HIS A 481 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N ALA A 486 " --> pdb=" O GLU A 482 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE A 487 " --> pdb=" O CYS A 483 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR A 488 " --> pdb=" O GLY A 484 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N LYS A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU A 491 " --> pdb=" O PHE A 487 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY A 493 " --> pdb=" O SER A 489 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N MET A 494 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N PHE A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS A 496 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP A 497 " --> pdb=" O GLY A 493 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N MET A 498 " --> pdb=" O MET A 494 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N HIS A 507 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN A 510 " --> pdb=" O VAL A 506 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN A 515 " --> pdb=" O HIS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 562 removed outlier: 3.617A pdb=" N LYS A 549 " --> pdb=" O PRO A 545 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN A 551 " --> pdb=" O MET A 547 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE A 554 " --> pdb=" O LEU A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 603 Processing helix chain 'A' and resid 609 through 618 removed outlier: 3.721A pdb=" N ILE A 613 " --> pdb=" O SER A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 634 Processing helix chain 'A' and resid 693 through 708 removed outlier: 4.166A pdb=" N ASP A 697 " --> pdb=" O GLN A 693 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N MET A 706 " --> pdb=" O ARG A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 721 removed outlier: 3.665A pdb=" N VAL A 716 " --> pdb=" O HIS A 712 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER A 717 " --> pdb=" O ASN A 713 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN A 721 " --> pdb=" O SER A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 742 removed outlier: 3.567A pdb=" N LYS A 734 " --> pdb=" O GLY A 730 " (cutoff:3.500A) Processing helix chain 'R' and resid 53 through 58 removed outlier: 4.274A pdb=" N ALA R 58 " --> pdb=" O ILE R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 91 Processing sheet with id=AA1, first strand: chain 'C' and resid 96 through 99 removed outlier: 3.522A pdb=" N LEU C 168 " --> pdb=" O LYS C 181 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LYS C 181 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N LEU C 170 " --> pdb=" O GLN C 179 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLN C 179 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLN C 178 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 9.469A pdb=" N VAL C 80 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N ALA C 121 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU C 123 " --> pdb=" O PRO C 82 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLY C 136 " --> pdb=" O ARG C 164 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ARG C 164 " --> pdb=" O GLY C 136 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR C 138 " --> pdb=" O ARG C 162 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 321 through 322 Processing sheet with id=AA3, first strand: chain 'C' and resid 349 through 350 Processing sheet with id=AA4, first strand: chain 'C' and resid 360 through 362 removed outlier: 3.519A pdb=" N LEU C 417 " --> pdb=" O LEU C 360 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 368 through 370 removed outlier: 3.586A pdb=" N GLN C 390 " --> pdb=" O ASN C 369 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS C 401 " --> pdb=" O THR C 387 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA C 389 " --> pdb=" O GLY C 399 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLY C 399 " --> pdb=" O ALA C 389 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N CYS C 391 " --> pdb=" O HIS C 397 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N HIS C 397 " --> pdb=" O CYS C 391 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 21 through 25 Processing sheet with id=AA7, first strand: chain 'D' and resid 52 through 55 Processing sheet with id=AA8, first strand: chain 'N' and resid 12 through 16 removed outlier: 6.842A pdb=" N LEU N 2 " --> pdb=" O SER N 65 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU N 67 " --> pdb=" O LEU N 2 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LYS N 4 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LEU N 69 " --> pdb=" O LYS N 4 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LYS N 6 " --> pdb=" O LEU N 69 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N LEU N 71 " --> pdb=" O LYS N 6 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'U' and resid 12 through 16 removed outlier: 3.995A pdb=" N SER U 65 " --> pdb=" O GLN U 2 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1007 through 1009 removed outlier: 6.515A pdb=" N ILE B1037 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL B 6 " --> pdb=" O ILE B1089 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 20 through 21 removed outlier: 3.637A pdb=" N LYS B 53 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N VAL B 43 " --> pdb=" O PRO B 51 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 63 through 65 removed outlier: 3.511A pdb=" N VAL B 63 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU B 65 " --> pdb=" O PHE B 78 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 78 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ILE B 88 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 121 through 124 removed outlier: 3.685A pdb=" N ILE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 163 through 169 removed outlier: 4.493A pdb=" N HIS B 163 " --> pdb=" O GLN B 183 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL B 181 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N VAL B 167 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N CYS B 179 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N PHE B 169 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N THR B 177 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE B 180 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU B 201 " --> pdb=" O SER B 196 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 163 through 169 removed outlier: 4.493A pdb=" N HIS B 163 " --> pdb=" O GLN B 183 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL B 181 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N VAL B 167 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N CYS B 179 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N PHE B 169 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N THR B 177 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE B 180 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ARG B 188 " --> pdb=" O VAL B 212 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 218 through 221 Processing sheet with id=AB8, first strand: chain 'B' and resid 258 through 263 removed outlier: 4.728A pdb=" N ARG B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU B 280 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP B 299 " --> pdb=" O GLU B 286 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 313 through 316 removed outlier: 6.359A pdb=" N LYS B 335 " --> pdb=" O ALA B 349 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ALA B 349 " --> pdb=" O LYS B 335 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 359 through 365 removed outlier: 7.088A pdb=" N CYS B 378 " --> pdb=" O VAL B 360 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N MET B 362 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL B 376 " --> pdb=" O MET B 362 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N VAL B 364 " --> pdb=" O GLN B 374 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLN B 374 " --> pdb=" O VAL B 364 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 359 through 365 removed outlier: 7.088A pdb=" N CYS B 378 " --> pdb=" O VAL B 360 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N MET B 362 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL B 376 " --> pdb=" O MET B 362 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N VAL B 364 " --> pdb=" O GLN B 374 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLN B 374 " --> pdb=" O VAL B 364 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 396 through 403 removed outlier: 5.591A pdb=" N GLU B 398 " --> pdb=" O THR B 703 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N THR B 703 " --> pdb=" O GLU B 398 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 410 through 413 removed outlier: 3.545A pdb=" N TRP B 411 " --> pdb=" O VAL B 426 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU B 442 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 457 through 463 removed outlier: 6.593A pdb=" N ILE B 471 " --> pdb=" O PHE B 458 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N CYS B 460 " --> pdb=" O ILE B 469 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE B 469 " --> pdb=" O CYS B 460 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ASN B 462 " --> pdb=" O GLN B 467 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N GLN B 467 " --> pdb=" O ASN B 462 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG B 477 " --> pdb=" O GLN B 470 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL B 476 " --> pdb=" O TRP B 490 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU B 478 " --> pdb=" O SER B 488 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER B 488 " --> pdb=" O LEU B 478 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N SER B 480 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU B 486 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 500 through 503 removed outlier: 6.856A pdb=" N LEU B 516 " --> pdb=" O HIS B 531 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N HIS B 531 " --> pdb=" O LEU B 516 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N TYR B 518 " --> pdb=" O ILE B 529 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN B 520 " --> pdb=" O ARG B 527 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG B 527 " --> pdb=" O GLN B 520 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.466A pdb=" N GLY B 559 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU B 541 " --> pdb=" O ALA B 557 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA B 557 " --> pdb=" O LEU B 541 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE B 568 " --> pdb=" O LEU B 577 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 588 through 596 removed outlier: 3.634A pdb=" N SER B 590 " --> pdb=" O ALA B 605 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ALA B 610 " --> pdb=" O LEU B 606 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU B 611 " --> pdb=" O LYS B 628 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LYS B 628 " --> pdb=" O LEU B 611 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N TYR B 613 " --> pdb=" O ARG B 626 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ARG B 626 " --> pdb=" O TYR B 613 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER B 624 " --> pdb=" O GLY B 615 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 637 through 643 removed outlier: 8.975A pdb=" N THR B 647 " --> pdb=" O SER B 661 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N SER B 661 " --> pdb=" O THR B 647 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 720 through 727 removed outlier: 4.008A pdb=" N SER B 720 " --> pdb=" O SER B 738 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU B 736 " --> pdb=" O ARG B 722 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ILE B 724 " --> pdb=" O GLY B 734 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLY B 734 " --> pdb=" O ILE B 724 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N TYR B 726 " --> pdb=" O CYS B 732 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N CYS B 732 " --> pdb=" O TYR B 726 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS B 803 " --> pdb=" O ILE B 793 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ASP B 795 " --> pdb=" O VAL B 801 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL B 801 " --> pdb=" O ASP B 795 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER B 764 " --> pdb=" O GLN B 806 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 811 through 819 removed outlier: 5.327A pdb=" N ALA B 813 " --> pdb=" O ALA B 834 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA B 834 " --> pdb=" O ALA B 813 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLN B 845 " --> pdb=" O MET B 835 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N GLY B 846 " --> pdb=" O GLU B 865 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N GLU B 865 " --> pdb=" O GLY B 846 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE B 848 " --> pdb=" O GLU B 863 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLU B 863 " --> pdb=" O ILE B 848 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL B 850 " --> pdb=" O VAL B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 890 through 893 removed outlier: 7.096A pdb=" N LEU B 890 " --> pdb=" O GLU B 902 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 915 through 917 removed outlier: 3.610A pdb=" N LYS B 915 " --> pdb=" O LEU B 922 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA B 946 " --> pdb=" O LEU B 932 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA B 934 " --> pdb=" O GLU B 944 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N GLU B 944 " --> pdb=" O ALA B 934 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LYS B 936 " --> pdb=" O PHE B 942 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N PHE B 942 " --> pdb=" O LYS B 936 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 954 through 961 removed outlier: 4.947A pdb=" N ALA B 956 " --> pdb=" O ALA B 968 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ASN B 964 " --> pdb=" O LEU B 960 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASN B 973 " --> pdb=" O GLU B 969 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY B 996 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLN B 978 " --> pdb=" O GLU B 994 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N GLU B 994 " --> pdb=" O GLN B 978 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1076 through 1078 Processing sheet with id=AD7, first strand: chain 'A' and resid 527 through 528 removed outlier: 7.063A pdb=" N LEU A 528 " --> pdb=" O TRP R 33 " (cutoff:3.500A) removed outlier: 9.134A pdb=" N TRP R 35 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL R 30 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLN A 570 " --> pdb=" O VAL R 30 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU R 32 " --> pdb=" O GLN A 568 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN A 568 " --> pdb=" O LEU R 32 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 575 through 578 Processing sheet with id=AD9, first strand: chain 'A' and resid 639 through 642 removed outlier: 3.951A pdb=" N SER A 642 " --> pdb=" O LYS A 653 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS A 653 " --> pdb=" O SER A 642 " (cutoff:3.500A) 815 hydrogen bonds defined for protein. 2274 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.47 Time building geometry restraints manager: 2.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4622 1.33 - 1.45: 4432 1.45 - 1.57: 11962 1.57 - 1.70: 0 1.70 - 1.82: 189 Bond restraints: 21205 Sorted by residual: bond pdb=" CA GLN D 92 " pdb=" CB GLN D 92 " ideal model delta sigma weight residual 1.524 1.568 -0.043 1.30e-02 5.92e+03 1.11e+01 bond pdb=" CA GLU N 28 " pdb=" CB GLU N 28 " ideal model delta sigma weight residual 1.529 1.560 -0.031 1.74e-02 3.30e+03 3.11e+00 bond pdb=" C1 Y70 C 502 " pdb=" C6 Y70 C 502 " ideal model delta sigma weight residual 1.419 1.387 0.032 2.00e-02 2.50e+03 2.52e+00 bond pdb=" N PRO N 37 " pdb=" CA PRO N 37 " ideal model delta sigma weight residual 1.457 1.476 -0.019 1.31e-02 5.83e+03 2.00e+00 bond pdb=" C6 Y70 C 502 " pdb=" N10 Y70 C 502 " ideal model delta sigma weight residual 1.343 1.367 -0.024 2.00e-02 2.50e+03 1.48e+00 ... (remaining 21200 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 28249 2.21 - 4.42: 374 4.42 - 6.63: 45 6.63 - 8.84: 7 8.84 - 11.05: 2 Bond angle restraints: 28677 Sorted by residual: angle pdb=" N VAL B 487 " pdb=" CA VAL B 487 " pdb=" C VAL B 487 " ideal model delta sigma weight residual 113.53 109.07 4.46 9.80e-01 1.04e+00 2.07e+01 angle pdb=" CA GLU N 28 " pdb=" CB GLU N 28 " pdb=" CG GLU N 28 " ideal model delta sigma weight residual 114.10 122.66 -8.56 2.00e+00 2.50e-01 1.83e+01 angle pdb=" N GLU N 28 " pdb=" CA GLU N 28 " pdb=" CB GLU N 28 " ideal model delta sigma weight residual 110.39 117.39 -7.00 1.66e+00 3.63e-01 1.78e+01 angle pdb=" C LYS N 27 " pdb=" N GLU N 28 " pdb=" CA GLU N 28 " ideal model delta sigma weight residual 120.72 113.73 6.99 1.67e+00 3.59e-01 1.75e+01 angle pdb=" N ILE A 669 " pdb=" CA ILE A 669 " pdb=" C ILE A 669 " ideal model delta sigma weight residual 111.88 107.77 4.11 1.06e+00 8.90e-01 1.50e+01 ... (remaining 28672 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 11545 17.94 - 35.89: 1104 35.89 - 53.83: 169 53.83 - 71.77: 30 71.77 - 89.71: 15 Dihedral angle restraints: 12863 sinusoidal: 5248 harmonic: 7615 Sorted by residual: dihedral pdb=" CA ARG B 928 " pdb=" C ARG B 928 " pdb=" N SER B 929 " pdb=" CA SER B 929 " ideal model delta harmonic sigma weight residual 180.00 159.65 20.35 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA PRO N 37 " pdb=" C PRO N 37 " pdb=" N PRO N 38 " pdb=" CA PRO N 38 " ideal model delta harmonic sigma weight residual -180.00 -160.01 -19.99 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA GLN B 466 " pdb=" C GLN B 466 " pdb=" N GLN B 467 " pdb=" CA GLN B 467 " ideal model delta harmonic sigma weight residual 180.00 160.94 19.06 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 12860 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2493 0.047 - 0.094: 552 0.094 - 0.141: 184 0.141 - 0.188: 3 0.188 - 0.235: 2 Chirality restraints: 3234 Sorted by residual: chirality pdb=" CA GLU N 28 " pdb=" N GLU N 28 " pdb=" C GLU N 28 " pdb=" CB GLU N 28 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB VAL A 98 " pdb=" CA VAL A 98 " pdb=" CG1 VAL A 98 " pdb=" CG2 VAL A 98 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA GLU D 140 " pdb=" N GLU D 140 " pdb=" C GLU D 140 " pdb=" CB GLU D 140 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.46e-01 ... (remaining 3231 not shown) Planarity restraints: 3680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 Y70 C 502 " 0.074 2.00e-02 2.50e+03 1.56e-01 7.95e+02 pdb=" C12 Y70 C 502 " 0.394 2.00e-02 2.50e+03 pdb=" C2 Y70 C 502 " 0.085 2.00e-02 2.50e+03 pdb=" C3 Y70 C 502 " 0.041 2.00e-02 2.50e+03 pdb=" C4 Y70 C 502 " -0.013 2.00e-02 2.50e+03 pdb=" C5 Y70 C 502 " -0.027 2.00e-02 2.50e+03 pdb=" C6 Y70 C 502 " 0.018 2.00e-02 2.50e+03 pdb=" C7 Y70 C 502 " -0.081 2.00e-02 2.50e+03 pdb=" C9 Y70 C 502 " -0.084 2.00e-02 2.50e+03 pdb=" N10 Y70 C 502 " 0.008 2.00e-02 2.50e+03 pdb=" N8 Y70 C 502 " 0.086 2.00e-02 2.50e+03 pdb=" O11 Y70 C 502 " -0.239 2.00e-02 2.50e+03 pdb=" O13 Y70 C 502 " -0.262 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 Y70 C 502 " 0.005 2.00e-02 2.50e+03 2.17e-02 5.87e+00 pdb=" C15 Y70 C 502 " 0.006 2.00e-02 2.50e+03 pdb=" C17 Y70 C 502 " -0.026 2.00e-02 2.50e+03 pdb=" N16 Y70 C 502 " 0.035 2.00e-02 2.50e+03 pdb=" O19 Y70 C 502 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 354 " 0.038 5.00e-02 4.00e+02 5.83e-02 5.43e+00 pdb=" N PRO A 355 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 355 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 355 " 0.032 5.00e-02 4.00e+02 ... (remaining 3677 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 322 2.64 - 3.21: 19585 3.21 - 3.77: 31271 3.77 - 4.34: 41653 4.34 - 4.90: 68361 Nonbonded interactions: 161192 Sorted by model distance: nonbonded pdb=" OG SER D 91 " pdb=" OE1 GLN D 92 " model vdw 2.079 3.040 nonbonded pdb=" OG SER A 468 " pdb=" OD1 ASP A 470 " model vdw 2.166 3.040 nonbonded pdb=" O THR A 159 " pdb=" NE2 GLN A 163 " model vdw 2.190 3.120 nonbonded pdb=" O VAL A 226 " pdb=" OG SER A 230 " model vdw 2.193 3.040 nonbonded pdb=" ND2 ASN B 392 " pdb=" O LEU B1012 " model vdw 2.202 3.120 ... (remaining 161187 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.900 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21228 Z= 0.139 Angle : 0.653 11.048 28692 Z= 0.342 Chirality : 0.043 0.235 3234 Planarity : 0.005 0.156 3680 Dihedral : 14.094 89.715 7927 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.04 % Allowed : 0.09 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.86 (0.17), residues: 2586 helix: 0.94 (0.20), residues: 689 sheet: -0.45 (0.22), residues: 608 loop : -1.48 (0.17), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG N 25 TYR 0.017 0.001 TYR D 45 PHE 0.025 0.001 PHE A 397 TRP 0.034 0.002 TRP D 93 HIS 0.008 0.001 HIS R 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (21205) covalent geometry : angle 0.64955 / 0.34 (28677) hydrogen bonds : bond 0.21969 / 14.75 ( 799) hydrogen bonds : angle 7.95514 / 5.55 ( 2274) metal coordination : bond 0.01128 / 0.51 ( 23) metal coordination : angle 3.07457 / 1.90 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5172 Ramachandran restraints generated. 2586 Oldfield, 0 Emsley, 2586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5172 Ramachandran restraints generated. 2586 Oldfield, 0 Emsley, 2586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 302 time to evaluate : 1.047 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: 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: D 8 LYS cc_start: 0.9252 (mmmm) cc_final: 0.8914 (mtmm) REVERT: I 184 GLN cc_start: 0.7092 (mp10) cc_final: 0.6757 (mp10) REVERT: N 51 ASN cc_start: 0.7965 (t0) cc_final: 0.7665 (t0) REVERT: B 80 LEU cc_start: 0.7579 (tp) cc_final: 0.7377 (tp) REVERT: A 494 MET cc_start: 0.7862 (mmt) cc_final: 0.7544 (mmp) REVERT: A 539 MET cc_start: 0.7542 (pmm) cc_final: 0.7148 (pmm) REVERT: A 601 MET cc_start: 0.8437 (ppp) cc_final: 0.8168 (ptt) outliers start: 1 outliers final: 0 residues processed: 303 average time/residue: 0.1620 time to fit residues: 75.4562 Evaluate side-chains 184 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 30.0000 chunk 71 optimal weight: 6.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 GLN D 77 ASN ** U 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 908 ASN ** B1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 GLN ** A 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.053190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.043417 restraints weight = 208368.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.044474 restraints weight = 115027.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.045202 restraints weight = 77069.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.045572 restraints weight = 58041.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.045934 restraints weight = 49359.999| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 21228 Z= 0.220 Angle : 0.700 12.122 28692 Z= 0.357 Chirality : 0.045 0.198 3234 Planarity : 0.004 0.056 3680 Dihedral : 4.566 32.572 2824 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.13 % Allowed : 9.08 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.90 (0.16), residues: 2586 helix: 0.87 (0.20), residues: 733 sheet: -0.54 (0.21), residues: 629 loop : -1.54 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 742 TYR 0.025 0.002 TYR D 45 PHE 0.018 0.002 PHE A 397 TRP 0.021 0.002 TRP D 93 HIS 0.010 0.001 HIS R 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.22 (21205) covalent geometry : angle 0.69324 / 0.36 (28677) hydrogen bonds : bond 0.04666 / 3.20 ( 799) hydrogen bonds : angle 5.93763 / 4.12 ( 2274) metal coordination : bond 0.01499 / 0.78 ( 23) metal coordination : angle 4.40842 / 2.61 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5172 Ramachandran restraints generated. 2586 Oldfield, 0 Emsley, 2586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5172 Ramachandran restraints generated. 2586 Oldfield, 0 Emsley, 2586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 193 time to evaluate : 0.855 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: 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: C 194 MET cc_start: 0.9375 (mmm) cc_final: 0.9110 (mmm) REVERT: C 254 MET cc_start: 0.9282 (mmt) cc_final: 0.8664 (mmt) REVERT: N 8 LEU cc_start: 0.9540 (OUTLIER) cc_final: 0.9262 (mm) REVERT: N 32 GLU cc_start: 0.9044 (pt0) cc_final: 0.8799 (pp20) REVERT: B 592 LEU cc_start: 0.9538 (tp) cc_final: 0.9289 (tt) REVERT: B 593 MET cc_start: 0.8829 (mtt) cc_final: 0.8604 (mtt) REVERT: B 912 LEU cc_start: 0.9605 (OUTLIER) cc_final: 0.9398 (mm) REVERT: A 173 MET cc_start: 0.9300 (OUTLIER) cc_final: 0.8966 (ppp) REVERT: A 390 MET cc_start: 0.9472 (tmm) cc_final: 0.9200 (ppp) REVERT: A 475 MET cc_start: 0.9450 (tpp) cc_final: 0.8943 (tpp) REVERT: A 479 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.8971 (mt) REVERT: A 494 MET cc_start: 0.8455 (mmt) cc_final: 0.8120 (mmp) REVERT: A 539 MET cc_start: 0.8489 (pmm) cc_final: 0.8211 (pmm) REVERT: A 601 MET cc_start: 0.9100 (ppp) cc_final: 0.8843 (ptt) REVERT: A 720 TYR cc_start: 0.9076 (m-80) cc_final: 0.8734 (m-10) outliers start: 26 outliers final: 17 residues processed: 209 average time/residue: 0.1495 time to fit residues: 48.6086 Evaluate side-chains 187 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain U residue 4 PHE Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 548 ASP Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 873 MET Chi-restraints excluded: chain B residue 912 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1006 VAL Chi-restraints excluded: chain B residue 1014 MET Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain R residue 69 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 155 optimal weight: 7.9990 chunk 243 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 233 optimal weight: 40.0000 chunk 166 optimal weight: 5.9990 chunk 242 optimal weight: 9.9990 chunk 113 optimal weight: 20.0000 chunk 111 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 2 optimal weight: 0.6980 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN ** I 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 184 GLN ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.049693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.040083 restraints weight = 212772.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.041107 restraints weight = 116833.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.041728 restraints weight = 78287.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.042251 restraints weight = 60213.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.042551 restraints weight = 49484.784| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 21228 Z= 0.253 Angle : 0.689 9.327 28692 Z= 0.354 Chirality : 0.045 0.170 3234 Planarity : 0.004 0.051 3680 Dihedral : 4.778 32.704 2824 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.62 % Allowed : 12.09 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.16), residues: 2586 helix: 0.78 (0.20), residues: 729 sheet: -0.66 (0.20), residues: 628 loop : -1.58 (0.17), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 15 TYR 0.020 0.002 TYR B 3 PHE 0.021 0.002 PHE A 554 TRP 0.028 0.002 TRP D 93 HIS 0.011 0.001 HIS R 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.25 (21205) covalent geometry : angle 0.67903 / 0.35 (28677) hydrogen bonds : bond 0.04181 / 2.87 ( 799) hydrogen bonds : angle 5.63418 / 3.91 ( 2274) metal coordination : bond 0.01695 / 0.97 ( 23) metal coordination : angle 5.13035 / 3.00 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5172 Ramachandran restraints generated. 2586 Oldfield, 0 Emsley, 2586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5172 Ramachandran restraints generated. 2586 Oldfield, 0 Emsley, 2586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 0.889 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 194 MET cc_start: 0.9389 (mmm) cc_final: 0.9188 (mmm) REVERT: C 254 MET cc_start: 0.9321 (mmt) cc_final: 0.8528 (mmt) REVERT: D 38 MET cc_start: 0.8459 (mmt) cc_final: 0.8018 (mpp) REVERT: I 166 CYS cc_start: 0.9142 (m) cc_final: 0.8721 (p) REVERT: I 184 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7624 (mm-40) REVERT: N 52 ASP cc_start: 0.8991 (m-30) cc_final: 0.8779 (t0) REVERT: N 73 LEU cc_start: 0.9173 (tp) cc_final: 0.8702 (tp) REVERT: U 56 LEU cc_start: 0.9668 (mp) cc_final: 0.9410 (pp) REVERT: B 282 MET cc_start: 0.8661 (tpt) cc_final: 0.8391 (tpt) REVERT: B 593 MET cc_start: 0.8862 (mtt) cc_final: 0.8633 (mtt) REVERT: B 910 MET cc_start: 0.8963 (ttm) cc_final: 0.8191 (tpp) REVERT: B 1054 MET cc_start: 0.9167 (ttt) cc_final: 0.8814 (tpt) REVERT: A 390 MET cc_start: 0.9580 (tmm) cc_final: 0.9270 (ppp) REVERT: A 475 MET cc_start: 0.9516 (tpp) cc_final: 0.9241 (tpp) REVERT: A 505 MET cc_start: 0.9162 (mmt) cc_final: 0.8612 (mmm) REVERT: A 539 MET cc_start: 0.8570 (pmm) cc_final: 0.8066 (pmm) REVERT: A 720 TYR cc_start: 0.9138 (m-10) cc_final: 0.8855 (m-10) outliers start: 37 outliers final: 25 residues processed: 196 average time/residue: 0.1563 time to fit residues: 48.1370 Evaluate side-chains 186 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain I residue 184 GLN Chi-restraints excluded: chain N residue 28 GLU Chi-restraints excluded: chain N residue 54 LYS Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain U residue 4 PHE Chi-restraints excluded: chain U residue 39 ASP Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 548 ASP Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 926 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1014 MET Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain R residue 92 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 87 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 chunk 174 optimal weight: 9.9990 chunk 153 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 149 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 GLN ** I 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 68 HIS ** U 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.049323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.039777 restraints weight = 213385.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.040805 restraints weight = 114314.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.041513 restraints weight = 75702.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.042004 restraints weight = 56686.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.042261 restraints weight = 46295.836| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21228 Z= 0.201 Angle : 0.640 9.627 28692 Z= 0.326 Chirality : 0.043 0.194 3234 Planarity : 0.004 0.099 3680 Dihedral : 4.704 33.803 2824 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.27 % Allowed : 13.79 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.98 (0.16), residues: 2586 helix: 0.82 (0.20), residues: 739 sheet: -0.71 (0.20), residues: 632 loop : -1.54 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 15 TYR 0.017 0.001 TYR B1114 PHE 0.016 0.001 PHE A 554 TRP 0.022 0.002 TRP D 93 HIS 0.009 0.001 HIS R 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.20 (21205) covalent geometry : angle 0.63306 / 0.33 (28677) hydrogen bonds : bond 0.03562 / 2.44 ( 799) hydrogen bonds : angle 5.35826 / 3.72 ( 2274) metal coordination : bond 0.01300 / 0.73 ( 23) metal coordination : angle 4.27618 / 2.67 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5172 Ramachandran restraints generated. 2586 Oldfield, 0 Emsley, 2586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5172 Ramachandran restraints generated. 2586 Oldfield, 0 Emsley, 2586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 173 time to evaluate : 0.849 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 254 MET cc_start: 0.9331 (mmt) cc_final: 0.8564 (mmt) REVERT: D 38 MET cc_start: 0.8336 (mmt) cc_final: 0.7961 (mpp) REVERT: I 166 CYS cc_start: 0.9145 (m) cc_final: 0.8714 (p) REVERT: I 184 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7991 (mm-40) REVERT: N 4 LYS cc_start: 0.9031 (mtmm) cc_final: 0.8813 (mtmm) REVERT: N 52 ASP cc_start: 0.9035 (m-30) cc_final: 0.8808 (t0) REVERT: N 73 LEU cc_start: 0.9197 (tp) cc_final: 0.8784 (tp) REVERT: U 1 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8675 (mtm) REVERT: U 56 LEU cc_start: 0.9691 (mp) cc_final: 0.9473 (pp) REVERT: B 282 MET cc_start: 0.8821 (tpt) cc_final: 0.8489 (tpt) REVERT: B 362 MET cc_start: 0.9105 (pmm) cc_final: 0.8661 (pmm) REVERT: B 593 MET cc_start: 0.8941 (mtt) cc_final: 0.8670 (mtt) REVERT: B 910 MET cc_start: 0.8875 (ttm) cc_final: 0.8048 (tpp) REVERT: B 1054 MET cc_start: 0.9188 (ttt) cc_final: 0.8934 (tpt) REVERT: A 187 MET cc_start: 0.9080 (ppp) cc_final: 0.8803 (ppp) REVERT: A 221 LEU cc_start: 0.9416 (tt) cc_final: 0.8962 (pp) REVERT: A 390 MET cc_start: 0.9630 (tmm) cc_final: 0.9284 (ppp) REVERT: A 437 MET cc_start: 0.9250 (ppp) cc_final: 0.9046 (ppp) REVERT: A 475 MET cc_start: 0.9565 (tpp) cc_final: 0.9334 (tpp) REVERT: A 505 MET cc_start: 0.9224 (mmt) cc_final: 0.8698 (mmm) REVERT: A 539 MET cc_start: 0.8591 (pmm) cc_final: 0.8113 (pmm) outliers start: 52 outliers final: 30 residues processed: 205 average time/residue: 0.1454 time to fit residues: 46.6015 Evaluate side-chains 193 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain I residue 144 ARG Chi-restraints excluded: chain I residue 184 GLN Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain N residue 23 VAL Chi-restraints excluded: chain N residue 28 GLU Chi-restraints excluded: chain N residue 54 LYS Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 4 PHE Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 598 SER Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 873 MET Chi-restraints excluded: chain B residue 926 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1006 VAL Chi-restraints excluded: chain B residue 1014 MET Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 92 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 210 optimal weight: 5.9990 chunk 226 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 175 optimal weight: 8.9990 chunk 123 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 76 optimal weight: 0.6980 chunk 114 optimal weight: 20.0000 chunk 53 optimal weight: 9.9990 chunk 225 optimal weight: 7.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 GLN C 236 ASN ** I 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 180 ASN I 184 GLN ** U 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 GLN ** A 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.047752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.038338 restraints weight = 215029.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.039337 restraints weight = 113856.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.040038 restraints weight = 75154.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.040481 restraints weight = 56387.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.040737 restraints weight = 46243.926| |-----------------------------------------------------------------------------| r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 21228 Z= 0.228 Angle : 0.671 9.670 28692 Z= 0.338 Chirality : 0.044 0.190 3234 Planarity : 0.004 0.056 3680 Dihedral : 4.761 35.166 2824 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.01 % Allowed : 15.06 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.99 (0.16), residues: 2586 helix: 0.83 (0.19), residues: 741 sheet: -0.73 (0.20), residues: 652 loop : -1.56 (0.17), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG U 42 TYR 0.021 0.002 TYR B1114 PHE 0.020 0.002 PHE A 554 TRP 0.023 0.002 TRP D 93 HIS 0.009 0.001 HIS R 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.23 (21205) covalent geometry : angle 0.66233 / 0.34 (28677) hydrogen bonds : bond 0.03574 / 2.46 ( 799) hydrogen bonds : angle 5.29520 / 3.68 ( 2274) metal coordination : bond 0.01487 / 0.84 ( 23) metal coordination : angle 4.78873 / 2.99 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5172 Ramachandran restraints generated. 2586 Oldfield, 0 Emsley, 2586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5172 Ramachandran restraints generated. 2586 Oldfield, 0 Emsley, 2586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 166 time to evaluate : 0.705 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 254 MET cc_start: 0.9368 (mmt) cc_final: 0.8588 (mmt) REVERT: D 38 MET cc_start: 0.8568 (mmt) cc_final: 0.8244 (mpp) REVERT: I 166 CYS cc_start: 0.9211 (m) cc_final: 0.8796 (p) REVERT: I 184 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.8005 (mm-40) REVERT: U 1 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8337 (mtm) REVERT: U 20 SER cc_start: 0.9673 (m) cc_final: 0.9333 (m) REVERT: U 56 LEU cc_start: 0.9727 (mp) cc_final: 0.9478 (pp) REVERT: B 282 MET cc_start: 0.8942 (tpt) cc_final: 0.8713 (tpt) REVERT: B 362 MET cc_start: 0.9076 (pmm) cc_final: 0.8758 (pmm) REVERT: B 593 MET cc_start: 0.9010 (mtt) cc_final: 0.8772 (mtt) REVERT: B 910 MET cc_start: 0.8932 (ttm) cc_final: 0.8150 (tpp) REVERT: A 251 MET cc_start: 0.9429 (mmm) cc_final: 0.9217 (mmm) REVERT: A 390 MET cc_start: 0.9681 (tmm) cc_final: 0.9295 (ppp) REVERT: A 437 MET cc_start: 0.9341 (ppp) cc_final: 0.9101 (ppp) REVERT: A 475 MET cc_start: 0.9634 (tpp) cc_final: 0.9370 (tpp) REVERT: A 505 MET cc_start: 0.9264 (mmt) cc_final: 0.8712 (mmm) REVERT: A 539 MET cc_start: 0.8618 (pmm) cc_final: 0.8048 (pmm) REVERT: A 720 TYR cc_start: 0.9322 (m-10) cc_final: 0.9035 (m-80) outliers start: 69 outliers final: 43 residues processed: 209 average time/residue: 0.1356 time to fit residues: 45.1718 Evaluate side-chains 202 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 157 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain I residue 144 ARG Chi-restraints excluded: chain I residue 184 GLN Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain N residue 23 VAL Chi-restraints excluded: chain N residue 28 GLU Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 4 PHE Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 598 SER Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 873 MET Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 926 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1006 VAL Chi-restraints excluded: chain B residue 1014 MET Chi-restraints excluded: chain B residue 1100 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 92 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 227 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 156 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 48 optimal weight: 0.5980 chunk 205 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 202 optimal weight: 2.9990 chunk 230 optimal weight: 7.9990 chunk 95 optimal weight: 0.0870 chunk 100 optimal weight: 6.9990 overall best weight: 3.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 184 GLN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 GLN A 511 HIS ** A 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.048272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.038984 restraints weight = 212861.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.039997 restraints weight = 111580.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.040700 restraints weight = 72843.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.041125 restraints weight = 54443.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.041430 restraints weight = 44628.000| |-----------------------------------------------------------------------------| r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21228 Z= 0.166 Angle : 0.647 12.416 28692 Z= 0.321 Chirality : 0.043 0.212 3234 Planarity : 0.004 0.053 3680 Dihedral : 4.672 36.461 2824 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.40 % Allowed : 15.98 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.92 (0.16), residues: 2586 helix: 0.96 (0.20), residues: 742 sheet: -0.70 (0.20), residues: 651 loop : -1.56 (0.17), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG N 42 TYR 0.017 0.001 TYR B 3 PHE 0.015 0.001 PHE A 554 TRP 0.017 0.002 TRP D 93 HIS 0.008 0.001 HIS R 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 (21205) covalent geometry : angle 0.64002 / 0.32 (28677) hydrogen bonds : bond 0.03332 / 2.28 ( 799) hydrogen bonds : angle 5.12957 / 3.57 ( 2274) metal coordination : bond 0.01102 / 0.61 ( 23) metal coordination : angle 4.17370 / 2.69 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5172 Ramachandran restraints generated. 2586 Oldfield, 0 Emsley, 2586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5172 Ramachandran restraints generated. 2586 Oldfield, 0 Emsley, 2586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 167 time to evaluate : 0.582 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 194 MET cc_start: 0.9483 (mmm) cc_final: 0.9204 (mmm) REVERT: C 254 MET cc_start: 0.9330 (mmt) cc_final: 0.8593 (mmt) REVERT: D 38 MET cc_start: 0.8569 (mmt) cc_final: 0.8248 (mpp) REVERT: D 139 ARG cc_start: 0.9328 (mmm-85) cc_final: 0.9041 (tpp80) REVERT: I 166 CYS cc_start: 0.9207 (m) cc_final: 0.8769 (p) REVERT: I 184 GLN cc_start: 0.8149 (mp-120) cc_final: 0.7939 (mm-40) REVERT: N 54 LYS cc_start: 0.9356 (pttt) cc_final: 0.9100 (ttpt) REVERT: N 73 LEU cc_start: 0.9241 (tp) cc_final: 0.8811 (tp) REVERT: U 1 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8197 (mtm) REVERT: B 282 MET cc_start: 0.9041 (tpt) cc_final: 0.8751 (tpt) REVERT: B 362 MET cc_start: 0.9061 (pmm) cc_final: 0.8739 (pmm) REVERT: B 593 MET cc_start: 0.8980 (mtt) cc_final: 0.8741 (mtt) REVERT: B 631 LEU cc_start: 0.9605 (OUTLIER) cc_final: 0.9227 (pp) REVERT: B 910 MET cc_start: 0.8894 (ttm) cc_final: 0.8167 (tpp) REVERT: A 390 MET cc_start: 0.9685 (tmm) cc_final: 0.9280 (ppp) REVERT: A 437 MET cc_start: 0.9337 (ppp) cc_final: 0.9078 (ppp) REVERT: A 475 MET cc_start: 0.9613 (tpp) cc_final: 0.9350 (tpp) REVERT: A 505 MET cc_start: 0.9293 (mmt) cc_final: 0.8771 (mmm) REVERT: A 523 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8029 (mm) REVERT: A 720 TYR cc_start: 0.9318 (m-10) cc_final: 0.9069 (m-10) outliers start: 55 outliers final: 44 residues processed: 206 average time/residue: 0.1269 time to fit residues: 41.2907 Evaluate side-chains 205 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 158 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain I residue 144 ARG Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain N residue 28 GLU Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 4 PHE Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 598 SER Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 873 MET Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 926 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1006 VAL Chi-restraints excluded: chain B residue 1014 MET Chi-restraints excluded: chain B residue 1100 ILE Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain R residue 68 CYS Chi-restraints excluded: chain R residue 92 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 142 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 chunk 198 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 164 optimal weight: 5.9990 chunk 248 optimal weight: 20.0000 chunk 171 optimal weight: 6.9990 chunk 211 optimal weight: 10.0000 chunk 184 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 GLN D 34 GLN ** I 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 HIS ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1034 ASN ** B1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 GLN ** A 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.038422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.027246 restraints weight = 185982.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.028137 restraints weight = 113716.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.028722 restraints weight = 81913.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.029189 restraints weight = 65769.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.029452 restraints weight = 55928.803| |-----------------------------------------------------------------------------| r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 21228 Z= 0.259 Angle : 0.722 11.656 28692 Z= 0.360 Chirality : 0.044 0.187 3234 Planarity : 0.006 0.288 3680 Dihedral : 5.007 41.458 2824 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.66 % Allowed : 16.50 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.08 (0.16), residues: 2586 helix: 0.77 (0.19), residues: 740 sheet: -0.81 (0.20), residues: 656 loop : -1.60 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG U 74 TYR 0.019 0.002 TYR B 3 PHE 0.019 0.002 PHE A 554 TRP 0.022 0.002 TRP D 93 HIS 0.010 0.002 HIS R 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.26 (21205) covalent geometry : angle 0.71182 / 0.36 (28677) hydrogen bonds : bond 0.03618 / 2.47 ( 799) hydrogen bonds : angle 5.29073 / 3.67 ( 2274) metal coordination : bond 0.01670 / 0.96 ( 23) metal coordination : angle 5.35650 / 3.28 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5172 Ramachandran restraints generated. 2586 Oldfield, 0 Emsley, 2586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5172 Ramachandran restraints generated. 2586 Oldfield, 0 Emsley, 2586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 158 time to evaluate : 0.891 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 254 MET cc_start: 0.9376 (mmt) cc_final: 0.8543 (mmt) REVERT: D 15 ARG cc_start: 0.9505 (mtp-110) cc_final: 0.9008 (ptp-110) REVERT: D 38 MET cc_start: 0.8748 (mmt) cc_final: 0.8253 (mpp) REVERT: D 139 ARG cc_start: 0.9362 (mmm-85) cc_final: 0.9080 (tpp80) REVERT: I 166 CYS cc_start: 0.9252 (m) cc_final: 0.8784 (p) REVERT: I 184 GLN cc_start: 0.8272 (mp-120) cc_final: 0.7899 (mm-40) REVERT: N 6 LYS cc_start: 0.9591 (ttmt) cc_final: 0.9162 (tppt) REVERT: N 42 ARG cc_start: 0.9323 (mtp85) cc_final: 0.8739 (mpp80) REVERT: U 1 MET cc_start: 0.8960 (mtm) cc_final: 0.8694 (ptp) REVERT: B 362 MET cc_start: 0.9065 (pmm) cc_final: 0.8788 (pmm) REVERT: B 593 MET cc_start: 0.8976 (mtt) cc_final: 0.8747 (mtt) REVERT: B 631 LEU cc_start: 0.9629 (OUTLIER) cc_final: 0.9314 (pp) REVERT: B 910 MET cc_start: 0.8988 (ttm) cc_final: 0.8175 (tpp) REVERT: A 322 MET cc_start: 0.9522 (OUTLIER) cc_final: 0.9290 (tmm) REVERT: A 390 MET cc_start: 0.9736 (tmm) cc_final: 0.9344 (ppp) REVERT: A 437 MET cc_start: 0.9412 (ppp) cc_final: 0.9137 (ppp) REVERT: A 475 MET cc_start: 0.9677 (tpp) cc_final: 0.9436 (tpp) REVERT: A 494 MET cc_start: 0.9091 (mmp) cc_final: 0.8647 (mmp) REVERT: A 505 MET cc_start: 0.9383 (mmt) cc_final: 0.8888 (mmm) REVERT: A 523 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8108 (mm) REVERT: A 539 MET cc_start: 0.8631 (pmm) cc_final: 0.7758 (pmm) REVERT: A 720 TYR cc_start: 0.9323 (m-10) cc_final: 0.9041 (m-80) outliers start: 61 outliers final: 48 residues processed: 206 average time/residue: 0.1401 time to fit residues: 45.3053 Evaluate side-chains 204 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 153 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain I residue 144 ARG Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain N residue 17 ILE Chi-restraints excluded: chain N residue 28 GLU Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain U residue 4 PHE Chi-restraints excluded: chain U residue 44 ILE Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 598 SER Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 926 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1006 VAL Chi-restraints excluded: chain B residue 1014 MET Chi-restraints excluded: chain B residue 1100 ILE Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain R residue 68 CYS Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 92 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 180 optimal weight: 30.0000 chunk 102 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 59 optimal weight: 0.3980 chunk 45 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 34 optimal weight: 30.0000 chunk 225 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 GLN ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 670 ASN ** B1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 GLN A 261 ASN A 321 GLN ** A 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 695 GLN ** R 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 98 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.039132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.027778 restraints weight = 178742.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.028712 restraints weight = 108658.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.029357 restraints weight = 77735.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.029715 restraints weight = 61847.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.030076 restraints weight = 53987.321| |-----------------------------------------------------------------------------| r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21228 Z= 0.145 Angle : 0.666 11.553 28692 Z= 0.326 Chirality : 0.044 0.230 3234 Planarity : 0.004 0.087 3680 Dihedral : 4.751 39.377 2824 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.27 % Allowed : 17.63 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.96 (0.16), residues: 2586 helix: 0.87 (0.19), residues: 746 sheet: -0.72 (0.20), residues: 651 loop : -1.56 (0.17), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG U 72 TYR 0.017 0.001 TYR B1114 PHE 0.012 0.001 PHE U 4 TRP 0.021 0.002 TRP B 953 HIS 0.008 0.001 HIS R 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (21205) covalent geometry : angle 0.66012 / 0.33 (28677) hydrogen bonds : bond 0.03276 / 2.24 ( 799) hydrogen bonds : angle 5.06660 / 3.51 ( 2274) metal coordination : bond 0.01072 / 0.56 ( 23) metal coordination : angle 3.95985 / 2.68 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5172 Ramachandran restraints generated. 2586 Oldfield, 0 Emsley, 2586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5172 Ramachandran restraints generated. 2586 Oldfield, 0 Emsley, 2586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 162 time to evaluate : 0.751 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 254 MET cc_start: 0.9334 (mmt) cc_final: 0.8615 (mmt) REVERT: D 15 ARG cc_start: 0.9531 (mtp-110) cc_final: 0.9087 (ptp90) REVERT: D 38 MET cc_start: 0.8728 (mmt) cc_final: 0.8323 (mpp) REVERT: D 50 PHE cc_start: 0.9574 (m-10) cc_final: 0.9357 (m-10) REVERT: D 97 LEU cc_start: 0.9688 (OUTLIER) cc_final: 0.9250 (mp) REVERT: D 139 ARG cc_start: 0.9324 (mmm-85) cc_final: 0.9049 (tpp80) REVERT: I 184 GLN cc_start: 0.8267 (mp-120) cc_final: 0.7862 (mm-40) REVERT: N 41 GLN cc_start: 0.7093 (OUTLIER) cc_final: 0.6624 (pm20) REVERT: N 73 LEU cc_start: 0.9363 (tp) cc_final: 0.8964 (tp) REVERT: U 1 MET cc_start: 0.8755 (mtm) cc_final: 0.8255 (ptp) REVERT: B 218 MET cc_start: 0.9262 (OUTLIER) cc_final: 0.9031 (tpp) REVERT: B 362 MET cc_start: 0.9085 (pmm) cc_final: 0.8763 (pmm) REVERT: B 593 MET cc_start: 0.9002 (mtt) cc_final: 0.8736 (mtt) REVERT: B 674 LYS cc_start: 0.9274 (mmmt) cc_final: 0.8742 (tppt) REVERT: B 794 ILE cc_start: 0.9545 (OUTLIER) cc_final: 0.9308 (tp) REVERT: B 910 MET cc_start: 0.8943 (ttm) cc_final: 0.8145 (tpp) REVERT: A 390 MET cc_start: 0.9736 (tmm) cc_final: 0.9332 (ppp) REVERT: A 437 MET cc_start: 0.9372 (ppp) cc_final: 0.9070 (ppp) REVERT: A 475 MET cc_start: 0.9663 (tpp) cc_final: 0.9415 (tpp) REVERT: A 505 MET cc_start: 0.9375 (mmt) cc_final: 0.8909 (mmm) REVERT: A 523 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8264 (mm) REVERT: A 539 MET cc_start: 0.8613 (pmm) cc_final: 0.7717 (pmm) REVERT: A 720 TYR cc_start: 0.9306 (m-10) cc_final: 0.9031 (m-80) outliers start: 52 outliers final: 44 residues processed: 198 average time/residue: 0.1433 time to fit residues: 43.6862 Evaluate side-chains 202 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 153 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain I residue 144 ARG Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain N residue 28 GLU Chi-restraints excluded: chain N residue 41 GLN Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain U residue 4 PHE Chi-restraints excluded: chain U residue 74 ARG Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 598 SER Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 873 MET Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 926 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1006 VAL Chi-restraints excluded: chain B residue 1014 MET Chi-restraints excluded: chain B residue 1100 ILE Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain R residue 68 CYS Chi-restraints excluded: chain R residue 92 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 61 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 253 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 104 optimal weight: 8.9990 chunk 223 optimal weight: 0.3980 chunk 156 optimal weight: 0.9980 chunk 137 optimal weight: 6.9990 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 180 ASN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.038542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.027300 restraints weight = 182490.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.028209 restraints weight = 111386.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.028815 restraints weight = 80084.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.029263 restraints weight = 64174.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.029528 restraints weight = 54769.235| |-----------------------------------------------------------------------------| r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21228 Z= 0.190 Angle : 0.708 15.730 28692 Z= 0.343 Chirality : 0.044 0.267 3234 Planarity : 0.004 0.057 3680 Dihedral : 4.757 38.925 2824 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.49 % Allowed : 17.77 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.99 (0.16), residues: 2586 helix: 0.87 (0.19), residues: 747 sheet: -0.77 (0.20), residues: 653 loop : -1.58 (0.17), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 42 TYR 0.016 0.001 TYR B 3 PHE 0.015 0.001 PHE A 554 TRP 0.017 0.002 TRP D 93 HIS 0.009 0.001 HIS R 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.19 (21205) covalent geometry : angle 0.70028 / 0.34 (28677) hydrogen bonds : bond 0.03350 / 2.29 ( 799) hydrogen bonds : angle 5.08426 / 3.53 ( 2274) metal coordination : bond 0.01214 / 0.67 ( 23) metal coordination : angle 4.62336 / 2.89 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5172 Ramachandran restraints generated. 2586 Oldfield, 0 Emsley, 2586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5172 Ramachandran restraints generated. 2586 Oldfield, 0 Emsley, 2586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 158 time to evaluate : 0.813 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 75 ASP cc_start: 0.9178 (m-30) cc_final: 0.8767 (t0) REVERT: C 194 MET cc_start: 0.9486 (mmm) cc_final: 0.9138 (mmm) REVERT: C 254 MET cc_start: 0.9360 (mmt) cc_final: 0.8599 (mmt) REVERT: D 38 MET cc_start: 0.9114 (mmt) cc_final: 0.8405 (mpp) REVERT: D 69 PHE cc_start: 0.9464 (m-80) cc_final: 0.9037 (t80) REVERT: D 97 LEU cc_start: 0.9670 (OUTLIER) cc_final: 0.9228 (mp) REVERT: I 184 GLN cc_start: 0.8346 (mp-120) cc_final: 0.7951 (mm-40) REVERT: N 41 GLN cc_start: 0.6958 (OUTLIER) cc_final: 0.6668 (pm20) REVERT: N 73 LEU cc_start: 0.9416 (tp) cc_final: 0.9002 (tp) REVERT: U 1 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8102 (ptp) REVERT: B 218 MET cc_start: 0.9269 (OUTLIER) cc_final: 0.8881 (tpp) REVERT: B 362 MET cc_start: 0.9063 (pmm) cc_final: 0.8780 (pmm) REVERT: B 593 MET cc_start: 0.8987 (mtt) cc_final: 0.8672 (mtt) REVERT: B 631 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9245 (pp) REVERT: B 674 LYS cc_start: 0.9260 (mmmt) cc_final: 0.8759 (tppt) REVERT: B 794 ILE cc_start: 0.9555 (OUTLIER) cc_final: 0.9311 (tp) REVERT: B 910 MET cc_start: 0.8974 (ttm) cc_final: 0.8188 (tpp) REVERT: A 390 MET cc_start: 0.9736 (tmm) cc_final: 0.9333 (ppp) REVERT: A 437 MET cc_start: 0.9356 (ppp) cc_final: 0.9062 (ppp) REVERT: A 475 MET cc_start: 0.9655 (tpp) cc_final: 0.9415 (tpp) REVERT: A 494 MET cc_start: 0.9151 (mmp) cc_final: 0.8712 (mmp) REVERT: A 505 MET cc_start: 0.9388 (mmt) cc_final: 0.8917 (mmm) REVERT: A 539 MET cc_start: 0.8599 (pmm) cc_final: 0.7657 (pmm) REVERT: A 720 TYR cc_start: 0.9332 (m-10) cc_final: 0.9046 (m-80) outliers start: 57 outliers final: 46 residues processed: 197 average time/residue: 0.1468 time to fit residues: 45.3982 Evaluate side-chains 205 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 153 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain I residue 144 ARG Chi-restraints excluded: chain I residue 180 ASN Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain N residue 17 ILE Chi-restraints excluded: chain N residue 28 GLU Chi-restraints excluded: chain N residue 41 GLN Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 4 PHE Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 598 SER Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 873 MET Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 926 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1006 VAL Chi-restraints excluded: chain B residue 1014 MET Chi-restraints excluded: chain B residue 1100 ILE Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 68 CYS Chi-restraints excluded: chain R residue 92 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 250 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 139 optimal weight: 9.9990 chunk 222 optimal weight: 0.1980 chunk 245 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 106 optimal weight: 9.9990 chunk 65 optimal weight: 8.9990 chunk 237 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 180 ASN ** B 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 HIS ** B 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 98 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.038881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.027713 restraints weight = 182115.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.028657 restraints weight = 109138.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.029304 restraints weight = 77406.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.029743 restraints weight = 61246.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.029997 restraints weight = 52111.088| |-----------------------------------------------------------------------------| r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21228 Z= 0.143 Angle : 0.694 12.415 28692 Z= 0.335 Chirality : 0.044 0.221 3234 Planarity : 0.004 0.074 3680 Dihedral : 4.699 39.414 2824 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.23 % Allowed : 18.38 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.96 (0.16), residues: 2586 helix: 0.87 (0.19), residues: 748 sheet: -0.66 (0.20), residues: 642 loop : -1.60 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG U 74 TYR 0.016 0.001 TYR B1114 PHE 0.012 0.001 PHE U 4 TRP 0.017 0.001 TRP B 953 HIS 0.008 0.001 HIS R 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (21205) covalent geometry : angle 0.68819 / 0.33 (28677) hydrogen bonds : bond 0.03246 / 2.21 ( 799) hydrogen bonds : angle 4.95581 / 3.44 ( 2274) metal coordination : bond 0.01062 / 0.54 ( 23) metal coordination : angle 3.89687 / 2.58 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5172 Ramachandran restraints generated. 2586 Oldfield, 0 Emsley, 2586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5172 Ramachandran restraints generated. 2586 Oldfield, 0 Emsley, 2586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 160 time to evaluate : 0.844 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 194 MET cc_start: 0.9505 (mmm) cc_final: 0.9226 (mmm) REVERT: C 254 MET cc_start: 0.9314 (mmt) cc_final: 0.8599 (mmt) REVERT: D 15 ARG cc_start: 0.9236 (mtm110) cc_final: 0.8934 (ptp-110) REVERT: D 38 MET cc_start: 0.9112 (mmt) cc_final: 0.8420 (mpp) REVERT: D 69 PHE cc_start: 0.9489 (m-80) cc_final: 0.9032 (t80) REVERT: D 97 LEU cc_start: 0.9668 (OUTLIER) cc_final: 0.9238 (mp) REVERT: I 184 GLN cc_start: 0.8344 (mp-120) cc_final: 0.7923 (mm-40) REVERT: N 24 GLU cc_start: 0.9314 (mp0) cc_final: 0.8562 (mp0) REVERT: N 28 GLU cc_start: 0.9635 (OUTLIER) cc_final: 0.9266 (pp20) REVERT: N 41 GLN cc_start: 0.7163 (OUTLIER) cc_final: 0.6711 (pm20) REVERT: N 73 LEU cc_start: 0.9376 (tp) cc_final: 0.8951 (tp) REVERT: U 1 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.7980 (ptp) REVERT: U 3 ILE cc_start: 0.9459 (pt) cc_final: 0.9085 (mp) REVERT: B 218 MET cc_start: 0.9239 (OUTLIER) cc_final: 0.8853 (tpp) REVERT: B 282 MET cc_start: 0.8545 (tpt) cc_final: 0.8299 (tpt) REVERT: B 362 MET cc_start: 0.9067 (pmm) cc_final: 0.8785 (pmm) REVERT: B 534 MET cc_start: 0.8909 (tpp) cc_final: 0.8357 (mmp) REVERT: B 593 MET cc_start: 0.8962 (mtt) cc_final: 0.8753 (mtt) REVERT: B 631 LEU cc_start: 0.9582 (OUTLIER) cc_final: 0.9198 (pp) REVERT: B 674 LYS cc_start: 0.9269 (mmmt) cc_final: 0.8818 (tppt) REVERT: B 910 MET cc_start: 0.8938 (ttm) cc_final: 0.8182 (tpp) REVERT: A 220 MET cc_start: 0.9371 (ppp) cc_final: 0.8636 (tmm) REVERT: A 437 MET cc_start: 0.9335 (ppp) cc_final: 0.9033 (ppp) REVERT: A 475 MET cc_start: 0.9633 (tpp) cc_final: 0.9388 (tpp) REVERT: A 494 MET cc_start: 0.9121 (mmp) cc_final: 0.8660 (mmp) REVERT: A 505 MET cc_start: 0.9393 (mmt) cc_final: 0.8936 (mmm) REVERT: A 539 MET cc_start: 0.8571 (pmm) cc_final: 0.7561 (pmm) REVERT: A 720 TYR cc_start: 0.9323 (m-10) cc_final: 0.9046 (m-80) outliers start: 51 outliers final: 42 residues processed: 194 average time/residue: 0.1563 time to fit residues: 47.5179 Evaluate side-chains 204 residues out of total 2334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 156 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain I residue 144 ARG Chi-restraints excluded: chain I residue 180 ASN Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain N residue 28 GLU Chi-restraints excluded: chain N residue 41 GLN Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 69 LEU Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 598 SER Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 873 MET Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 926 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1006 VAL Chi-restraints excluded: chain B residue 1100 ILE Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 68 CYS Chi-restraints excluded: chain R residue 92 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 163 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 226 optimal weight: 0.9980 chunk 155 optimal weight: 10.0000 chunk 172 optimal weight: 8.9990 chunk 222 optimal weight: 0.9980 chunk 69 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 GLN ** A 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.039076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.027925 restraints weight = 175264.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.028853 restraints weight = 106496.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.029504 restraints weight = 76132.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.029949 restraints weight = 60052.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.030282 restraints weight = 50911.439| |-----------------------------------------------------------------------------| r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21228 Z= 0.126 Angle : 0.699 12.102 28692 Z= 0.337 Chirality : 0.044 0.220 3234 Planarity : 0.004 0.060 3680 Dihedral : 4.634 39.324 2824 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.27 % Allowed : 18.46 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.16), residues: 2586 helix: 0.87 (0.19), residues: 751 sheet: -0.65 (0.20), residues: 649 loop : -1.63 (0.17), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG U 54 TYR 0.015 0.001 TYR I 181 PHE 0.012 0.001 PHE C 165 TRP 0.019 0.001 TRP B 953 HIS 0.007 0.001 HIS R 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (21205) covalent geometry : angle 0.69438 / 0.34 (28677) hydrogen bonds : bond 0.03161 / 2.15 ( 799) hydrogen bonds : angle 4.86089 / 3.39 ( 2274) metal coordination : bond 0.01233 / 0.56 ( 23) metal coordination : angle 3.68920 / 2.49 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3501.35 seconds wall clock time: 61 minutes 35.34 seconds (3695.34 seconds total)