Starting phenix.real_space_refine on Fri Mar 6 13:27:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zm1_11277/03_2026/6zm1_11277.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zm1_11277/03_2026/6zm1_11277.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6zm1_11277/03_2026/6zm1_11277.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zm1_11277/03_2026/6zm1_11277.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zm1_11277/03_2026/6zm1_11277.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zm1_11277/03_2026/6zm1_11277.map" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 10980 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 79 5.16 5 C 14254 2.51 5 N 3810 2.21 5 O 4400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 110 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22543 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4358 Classifications: {'peptide': 552} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 532} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 7335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 933, 7335 Classifications: {'peptide': 933} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 900} Chain: "C" Number of atoms: 4457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4457 Classifications: {'peptide': 555} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 535} Chain: "D" Number of atoms: 6393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6393 Classifications: {'peptide': 804} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 776} Time building chain proxies: 5.01, per 1000 atoms: 0.22 Number of scatterers: 22543 At special positions: 0 Unit cell: (142.31, 148.73, 131.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 79 16.00 O 4400 8.00 N 3810 7.00 C 14254 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 299 " distance=2.05 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 389 " distance=2.05 Simple disulfide: pdb=" SG CYS C 298 " - pdb=" SG CYS C 299 " distance=2.04 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 389 " distance=2.11 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 997.6 milliseconds 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5176 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 23 sheets defined 25.7% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 1 through 5 Processing helix chain 'A' and resid 17 through 21 removed outlier: 3.737A pdb=" N ALA A 20 " --> pdb=" O ASP A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 34 Processing helix chain 'A' and resid 69 through 77 Processing helix chain 'A' and resid 84 through 108 removed outlier: 4.211A pdb=" N ASN A 88 " --> pdb=" O ASP A 84 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N CYS A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 118 through 141 Processing helix chain 'A' and resid 153 through 157 removed outlier: 3.625A pdb=" N TYR A 157 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 185 removed outlier: 4.333A pdb=" N ASP A 177 " --> pdb=" O LYS A 173 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE A 178 " --> pdb=" O ILE A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 213 removed outlier: 3.907A pdb=" N TYR A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 236 Processing helix chain 'A' and resid 238 through 244 removed outlier: 3.886A pdb=" N MET A 242 " --> pdb=" O ASP A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 289 Processing helix chain 'A' and resid 305 through 313 removed outlier: 3.759A pdb=" N VAL A 309 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS A 313 " --> pdb=" O VAL A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 344 removed outlier: 3.909A pdb=" N HIS A 343 " --> pdb=" O PRO A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 422 Processing helix chain 'A' and resid 426 through 442 Processing helix chain 'A' and resid 447 through 451 removed outlier: 4.151A pdb=" N LYS A 451 " --> pdb=" O PHE A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 485 Processing helix chain 'A' and resid 491 through 499 Processing helix chain 'A' and resid 501 through 513 Processing helix chain 'A' and resid 517 through 521 removed outlier: 3.676A pdb=" N ASN A 521 " --> pdb=" O ILE A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 542 removed outlier: 3.548A pdb=" N ILE A 539 " --> pdb=" O PRO A 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 97 removed outlier: 3.635A pdb=" N ASP B 96 " --> pdb=" O ARG B 93 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU B 97 " --> pdb=" O LYS B 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 93 through 97' Processing helix chain 'B' and resid 108 through 113 removed outlier: 3.930A pdb=" N GLY B 113 " --> pdb=" O ILE B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 249 Processing helix chain 'B' and resid 377 through 384 Processing helix chain 'B' and resid 409 through 417 Processing helix chain 'B' and resid 604 through 608 removed outlier: 3.726A pdb=" N LYS B 608 " --> pdb=" O ASN B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 729 Processing helix chain 'B' and resid 781 through 786 removed outlier: 3.813A pdb=" N GLY B 786 " --> pdb=" O VAL B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 822 Processing helix chain 'B' and resid 890 through 896 removed outlier: 3.948A pdb=" N PHE B 896 " --> pdb=" O LYS B 892 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 914 removed outlier: 3.596A pdb=" N ASN B 913 " --> pdb=" O ARG B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 943 Processing helix chain 'B' and resid 961 through 967 Processing helix chain 'C' and resid 17 through 23 removed outlier: 3.993A pdb=" N ALA C 20 " --> pdb=" O ASP C 17 " (cutoff:3.500A) Proline residue: C 22 - end of helix Processing helix chain 'C' and resid 24 through 39 removed outlier: 4.556A pdb=" N TRP C 36 " --> pdb=" O ALA C 32 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA C 37 " --> pdb=" O TYR C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 53 removed outlier: 3.574A pdb=" N VAL C 53 " --> pdb=" O TRP C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 77 Processing helix chain 'C' and resid 84 through 110 removed outlier: 3.940A pdb=" N GLN C 110 " --> pdb=" O GLN C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'C' and resid 118 through 142 Processing helix chain 'C' and resid 154 through 160 Processing helix chain 'C' and resid 166 through 185 removed outlier: 3.652A pdb=" N ASP C 177 " --> pdb=" O LYS C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 213 removed outlier: 4.044A pdb=" N TYR C 213 " --> pdb=" O LEU C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 236 removed outlier: 3.654A pdb=" N LEU C 230 " --> pdb=" O ASN C 226 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN C 232 " --> pdb=" O GLU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 244 Processing helix chain 'C' and resid 252 through 262 removed outlier: 3.550A pdb=" N LEU C 258 " --> pdb=" O MET C 255 " (cutoff:3.500A) Proline residue: C 259 - end of helix removed outlier: 3.597A pdb=" N GLU C 262 " --> pdb=" O PRO C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 289 Processing helix chain 'C' and resid 293 through 297 Processing helix chain 'C' and resid 305 through 312 removed outlier: 3.736A pdb=" N PHE C 312 " --> pdb=" O LEU C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 344 Processing helix chain 'C' and resid 407 through 421 Processing helix chain 'C' and resid 425 through 442 Processing helix chain 'C' and resid 469 through 485 Processing helix chain 'C' and resid 490 through 499 Processing helix chain 'C' and resid 500 through 514 removed outlier: 4.515A pdb=" N SER C 514 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 522 removed outlier: 3.889A pdb=" N ASN C 521 " --> pdb=" O ILE C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 543 removed outlier: 3.784A pdb=" N ASN C 543 " --> pdb=" O ILE C 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 248 Processing helix chain 'D' and resid 251 through 255 removed outlier: 3.524A pdb=" N ASN D 255 " --> pdb=" O PRO D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 300 Processing helix chain 'D' and resid 376 through 384 Processing helix chain 'D' and resid 409 through 417 Processing helix chain 'D' and resid 535 through 539 Processing helix chain 'D' and resid 584 through 587 Processing helix chain 'D' and resid 602 through 608 removed outlier: 5.110A pdb=" N ASN D 605 " --> pdb=" O THR D 602 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N PHE D 606 " --> pdb=" O GLN D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 725 through 729 Processing helix chain 'D' and resid 779 through 786 removed outlier: 3.521A pdb=" N GLY D 786 " --> pdb=" O VAL D 782 " (cutoff:3.500A) Processing helix chain 'D' and resid 815 through 821 removed outlier: 3.713A pdb=" N VAL D 819 " --> pdb=" O SER D 815 " (cutoff:3.500A) Processing helix chain 'D' and resid 889 through 895 removed outlier: 3.863A pdb=" N LYS D 893 " --> pdb=" O ASP D 889 " (cutoff:3.500A) Processing helix chain 'D' and resid 908 through 914 removed outlier: 3.868A pdb=" N LEU D 911 " --> pdb=" O GLY D 908 " (cutoff:3.500A) Processing helix chain 'D' and resid 939 through 941 No H-bonds generated for 'chain 'D' and resid 939 through 941' Processing helix chain 'D' and resid 961 through 966 Processing helix chain 'D' and resid 967 through 969 No H-bonds generated for 'chain 'D' and resid 967 through 969' Processing sheet with id=A, first strand: chain 'A' and resid 269 through 271 removed outlier: 4.075A pdb=" N TRP A 269 " --> pdb=" O ILE A 405 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE A 405 " --> pdb=" O TRP A 269 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE A 271 " --> pdb=" O ILE A 403 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ILE A 403 " --> pdb=" O ILE A 271 " (cutoff:3.500A) No H-bonds generated for sheet with id=A Processing sheet with id=B, first strand: chain 'B' and resid 85 through 87 removed outlier: 4.019A pdb=" N THR B 90 " --> pdb=" O THR B 87 " (cutoff:3.500A) Processing sheet with id=C, first strand: chain 'B' and resid 101 through 104 removed outlier: 4.364A pdb=" N ILE B 179 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER B 178 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU B 156 " --> pdb=" O ILE B 200 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ILE B 202 " --> pdb=" O LEU B 156 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ILE B 158 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR B 157 " --> pdb=" O THR B 164 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL B 162 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'B' and resid 128 through 132 Processing sheet with id=E, first strand: chain 'B' and resid 338 through 342 removed outlier: 3.671A pdb=" N TYR B 327 " --> pdb=" O TYR B 308 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL B 304 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE B 305 " --> pdb=" O SER B 221 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 218 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B1012 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL B 220 " --> pdb=" O PHE B1010 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASN B 953 " --> pdb=" O PHE B 877 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP B 873 " --> pdb=" O GLY B 957 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU B 760 " --> pdb=" O THR B 756 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY B 745 " --> pdb=" O TYR B 711 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR B 711 " --> pdb=" O GLY B 745 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN B 749 " --> pdb=" O SER B 707 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY B 706 " --> pdb=" O PHE B 697 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR B 712 " --> pdb=" O THR B 691 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN B 627 " --> pdb=" O GLU B 686 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS B 617 " --> pdb=" O ASP B 696 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N GLY B 626 " --> pdb=" O THR B 591 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N THR B 591 " --> pdb=" O GLY B 626 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR B 574 " --> pdb=" O SER B 594 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU B 514 " --> pdb=" O TYR B 552 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 554 " --> pdb=" O ASN B 512 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY B 508 " --> pdb=" O PHE B 558 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET B 506 " --> pdb=" O LYS B 560 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N MET B 509 " --> pdb=" O ALA B 490 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA B 490 " --> pdb=" O MET B 509 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP B 488 " --> pdb=" O LEU B 511 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'B' and resid 221 through 224 Processing sheet with id=G, first strand: chain 'B' and resid 311 through 313 removed outlier: 3.794A pdb=" N ARG B 345 " --> pdb=" O SER B 324 " (cutoff:3.500A) Processing sheet with id=H, first strand: chain 'B' and resid 365 through 368 removed outlier: 3.703A pdb=" N ARG B 426 " --> pdb=" O ASN B 366 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA B 452 " --> pdb=" O TRP B 483 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N HIS B 482 " --> pdb=" O SER B 517 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N HIS B 518 " --> pdb=" O ALA B 548 " (cutoff:3.500A) Processing sheet with id=I, first strand: chain 'B' and resid 458 through 460 removed outlier: 3.785A pdb=" N ALA B 475 " --> pdb=" O THR B 460 " (cutoff:3.500A) Processing sheet with id=J, first strand: chain 'B' and resid 719 through 722 removed outlier: 3.570A pdb=" N ILE B 736 " --> pdb=" O THR B 720 " (cutoff:3.500A) Processing sheet with id=K, first strand: chain 'B' and resid 879 through 881 Processing sheet with id=L, first strand: chain 'B' and resid 259 through 265 removed outlier: 6.803A pdb=" N GLY B 264 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LEU B 273 " --> pdb=" O GLY B 264 " (cutoff:3.500A) Processing sheet with id=M, first strand: chain 'B' and resid 740 through 744 removed outlier: 3.605A pdb=" N GLU B 777 " --> pdb=" O ALA B 740 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LYS B 742 " --> pdb=" O ILE B 775 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ILE B 775 " --> pdb=" O LYS B 742 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N GLN B 744 " --> pdb=" O ASN B 773 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASN B 773 " --> pdb=" O GLN B 744 " (cutoff:3.500A) Processing sheet with id=N, first strand: chain 'B' and resid 804 through 806 removed outlier: 3.765A pdb=" N TYR B 853 " --> pdb=" O GLN B 804 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY B 806 " --> pdb=" O TRP B 851 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N TRP B 851 " --> pdb=" O GLY B 806 " (cutoff:3.500A) Processing sheet with id=O, first strand: chain 'C' and resid 390 through 392 Processing sheet with id=P, first strand: chain 'D' and resid 302 through 312 removed outlier: 3.581A pdb=" N ARG D 972 " --> pdb=" O GLY D1015 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N PHE D 877 " --> pdb=" O ARG D 952 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE D 954 " --> pdb=" O THR D 875 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR D 875 " --> pdb=" O ILE D 954 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU D 956 " --> pdb=" O ASP D 873 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASP D 873 " --> pdb=" O LEU D 956 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ALA D 740 " --> pdb=" O LEU D 776 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N GLY D 626 " --> pdb=" O THR D 591 " (cutoff:3.500A) removed outlier: 9.809A pdb=" N THR D 591 " --> pdb=" O GLY D 626 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ARG D 457 " --> pdb=" O ARG D 421 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ARG D 421 " --> pdb=" O ARG D 457 " (cutoff:3.500A) Processing sheet with id=Q, first strand: chain 'D' and resid 719 through 722 Processing sheet with id=R, first strand: chain 'D' and resid 765 through 769 Processing sheet with id=S, first strand: chain 'D' and resid 885 through 887 Processing sheet with id=T, first strand: chain 'D' and resid 948 through 951 removed outlier: 4.268A pdb=" N LEU D 983 " --> pdb=" O LEU D 951 " (cutoff:3.500A) Processing sheet with id=U, first strand: chain 'D' and resid 259 through 265 removed outlier: 6.706A pdb=" N GLY D 264 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LEU D 273 " --> pdb=" O GLY D 264 " (cutoff:3.500A) Processing sheet with id=V, first strand: chain 'D' and resid 638 through 640 removed outlier: 3.708A pdb=" N GLN D 677 " --> pdb=" O ILE D 638 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ALA D 640 " --> pdb=" O ARG D 675 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ARG D 675 " --> pdb=" O ALA D 640 " (cutoff:3.500A) Processing sheet with id=W, first strand: chain 'D' and resid 804 through 807 removed outlier: 6.361A pdb=" N GLY D 806 " --> pdb=" O TRP D 851 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N TRP D 851 " --> pdb=" O GLY D 806 " (cutoff:3.500A) 907 hydrogen bonds defined for protein. 2475 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: 4.43 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7388 1.34 - 1.47: 6151 1.47 - 1.60: 9413 1.60 - 1.73: 0 1.73 - 1.86: 140 Bond restraints: 23092 Sorted by residual: bond pdb=" CB ASN D 470 " pdb=" CG ASN D 470 " ideal model delta sigma weight residual 1.516 1.449 0.067 2.50e-02 1.60e+03 7.23e+00 bond pdb=" CB ASN D 785 " pdb=" CG ASN D 785 " ideal model delta sigma weight residual 1.516 1.466 0.050 2.50e-02 1.60e+03 4.03e+00 bond pdb=" CB ASP D 292 " pdb=" CG ASP D 292 " ideal model delta sigma weight residual 1.516 1.563 -0.047 2.50e-02 1.60e+03 3.56e+00 bond pdb=" C THR D 469 " pdb=" N ASN D 470 " ideal model delta sigma weight residual 1.336 1.307 0.029 1.55e-02 4.16e+03 3.47e+00 bond pdb=" CG GLN C 197 " pdb=" CD GLN C 197 " ideal model delta sigma weight residual 1.516 1.470 0.046 2.50e-02 1.60e+03 3.34e+00 ... (remaining 23087 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 29839 1.93 - 3.85: 1325 3.85 - 5.78: 130 5.78 - 7.70: 29 7.70 - 9.63: 17 Bond angle restraints: 31340 Sorted by residual: angle pdb=" CA TRP D 599 " pdb=" CB TRP D 599 " pdb=" CG TRP D 599 " ideal model delta sigma weight residual 113.60 122.40 -8.80 1.90e+00 2.77e-01 2.14e+01 angle pdb=" C CYS A 298 " pdb=" N CYS A 299 " pdb=" CA CYS A 299 " ideal model delta sigma weight residual 121.70 129.30 -7.60 1.80e+00 3.09e-01 1.78e+01 angle pdb=" C GLY B 167 " pdb=" N MET B 168 " pdb=" CA MET B 168 " ideal model delta sigma weight residual 121.54 129.54 -8.00 1.91e+00 2.74e-01 1.75e+01 angle pdb=" C ASP A 388 " pdb=" N CYS A 389 " pdb=" CA CYS A 389 " ideal model delta sigma weight residual 120.28 126.18 -5.90 1.44e+00 4.82e-01 1.68e+01 angle pdb=" C LEU A 421 " pdb=" N ASN A 422 " pdb=" CA ASN A 422 " ideal model delta sigma weight residual 121.54 129.27 -7.73 1.91e+00 2.74e-01 1.64e+01 ... (remaining 31335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 11882 17.85 - 35.70: 1228 35.70 - 53.55: 277 53.55 - 71.41: 65 71.41 - 89.26: 36 Dihedral angle restraints: 13488 sinusoidal: 5289 harmonic: 8199 Sorted by residual: dihedral pdb=" CA ASN D 470 " pdb=" C ASN D 470 " pdb=" N ASN D 471 " pdb=" CA ASN D 471 " ideal model delta harmonic sigma weight residual -180.00 -150.56 -29.44 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA CYS A 387 " pdb=" C CYS A 387 " pdb=" N ASP A 388 " pdb=" CA ASP A 388 " ideal model delta harmonic sigma weight residual 180.00 151.32 28.68 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA THR D 645 " pdb=" C THR D 645 " pdb=" N THR D 646 " pdb=" CA THR D 646 " ideal model delta harmonic sigma weight residual 180.00 -152.64 -27.36 0 5.00e+00 4.00e-02 2.99e+01 ... (remaining 13485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 2843 0.080 - 0.160: 395 0.160 - 0.239: 20 0.239 - 0.319: 4 0.319 - 0.399: 1 Chirality restraints: 3263 Sorted by residual: chirality pdb=" CB ILE D 377 " pdb=" CA ILE D 377 " pdb=" CG1 ILE D 377 " pdb=" CG2 ILE D 377 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.98e+00 chirality pdb=" CB ILE B 212 " pdb=" CA ILE B 212 " pdb=" CG1 ILE B 212 " pdb=" CG2 ILE B 212 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CB VAL B 668 " pdb=" CA VAL B 668 " pdb=" CG1 VAL B 668 " pdb=" CG2 VAL B 668 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 3260 not shown) Planarity restraints: 4129 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 384 " 0.049 5.00e-02 4.00e+02 7.41e-02 8.79e+00 pdb=" N PRO D 385 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO D 385 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 385 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 303 " 0.048 5.00e-02 4.00e+02 7.35e-02 8.65e+00 pdb=" N PRO C 304 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO C 304 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 304 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 826 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.06e+00 pdb=" CD GLU B 826 " -0.039 2.00e-02 2.50e+03 pdb=" OE1 GLU B 826 " 0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU B 826 " 0.013 2.00e-02 2.50e+03 ... (remaining 4126 not shown) Histogram of nonbonded interaction distances: 0.83 - 1.64: 11 1.64 - 2.46: 164 2.46 - 3.27: 23366 3.27 - 4.09: 57121 4.09 - 4.90: 104687 Warning: very small nonbonded interaction distances. Nonbonded interactions: 185349 Sorted by model distance: nonbonded pdb=" O GLY B 547 " pdb=" OD2 ASP D 537 " model vdw 0.828 3.040 nonbonded pdb=" O VAL C 14 " pdb=" N TYR D 639 " model vdw 1.047 3.120 nonbonded pdb=" CD LYS C 370 " pdb=" CB ALA D 256 " model vdw 1.063 3.860 nonbonded pdb=" CD1 PHE C 536 " pdb=" OE2 GLU D 846 " model vdw 1.078 3.340 nonbonded pdb=" NH1 ARG C 7 " pdb=" NH2 ARG D 513 " model vdw 1.104 3.200 ... (remaining 185344 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 1 through 77 or (resid 78 and (name N or name CA or name C \ or name O or name CB )) or resid 79 through 141 or (resid 142 and (name N or na \ me CA or name C or name O or name CB )) or resid 143 through 230 or (resid 231 a \ nd (name N or name CA or name C or name O or name CB )) or resid 232 through 254 \ or (resid 255 and (name N or name CA or name C or name O or name CB )) or resid \ 256 through 312 or (resid 313 and (name N or name CA or name C or name O or nam \ e CB )) or resid 314 through 318 or (resid 319 and (name N or name CA or name C \ or name O or name CB )) or resid 320 through 329 or (resid 330 and (name N or na \ me CA or name C or name O or name CB )) or resid 331 through 335 or (resid 336 a \ nd (name N or name CA or name C or name O or name CB )) or resid 337 through 352 \ or (resid 353 and (name N or name CA or name C or name O or name CB )) or resid \ 354 through 391 or (resid 392 and (name N or name CA or name C or name O or nam \ e CB )) or resid 393 through 422 or (resid 423 and (name N or name CA or name C \ or name O or name CB )) or resid 424 through 429 or (resid 430 and (name N or na \ me CA or name C or name O or name CB )) or resid 431 through 444 or (resid 445 a \ nd (name N or name CA or name C or name O or name CB )) or resid 446 through 449 \ or (resid 450 and (name N or name CA or name C or name O or name CB )) or resid \ 451 or (resid 452 and (name N or name CA or name C or name O or name CB )) or r \ esid 453 through 471 or (resid 472 through 473 and (name N or name CA or name C \ or name O or name CB )) or resid 474 or (resid 475 through 476 and (name N or na \ me CA or name C or name O or name CB )) or resid 477 through 501 or (resid 502 a \ nd (name N or name CA or name C or name O or name CB )) or resid 503 through 511 \ or (resid 512 through 513 and (name N or name CA or name C or name O or name CB \ )) or resid 514 through 519 or (resid 520 and (name N or name CA or name C or n \ ame O or name CB )) or resid 521 through 552)) } ncs_group { reference = (chain 'B' and resid 213 through 1016) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.390 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6085 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 : 0.007 0.452 23097 Z= 0.433 Angle : 0.908 9.625 31348 Z= 0.510 Chirality : 0.055 0.399 3263 Planarity : 0.006 0.074 4129 Dihedral : 16.150 89.256 8300 Min Nonbonded Distance : 0.828 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.49 % Favored : 93.30 % Rotamer: Outliers : 0.55 % Allowed : 15.28 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -3.15 (0.14), residues: 2836 helix: -2.69 (0.15), residues: 623 sheet: -1.56 (0.18), residues: 741 loop : -2.05 (0.14), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 367 TYR 0.027 0.003 TYR B 422 PHE 0.026 0.003 PHE D 942 TRP 0.030 0.003 TRP D 425 HIS 0.009 0.002 HIS D 362 Details of bonding type rmsd covalent geometry : bond 0.00673 (23092) covalent geometry : angle 0.90708 (31340) SS BOND : bond 0.04131 ( 4) SS BOND : angle 2.81610 ( 8) hydrogen bonds : bond 0.21959 ( 899) hydrogen bonds : angle 8.37197 ( 2475) Misc. bond : bond 0.45229 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 510 time to evaluate : 0.892 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 THR cc_start: 0.8780 (OUTLIER) cc_final: 0.8537 (t) REVERT: B 450 ASP cc_start: 0.5995 (t70) cc_final: 0.5697 (t70) REVERT: B 480 GLN cc_start: 0.8208 (tp40) cc_final: 0.7988 (tt0) REVERT: B 487 MET cc_start: 0.7673 (ptm) cc_final: 0.7467 (ptm) REVERT: B 489 ASN cc_start: 0.5012 (p0) cc_final: 0.4723 (p0) REVERT: B 507 ILE cc_start: 0.8098 (pt) cc_final: 0.7688 (tt) REVERT: B 526 PHE cc_start: 0.8434 (m-80) cc_final: 0.8111 (m-10) REVERT: B 630 ILE cc_start: 0.8576 (pt) cc_final: 0.8019 (mp) REVERT: B 948 PHE cc_start: 0.7256 (p90) cc_final: 0.6747 (p90) REVERT: C 50 ASN cc_start: 0.8069 (m110) cc_final: 0.7867 (m-40) REVERT: C 57 ASP cc_start: 0.8526 (m-30) cc_final: 0.7985 (t0) REVERT: C 97 CYS cc_start: 0.7408 (m) cc_final: 0.7198 (m) REVERT: C 160 LEU cc_start: 0.7176 (mt) cc_final: 0.6823 (mt) REVERT: C 276 ASN cc_start: 0.7525 (m-40) cc_final: 0.7299 (m-40) REVERT: C 284 LEU cc_start: 0.9281 (mt) cc_final: 0.8935 (mp) REVERT: C 312 PHE cc_start: 0.7743 (m-80) cc_final: 0.7250 (m-10) REVERT: C 412 LEU cc_start: 0.7710 (mt) cc_final: 0.7505 (mt) REVERT: C 450 TYR cc_start: 0.6682 (m-10) cc_final: 0.6269 (m-10) REVERT: C 485 PHE cc_start: 0.7516 (m-80) cc_final: 0.6873 (m-10) REVERT: D 234 THR cc_start: 0.8142 (m) cc_final: 0.7810 (p) REVERT: D 293 THR cc_start: 0.8049 (m) cc_final: 0.6681 (p) REVERT: D 414 LEU cc_start: 0.8611 (mt) cc_final: 0.8403 (mp) REVERT: D 450 ASP cc_start: 0.7421 (t0) cc_final: 0.6978 (t70) REVERT: D 470 ASN cc_start: 0.6164 (t0) cc_final: 0.5890 (t0) REVERT: D 487 MET cc_start: 0.7662 (tmm) cc_final: 0.6198 (tmm) REVERT: D 669 LEU cc_start: 0.8779 (mt) cc_final: 0.8445 (mp) REVERT: D 867 LEU cc_start: 0.8010 (mt) cc_final: 0.7197 (mm) REVERT: D 954 ILE cc_start: 0.6990 (tt) cc_final: 0.5048 (tt) outliers start: 13 outliers final: 2 residues processed: 519 average time/residue: 0.1673 time to fit residues: 133.4900 Evaluate side-chains 261 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 258 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.0270 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.2980 overall best weight: 1.0644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN A 215 GLN A 226 ASN A 263 ASN A 283 ASN A 506 ASN A 538 GLN B 112 GLN B 122 GLN B 174 ASN B 434 ASN B 562 ASN B 587 HIS B 628 GLN ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 743 ASN B 754 ASN C 43 ASN C 179 GLN C 256 ASN ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 480 GLN D 501 HIS D 586 ASN D 692 ASN D 754 ASN D 767 ASN D 980 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.077922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.061783 restraints weight = 121032.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.063161 restraints weight = 85927.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.063591 restraints weight = 58492.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.063774 restraints weight = 53826.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.063925 restraints weight = 51263.702| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23097 Z= 0.135 Angle : 0.637 10.147 31348 Z= 0.347 Chirality : 0.045 0.162 3263 Planarity : 0.005 0.070 4129 Dihedral : 5.416 31.739 3146 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.53 % Favored : 96.40 % Rotamer: Outliers : 0.21 % Allowed : 3.66 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.78 (0.15), residues: 2836 helix: -0.83 (0.19), residues: 639 sheet: -0.85 (0.19), residues: 719 loop : -1.46 (0.15), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 582 TYR 0.027 0.001 TYR A 157 PHE 0.056 0.002 PHE C 178 TRP 0.026 0.002 TRP C 498 HIS 0.011 0.001 HIS D 362 Details of bonding type rmsd covalent geometry : bond 0.00286 (23092) covalent geometry : angle 0.63310 (31340) SS BOND : bond 0.00947 ( 4) SS BOND : angle 4.19219 ( 8) hydrogen bonds : bond 0.04377 ( 899) hydrogen bonds : angle 5.52249 ( 2475) Misc. bond : bond 0.00051 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 334 time to evaluate : 0.836 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: A 242 MET cc_start: 0.8946 (mpp) cc_final: 0.8609 (mpp) REVERT: A 288 MET cc_start: 0.7283 (tmm) cc_final: 0.6774 (tmm) REVERT: A 413 MET cc_start: 0.9374 (mtm) cc_final: 0.8955 (mtp) REVERT: A 474 MET cc_start: 0.9337 (mmt) cc_final: 0.8685 (mmt) REVERT: B 229 MET cc_start: 0.8082 (mtm) cc_final: 0.7803 (pmm) REVERT: B 276 MET cc_start: 0.7663 (tpt) cc_final: 0.7114 (tpt) REVERT: B 288 MET cc_start: 0.8836 (tpt) cc_final: 0.8625 (mmm) REVERT: B 296 PHE cc_start: 0.7275 (m-10) cc_final: 0.6962 (m-10) REVERT: B 336 ASP cc_start: 0.8093 (m-30) cc_final: 0.7096 (t70) REVERT: B 347 ASN cc_start: 0.8962 (m-40) cc_final: 0.8473 (m-40) REVERT: B 511 LEU cc_start: 0.8211 (mt) cc_final: 0.7578 (mt) REVERT: B 519 PHE cc_start: 0.8615 (p90) cc_final: 0.8210 (p90) REVERT: B 682 ASN cc_start: 0.8418 (t0) cc_final: 0.8027 (p0) REVERT: B 720 THR cc_start: 0.8302 (t) cc_final: 0.7852 (m) REVERT: C 35 ILE cc_start: 0.8475 (tp) cc_final: 0.8124 (tp) REVERT: C 152 MET cc_start: 0.7362 (ttt) cc_final: 0.7076 (ttt) REVERT: C 277 ASP cc_start: 0.4090 (p0) cc_final: 0.3650 (p0) REVERT: C 284 LEU cc_start: 0.9634 (mt) cc_final: 0.9408 (mp) REVERT: C 347 MET cc_start: 0.7724 (mpp) cc_final: 0.7132 (mpp) REVERT: C 409 ASP cc_start: 0.8703 (m-30) cc_final: 0.8368 (m-30) REVERT: C 412 LEU cc_start: 0.9002 (mt) cc_final: 0.8730 (mt) REVERT: C 474 MET cc_start: 0.9254 (mmm) cc_final: 0.8186 (mmm) REVERT: C 485 PHE cc_start: 0.6066 (m-80) cc_final: 0.5452 (m-10) REVERT: C 487 MET cc_start: 0.8384 (mmm) cc_final: 0.8063 (mtp) REVERT: D 368 THR cc_start: 0.6082 (m) cc_final: 0.5736 (p) REVERT: D 427 MET cc_start: 0.7857 (mpp) cc_final: 0.7471 (mpp) REVERT: D 450 ASP cc_start: 0.7866 (t0) cc_final: 0.7485 (t70) REVERT: D 504 ASP cc_start: 0.9116 (m-30) cc_final: 0.8666 (m-30) REVERT: D 621 SER cc_start: 0.6300 (p) cc_final: 0.5495 (p) REVERT: D 669 LEU cc_start: 0.8318 (mt) cc_final: 0.8057 (mm) REVERT: D 692 ASN cc_start: 0.6257 (m-40) cc_final: 0.5639 (m-40) REVERT: D 929 ARG cc_start: 0.7479 (ttt180) cc_final: 0.7107 (ttp-110) outliers start: 5 outliers final: 2 residues processed: 337 average time/residue: 0.1602 time to fit residues: 84.8448 Evaluate side-chains 216 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 214 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 131 optimal weight: 6.9990 chunk 195 optimal weight: 3.9990 chunk 11 optimal weight: 0.4980 chunk 42 optimal weight: 0.8980 chunk 276 optimal weight: 20.0000 chunk 12 optimal weight: 8.9990 chunk 264 optimal weight: 20.0000 chunk 249 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 228 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN A 134 HIS A 167 ASN A 549 ASN B 112 GLN B 174 ASN B 262 ASN B 362 HIS B 501 HIS B 586 ASN ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 ASN C 263 ASN C 272 GLN C 327 ASN C 401 ASN ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 ASN D 677 GLN D 690 GLN D 999 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.071806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.055102 restraints weight = 128378.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.056284 restraints weight = 91986.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.056709 restraints weight = 62243.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.056935 restraints weight = 59001.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.057057 restraints weight = 53465.078| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 23097 Z= 0.166 Angle : 0.639 11.007 31348 Z= 0.346 Chirality : 0.045 0.209 3263 Planarity : 0.005 0.079 4129 Dihedral : 5.170 33.303 3146 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.80 % Favored : 95.17 % Rotamer: Outliers : 0.04 % Allowed : 3.79 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.14 (0.15), residues: 2836 helix: -0.18 (0.20), residues: 634 sheet: -0.45 (0.19), residues: 739 loop : -1.13 (0.16), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 588 TYR 0.024 0.002 TYR A 157 PHE 0.026 0.002 PHE D 592 TRP 0.022 0.002 TRP D 685 HIS 0.009 0.002 HIS D 362 Details of bonding type rmsd covalent geometry : bond 0.00358 (23092) covalent geometry : angle 0.63604 (31340) SS BOND : bond 0.01497 ( 4) SS BOND : angle 3.81140 ( 8) hydrogen bonds : bond 0.04107 ( 899) hydrogen bonds : angle 5.17223 ( 2475) Misc. bond : bond 0.00114 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 274 time to evaluate : 0.865 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: A 242 MET cc_start: 0.9000 (mpp) cc_final: 0.8729 (mpp) REVERT: A 288 MET cc_start: 0.7465 (tmm) cc_final: 0.6952 (tmm) REVERT: A 413 MET cc_start: 0.9314 (mtm) cc_final: 0.8873 (mtp) REVERT: A 474 MET cc_start: 0.9375 (mmt) cc_final: 0.8656 (mmt) REVERT: B 276 MET cc_start: 0.7786 (tpt) cc_final: 0.7280 (tpt) REVERT: B 288 MET cc_start: 0.8822 (tpt) cc_final: 0.8284 (mmm) REVERT: B 336 ASP cc_start: 0.8260 (m-30) cc_final: 0.7541 (t70) REVERT: B 347 ASN cc_start: 0.8064 (m-40) cc_final: 0.7696 (p0) REVERT: B 485 LYS cc_start: 0.7471 (tttt) cc_final: 0.6916 (tttt) REVERT: B 509 MET cc_start: 0.8093 (ppp) cc_final: 0.7496 (pmm) REVERT: B 747 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7208 (tm-30) REVERT: B 1006 VAL cc_start: 0.8907 (t) cc_final: 0.8373 (t) REVERT: C 137 LEU cc_start: 0.9260 (mt) cc_final: 0.8810 (mt) REVERT: C 140 LEU cc_start: 0.9325 (mt) cc_final: 0.8499 (mt) REVERT: C 144 ILE cc_start: 0.8852 (pt) cc_final: 0.8482 (pt) REVERT: C 174 ILE cc_start: 0.9278 (mm) cc_final: 0.8704 (tp) REVERT: C 255 MET cc_start: 0.9247 (mpp) cc_final: 0.8692 (mpp) REVERT: C 256 ASN cc_start: 0.8036 (m-40) cc_final: 0.7578 (m110) REVERT: C 277 ASP cc_start: 0.5208 (p0) cc_final: 0.4574 (p0) REVERT: C 347 MET cc_start: 0.7842 (mpp) cc_final: 0.7229 (mpp) REVERT: C 400 LEU cc_start: 0.9049 (tt) cc_final: 0.8830 (pp) REVERT: C 412 LEU cc_start: 0.8838 (mt) cc_final: 0.8581 (mt) REVERT: C 474 MET cc_start: 0.9299 (mmm) cc_final: 0.8278 (mmm) REVERT: C 516 CYS cc_start: 0.8206 (t) cc_final: 0.7178 (m) REVERT: C 538 GLN cc_start: 0.8669 (mm-40) cc_final: 0.8066 (mm110) REVERT: D 379 GLU cc_start: 0.8994 (pp20) cc_final: 0.8747 (pp20) REVERT: D 477 GLU cc_start: 0.8184 (tt0) cc_final: 0.7899 (tt0) REVERT: D 514 GLU cc_start: 0.6905 (tm-30) cc_final: 0.6634 (tm-30) REVERT: D 534 MET cc_start: 0.7615 (mmm) cc_final: 0.7376 (mmm) REVERT: D 669 LEU cc_start: 0.8273 (mt) cc_final: 0.7936 (mm) REVERT: D 728 LEU cc_start: 0.8970 (mt) cc_final: 0.8567 (mt) REVERT: D 835 TYR cc_start: 0.7056 (m-80) cc_final: 0.6700 (m-80) REVERT: D 889 ASP cc_start: 0.7577 (m-30) cc_final: 0.6723 (p0) outliers start: 1 outliers final: 0 residues processed: 274 average time/residue: 0.1495 time to fit residues: 65.7096 Evaluate side-chains 189 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 119 optimal weight: 9.9990 chunk 46 optimal weight: 20.0000 chunk 175 optimal weight: 8.9990 chunk 268 optimal weight: 2.9990 chunk 120 optimal weight: 8.9990 chunk 230 optimal weight: 6.9990 chunk 161 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 235 optimal weight: 1.9990 chunk 271 optimal weight: 7.9990 chunk 99 optimal weight: 0.0370 overall best weight: 3.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN ** A 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 ASN B 243 GLN B 247 ASN B 562 ASN B 586 ASN B 628 GLN ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 743 ASN ** B 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 945 ASN C 260 GLN ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 642 ASN ** D 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.067871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.052258 restraints weight = 131596.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.052743 restraints weight = 105866.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.053282 restraints weight = 77333.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.053485 restraints weight = 69171.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.053652 restraints weight = 64284.519| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.5677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23097 Z= 0.167 Angle : 0.614 8.859 31348 Z= 0.332 Chirality : 0.044 0.177 3263 Planarity : 0.004 0.055 4129 Dihedral : 5.084 34.415 3146 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.23 % Favored : 95.73 % Rotamer: Outliers : 0.04 % Allowed : 3.12 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.88 (0.16), residues: 2836 helix: 0.11 (0.21), residues: 623 sheet: -0.34 (0.19), residues: 750 loop : -0.97 (0.16), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 406 TYR 0.030 0.002 TYR C 203 PHE 0.032 0.002 PHE C 135 TRP 0.024 0.002 TRP D 685 HIS 0.012 0.002 HIS D 362 Details of bonding type rmsd covalent geometry : bond 0.00357 (23092) covalent geometry : angle 0.61179 (31340) SS BOND : bond 0.01103 ( 4) SS BOND : angle 3.62053 ( 8) hydrogen bonds : bond 0.03952 ( 899) hydrogen bonds : angle 5.01906 ( 2475) Misc. bond : bond 0.00090 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 233 time to evaluate : 0.942 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: A 242 MET cc_start: 0.9015 (mpp) cc_final: 0.8751 (mpp) REVERT: A 288 MET cc_start: 0.7756 (tmm) cc_final: 0.7093 (tmm) REVERT: A 413 MET cc_start: 0.9334 (mtm) cc_final: 0.9049 (mtp) REVERT: A 474 MET cc_start: 0.9420 (mmt) cc_final: 0.8699 (mmt) REVERT: B 276 MET cc_start: 0.7389 (tpt) cc_final: 0.6816 (tpt) REVERT: B 288 MET cc_start: 0.8901 (tpt) cc_final: 0.8397 (mmm) REVERT: B 314 ASN cc_start: 0.8626 (t0) cc_final: 0.7959 (t0) REVERT: B 336 ASP cc_start: 0.8424 (m-30) cc_final: 0.7883 (t70) REVERT: B 347 ASN cc_start: 0.7949 (m-40) cc_final: 0.7641 (p0) REVERT: B 379 GLU cc_start: 0.7974 (pp20) cc_final: 0.7700 (pp20) REVERT: B 485 LYS cc_start: 0.7312 (tttt) cc_final: 0.6979 (tttp) REVERT: B 741 MET cc_start: 0.7499 (ttm) cc_final: 0.7224 (ttp) REVERT: C 129 LEU cc_start: 0.9331 (mt) cc_final: 0.8893 (mt) REVERT: C 157 TYR cc_start: 0.9008 (m-80) cc_final: 0.8387 (m-80) REVERT: C 255 MET cc_start: 0.9367 (mpp) cc_final: 0.9074 (mpp) REVERT: C 256 ASN cc_start: 0.8067 (m-40) cc_final: 0.7631 (m110) REVERT: C 347 MET cc_start: 0.8078 (mpp) cc_final: 0.7463 (mpp) REVERT: C 450 TYR cc_start: 0.7902 (m-10) cc_final: 0.7183 (m-80) REVERT: C 474 MET cc_start: 0.9315 (mmm) cc_final: 0.8308 (mmm) REVERT: C 516 CYS cc_start: 0.8782 (t) cc_final: 0.7741 (m) REVERT: C 538 GLN cc_start: 0.8611 (mm-40) cc_final: 0.8349 (mm110) REVERT: D 449 LEU cc_start: 0.8289 (tt) cc_final: 0.8053 (tt) REVERT: D 514 GLU cc_start: 0.7223 (tm-30) cc_final: 0.6744 (tm-30) REVERT: D 534 MET cc_start: 0.8292 (mmm) cc_final: 0.7717 (mmt) REVERT: D 625 THR cc_start: 0.9108 (p) cc_final: 0.8689 (p) REVERT: D 835 TYR cc_start: 0.7011 (m-80) cc_final: 0.6427 (m-80) outliers start: 1 outliers final: 1 residues processed: 233 average time/residue: 0.1534 time to fit residues: 57.6563 Evaluate side-chains 178 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 177 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 186 optimal weight: 0.0370 chunk 246 optimal weight: 5.9990 chunk 47 optimal weight: 40.0000 chunk 239 optimal weight: 20.0000 chunk 278 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 224 optimal weight: 3.9990 chunk 208 optimal weight: 20.0000 chunk 205 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 214 optimal weight: 4.9990 overall best weight: 3.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 50 ASN A 72 ASN A 102 ASN ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 ASN ** B 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 934 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.064272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.048503 restraints weight = 130541.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.048969 restraints weight = 90921.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.049552 restraints weight = 68409.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.049771 restraints weight = 62256.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.049874 restraints weight = 56560.403| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.6456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 23097 Z= 0.192 Angle : 0.630 9.984 31348 Z= 0.340 Chirality : 0.044 0.156 3263 Planarity : 0.004 0.054 4129 Dihedral : 5.055 34.053 3146 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.01 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 2836 helix: 0.18 (0.21), residues: 640 sheet: -0.35 (0.19), residues: 753 loop : -1.04 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 457 TYR 0.024 0.002 TYR B 191 PHE 0.017 0.002 PHE C 178 TRP 0.020 0.002 TRP D 735 HIS 0.010 0.002 HIS D 362 Details of bonding type rmsd covalent geometry : bond 0.00415 (23092) covalent geometry : angle 0.62779 (31340) SS BOND : bond 0.01704 ( 4) SS BOND : angle 3.56529 ( 8) hydrogen bonds : bond 0.03877 ( 899) hydrogen bonds : angle 4.99709 ( 2475) Misc. bond : bond 0.00110 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.916 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: A 136 MET cc_start: 0.9730 (mtm) cc_final: 0.9427 (mtm) REVERT: A 242 MET cc_start: 0.9160 (mpp) cc_final: 0.8792 (mpp) REVERT: A 413 MET cc_start: 0.9420 (mtm) cc_final: 0.9186 (mtp) REVERT: A 474 MET cc_start: 0.9479 (mmt) cc_final: 0.8774 (mmt) REVERT: B 212 ILE cc_start: 0.8362 (mp) cc_final: 0.8142 (mm) REVERT: B 276 MET cc_start: 0.7740 (tpt) cc_final: 0.7151 (tpt) REVERT: B 288 MET cc_start: 0.9051 (tpt) cc_final: 0.8552 (mmm) REVERT: B 336 ASP cc_start: 0.8223 (m-30) cc_final: 0.7848 (t70) REVERT: B 347 ASN cc_start: 0.7593 (m-40) cc_final: 0.7316 (m110) REVERT: B 379 GLU cc_start: 0.8142 (pp20) cc_final: 0.7888 (pp20) REVERT: B 485 LYS cc_start: 0.7681 (tttt) cc_final: 0.7242 (tttm) REVERT: B 487 MET cc_start: 0.7654 (ppp) cc_final: 0.7232 (ppp) REVERT: B 509 MET cc_start: 0.7984 (ppp) cc_final: 0.7711 (ppp) REVERT: B 741 MET cc_start: 0.7633 (ttm) cc_final: 0.7403 (ttp) REVERT: B 948 PHE cc_start: 0.8425 (p90) cc_final: 0.7974 (p90) REVERT: C 41 ASP cc_start: 0.6717 (p0) cc_final: 0.6204 (p0) REVERT: C 136 MET cc_start: 0.9034 (tmm) cc_final: 0.8717 (tmm) REVERT: C 157 TYR cc_start: 0.9055 (m-80) cc_final: 0.8778 (m-80) REVERT: C 255 MET cc_start: 0.9265 (mpp) cc_final: 0.8989 (mpp) REVERT: C 347 MET cc_start: 0.8126 (mpp) cc_final: 0.7677 (mpp) REVERT: C 412 LEU cc_start: 0.8937 (mt) cc_final: 0.8577 (mt) REVERT: C 474 MET cc_start: 0.9456 (mmm) cc_final: 0.8378 (mmm) REVERT: C 487 MET cc_start: 0.8311 (mmm) cc_final: 0.8041 (tpp) REVERT: C 516 CYS cc_start: 0.8998 (t) cc_final: 0.7924 (m) REVERT: C 538 GLN cc_start: 0.8765 (mm-40) cc_final: 0.8218 (mm110) REVERT: D 217 ASP cc_start: 0.8656 (m-30) cc_final: 0.7837 (t0) REVERT: D 514 GLU cc_start: 0.7130 (tm-30) cc_final: 0.6662 (tm-30) REVERT: D 615 ASP cc_start: 0.8781 (p0) cc_final: 0.8359 (p0) REVERT: D 618 LEU cc_start: 0.9499 (tp) cc_final: 0.9264 (pp) REVERT: D 625 THR cc_start: 0.9208 (p) cc_final: 0.8936 (p) REVERT: D 835 TYR cc_start: 0.7856 (m-80) cc_final: 0.7365 (m-10) REVERT: D 941 TYR cc_start: 0.7193 (t80) cc_final: 0.6667 (t80) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.1477 time to fit residues: 47.3106 Evaluate side-chains 155 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 239 optimal weight: 6.9990 chunk 199 optimal weight: 1.9990 chunk 223 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 262 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 232 optimal weight: 9.9990 chunk 63 optimal weight: 0.2980 chunk 120 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 ASN B 366 ASN B 518 HIS B 632 ASN ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 849 GLN C 220 ASN ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 HIS ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.063669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.048123 restraints weight = 131250.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.048735 restraints weight = 88341.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.049495 restraints weight = 63838.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.049568 restraints weight = 56203.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.049650 restraints weight = 51318.300| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.6900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 23097 Z= 0.158 Angle : 0.605 9.006 31348 Z= 0.323 Chirality : 0.044 0.193 3263 Planarity : 0.004 0.053 4129 Dihedral : 4.911 34.875 3146 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.34 % Favored : 95.63 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.75 (0.16), residues: 2836 helix: 0.44 (0.21), residues: 634 sheet: -0.31 (0.19), residues: 743 loop : -0.97 (0.16), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 457 TYR 0.020 0.001 TYR C 203 PHE 0.019 0.002 PHE D 322 TRP 0.015 0.002 TRP D 295 HIS 0.012 0.001 HIS D 362 Details of bonding type rmsd covalent geometry : bond 0.00341 (23092) covalent geometry : angle 0.60188 (31340) SS BOND : bond 0.00607 ( 4) SS BOND : angle 3.80751 ( 8) hydrogen bonds : bond 0.03611 ( 899) hydrogen bonds : angle 4.89676 ( 2475) Misc. bond : bond 0.00107 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.851 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: A 136 MET cc_start: 0.9635 (mtm) cc_final: 0.9312 (mtm) REVERT: A 242 MET cc_start: 0.9154 (mpp) cc_final: 0.8702 (mpp) REVERT: A 474 MET cc_start: 0.9433 (mmt) cc_final: 0.8710 (mmt) REVERT: B 276 MET cc_start: 0.7420 (tpt) cc_final: 0.6722 (tpt) REVERT: B 288 MET cc_start: 0.8735 (tpt) cc_final: 0.8268 (mmm) REVERT: B 336 ASP cc_start: 0.8377 (m-30) cc_final: 0.7921 (t70) REVERT: B 379 GLU cc_start: 0.8005 (pp20) cc_final: 0.7778 (pp20) REVERT: B 487 MET cc_start: 0.7743 (ppp) cc_final: 0.7535 (ppp) REVERT: B 509 MET cc_start: 0.8081 (ppp) cc_final: 0.7699 (tmm) REVERT: B 741 MET cc_start: 0.7753 (ttm) cc_final: 0.7415 (ttp) REVERT: B 948 PHE cc_start: 0.8321 (p90) cc_final: 0.7845 (p90) REVERT: C 41 ASP cc_start: 0.6644 (p0) cc_final: 0.6129 (p0) REVERT: C 136 MET cc_start: 0.8871 (tmm) cc_final: 0.8653 (tmm) REVERT: C 157 TYR cc_start: 0.8993 (m-80) cc_final: 0.8378 (m-80) REVERT: C 255 MET cc_start: 0.9259 (mpp) cc_final: 0.9039 (mpp) REVERT: C 347 MET cc_start: 0.8030 (mpp) cc_final: 0.7768 (mpp) REVERT: C 412 LEU cc_start: 0.8735 (mt) cc_final: 0.8520 (mt) REVERT: C 474 MET cc_start: 0.9051 (mmm) cc_final: 0.8259 (mmm) REVERT: C 487 MET cc_start: 0.8142 (mmm) cc_final: 0.7717 (tpp) REVERT: C 538 GLN cc_start: 0.8566 (mm-40) cc_final: 0.8085 (mm110) REVERT: D 217 ASP cc_start: 0.8525 (m-30) cc_final: 0.7724 (t0) REVERT: D 229 MET cc_start: 0.7960 (tpt) cc_final: 0.7739 (tpp) REVERT: D 294 ASP cc_start: 0.8475 (t0) cc_final: 0.8268 (t0) REVERT: D 468 GLN cc_start: 0.7649 (mm-40) cc_final: 0.6809 (tp40) REVERT: D 477 GLU cc_start: 0.8730 (tt0) cc_final: 0.8366 (tt0) REVERT: D 534 MET cc_start: 0.8621 (mmt) cc_final: 0.7558 (mmt) REVERT: D 618 LEU cc_start: 0.9403 (tp) cc_final: 0.9163 (pp) REVERT: D 833 ILE cc_start: 0.8073 (mm) cc_final: 0.7794 (mm) REVERT: D 835 TYR cc_start: 0.7708 (m-80) cc_final: 0.7299 (m-10) REVERT: D 941 TYR cc_start: 0.7477 (t80) cc_final: 0.6949 (t80) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.1535 time to fit residues: 47.9873 Evaluate side-chains 155 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 282 optimal weight: 5.9990 chunk 111 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 chunk 253 optimal weight: 5.9990 chunk 197 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 chunk 251 optimal weight: 20.0000 chunk 146 optimal weight: 3.9990 chunk 222 optimal weight: 8.9990 chunk 155 optimal weight: 10.0000 chunk 262 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 102 ASN ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 GLN B 174 ASN ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 ASN ** B 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 GLN C 81 ASN C 232 GLN ** C 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 677 GLN ** D 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 785 ASN D 989 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.060229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.045986 restraints weight = 138183.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.045990 restraints weight = 100931.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.046598 restraints weight = 81147.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.046945 restraints weight = 67308.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.047130 restraints weight = 61165.508| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.7796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 23097 Z= 0.264 Angle : 0.737 13.267 31348 Z= 0.396 Chirality : 0.047 0.180 3263 Planarity : 0.005 0.055 4129 Dihedral : 5.536 35.979 3146 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.45 % Favored : 93.51 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.17 (0.15), residues: 2836 helix: -0.06 (0.20), residues: 643 sheet: -0.51 (0.19), residues: 717 loop : -1.20 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 100 TYR 0.032 0.002 TYR B 191 PHE 0.027 0.003 PHE B 296 TRP 0.022 0.002 TRP D 295 HIS 0.023 0.002 HIS A 302 Details of bonding type rmsd covalent geometry : bond 0.00564 (23092) covalent geometry : angle 0.73414 (31340) SS BOND : bond 0.01226 ( 4) SS BOND : angle 3.97399 ( 8) hydrogen bonds : bond 0.04445 ( 899) hydrogen bonds : angle 5.43013 ( 2475) Misc. bond : bond 0.00047 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.913 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: A 136 MET cc_start: 0.9671 (mtm) cc_final: 0.9465 (mtp) REVERT: A 242 MET cc_start: 0.9276 (mpp) cc_final: 0.8859 (mpp) REVERT: A 474 MET cc_start: 0.9485 (mmt) cc_final: 0.8739 (mmt) REVERT: A 487 MET cc_start: 0.8664 (pmm) cc_final: 0.8446 (pmm) REVERT: B 276 MET cc_start: 0.7975 (tpt) cc_final: 0.7391 (tpt) REVERT: B 288 MET cc_start: 0.8864 (tpt) cc_final: 0.8571 (mmm) REVERT: B 336 ASP cc_start: 0.8389 (m-30) cc_final: 0.7509 (t70) REVERT: B 379 GLU cc_start: 0.8308 (pp20) cc_final: 0.8083 (pp20) REVERT: B 526 PHE cc_start: 0.8431 (m-10) cc_final: 0.8216 (m-10) REVERT: B 597 LEU cc_start: 0.9089 (pp) cc_final: 0.8884 (mp) REVERT: B 876 MET cc_start: 0.8998 (ptt) cc_final: 0.8781 (ttp) REVERT: B 948 PHE cc_start: 0.8377 (p90) cc_final: 0.7937 (p90) REVERT: C 41 ASP cc_start: 0.6780 (p0) cc_final: 0.6453 (p0) REVERT: C 136 MET cc_start: 0.8954 (tmm) cc_final: 0.8728 (tmm) REVERT: C 157 TYR cc_start: 0.9134 (m-80) cc_final: 0.8529 (m-80) REVERT: C 347 MET cc_start: 0.8091 (mpp) cc_final: 0.7703 (mpp) REVERT: C 412 LEU cc_start: 0.8807 (mt) cc_final: 0.8581 (mt) REVERT: C 474 MET cc_start: 0.9216 (mmm) cc_final: 0.8379 (mmm) REVERT: C 538 GLN cc_start: 0.8661 (mm-40) cc_final: 0.8213 (mm110) REVERT: D 217 ASP cc_start: 0.8423 (m-30) cc_final: 0.7736 (t0) REVERT: D 346 MET cc_start: 0.7811 (mmp) cc_final: 0.7464 (mmp) REVERT: D 449 LEU cc_start: 0.8148 (tt) cc_final: 0.7766 (tt) REVERT: D 465 GLU cc_start: 0.7430 (pt0) cc_final: 0.7154 (mm-30) REVERT: D 468 GLN cc_start: 0.8020 (mm-40) cc_final: 0.7248 (tp40) REVERT: D 477 GLU cc_start: 0.8763 (tt0) cc_final: 0.7874 (tm-30) REVERT: D 618 LEU cc_start: 0.9461 (tp) cc_final: 0.9208 (pp) REVERT: D 771 TYR cc_start: 0.8529 (p90) cc_final: 0.7997 (p90) REVERT: D 835 TYR cc_start: 0.8258 (m-80) cc_final: 0.7847 (m-80) REVERT: D 941 TYR cc_start: 0.8072 (t80) cc_final: 0.7570 (t80) REVERT: D 951 LEU cc_start: 0.7184 (mp) cc_final: 0.6688 (tp) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.1415 time to fit residues: 41.1418 Evaluate side-chains 142 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 238 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 152 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 202 optimal weight: 20.0000 chunk 56 optimal weight: 5.9990 chunk 226 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 134 HIS A 139 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 ASN ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 677 GLN ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 804 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.061457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.046666 restraints weight = 132610.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.047061 restraints weight = 89097.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.047865 restraints weight = 68075.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.047935 restraints weight = 56330.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.048007 restraints weight = 54229.128| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.7870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 23097 Z= 0.139 Angle : 0.612 9.532 31348 Z= 0.326 Chirality : 0.045 0.153 3263 Planarity : 0.004 0.056 4129 Dihedral : 5.028 35.533 3146 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.41 % Favored : 95.56 % Rotamer: Outliers : 0.08 % Allowed : 1.01 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.89 (0.16), residues: 2836 helix: 0.28 (0.21), residues: 652 sheet: -0.40 (0.19), residues: 741 loop : -1.04 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 100 TYR 0.022 0.001 TYR C 203 PHE 0.020 0.002 PHE B 606 TRP 0.017 0.001 TRP D 535 HIS 0.005 0.001 HIS B 501 Details of bonding type rmsd covalent geometry : bond 0.00306 (23092) covalent geometry : angle 0.60783 (31340) SS BOND : bond 0.01635 ( 4) SS BOND : angle 4.42331 ( 8) hydrogen bonds : bond 0.03659 ( 899) hydrogen bonds : angle 5.00431 ( 2475) Misc. bond : bond 0.00071 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 188 time to evaluate : 0.822 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: A 126 MET cc_start: 0.9090 (mtm) cc_final: 0.8676 (ttp) REVERT: A 136 MET cc_start: 0.9644 (mtm) cc_final: 0.9399 (mtp) REVERT: A 242 MET cc_start: 0.9218 (mpp) cc_final: 0.8792 (mpp) REVERT: A 474 MET cc_start: 0.9483 (mmt) cc_final: 0.8694 (mmt) REVERT: A 487 MET cc_start: 0.8556 (pmm) cc_final: 0.8312 (pmm) REVERT: B 109 ILE cc_start: 0.8717 (mt) cc_final: 0.8439 (mt) REVERT: B 276 MET cc_start: 0.7699 (tpt) cc_final: 0.7385 (tpt) REVERT: B 288 MET cc_start: 0.8634 (tpt) cc_final: 0.8369 (mmm) REVERT: B 336 ASP cc_start: 0.8390 (m-30) cc_final: 0.7478 (t70) REVERT: B 379 GLU cc_start: 0.8250 (pp20) cc_final: 0.7994 (pp20) REVERT: B 485 LYS cc_start: 0.7506 (tttt) cc_final: 0.6876 (tttp) REVERT: B 509 MET cc_start: 0.8065 (ppp) cc_final: 0.7799 (tmm) REVERT: B 526 PHE cc_start: 0.8594 (m-10) cc_final: 0.7898 (m-10) REVERT: B 530 THR cc_start: 0.8484 (p) cc_final: 0.7738 (p) REVERT: B 677 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.7234 (pp30) REVERT: B 876 MET cc_start: 0.8993 (ptt) cc_final: 0.8670 (ttp) REVERT: B 948 PHE cc_start: 0.8351 (p90) cc_final: 0.7871 (p90) REVERT: C 41 ASP cc_start: 0.6576 (p0) cc_final: 0.6300 (p0) REVERT: C 136 MET cc_start: 0.8904 (tmm) cc_final: 0.8585 (tmm) REVERT: C 157 TYR cc_start: 0.8990 (m-80) cc_final: 0.8637 (m-80) REVERT: C 347 MET cc_start: 0.7922 (mpp) cc_final: 0.7545 (mpp) REVERT: C 412 LEU cc_start: 0.8733 (mt) cc_final: 0.8510 (mt) REVERT: C 474 MET cc_start: 0.9177 (mmm) cc_final: 0.8329 (mmm) REVERT: C 487 MET cc_start: 0.8298 (mmm) cc_final: 0.7771 (mtp) REVERT: C 538 GLN cc_start: 0.8614 (mm-40) cc_final: 0.8269 (mm110) REVERT: D 217 ASP cc_start: 0.8548 (m-30) cc_final: 0.7829 (t0) REVERT: D 346 MET cc_start: 0.7710 (mmp) cc_final: 0.7482 (mmp) REVERT: D 449 LEU cc_start: 0.8193 (tt) cc_final: 0.7932 (tt) REVERT: D 451 TYR cc_start: 0.8077 (t80) cc_final: 0.7271 (t80) REVERT: D 468 GLN cc_start: 0.7798 (mm-40) cc_final: 0.7541 (tp40) REVERT: D 480 GLN cc_start: 0.7618 (mm-40) cc_final: 0.6870 (mm-40) REVERT: D 487 MET cc_start: 0.7349 (tmm) cc_final: 0.7096 (tmm) REVERT: D 509 MET cc_start: 0.8267 (pmm) cc_final: 0.8057 (pmm) REVERT: D 618 LEU cc_start: 0.9449 (tp) cc_final: 0.9132 (pp) REVERT: D 771 TYR cc_start: 0.8538 (p90) cc_final: 0.8013 (p90) REVERT: D 835 TYR cc_start: 0.8299 (m-80) cc_final: 0.7772 (m-80) REVERT: D 941 TYR cc_start: 0.7962 (t80) cc_final: 0.7475 (t80) outliers start: 2 outliers final: 1 residues processed: 189 average time/residue: 0.1381 time to fit residues: 42.7845 Evaluate side-chains 147 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 145 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 95 optimal weight: 7.9990 chunk 6 optimal weight: 30.0000 chunk 212 optimal weight: 9.9990 chunk 156 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 176 optimal weight: 6.9990 chunk 231 optimal weight: 30.0000 chunk 202 optimal weight: 9.9990 chunk 163 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 ASN ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN ** B 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 785 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.058950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.044701 restraints weight = 139892.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.044923 restraints weight = 94424.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.045517 restraints weight = 76408.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.045855 restraints weight = 60180.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.045935 restraints weight = 56580.395| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.8412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 23097 Z= 0.239 Angle : 0.712 12.284 31348 Z= 0.380 Chirality : 0.046 0.175 3263 Planarity : 0.005 0.059 4129 Dihedral : 5.427 35.116 3146 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.52 % Favored : 93.44 % Rotamer: Outliers : 0.04 % Allowed : 0.76 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.10 (0.16), residues: 2836 helix: 0.13 (0.21), residues: 638 sheet: -0.57 (0.18), residues: 741 loop : -1.16 (0.16), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 457 TYR 0.030 0.002 TYR B 191 PHE 0.029 0.002 PHE D 788 TRP 0.015 0.002 TRP B 486 HIS 0.006 0.001 HIS D 799 Details of bonding type rmsd covalent geometry : bond 0.00512 (23092) covalent geometry : angle 0.70845 (31340) SS BOND : bond 0.01079 ( 4) SS BOND : angle 4.59148 ( 8) hydrogen bonds : bond 0.04213 ( 899) hydrogen bonds : angle 5.29211 ( 2475) Misc. bond : bond 0.00119 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 MET cc_start: 0.9112 (mtm) cc_final: 0.8663 (ttm) REVERT: A 136 MET cc_start: 0.9664 (mtm) cc_final: 0.9430 (mtp) REVERT: A 242 MET cc_start: 0.9284 (mpp) cc_final: 0.8853 (mpp) REVERT: A 474 MET cc_start: 0.9477 (mmt) cc_final: 0.8693 (mmt) REVERT: A 487 MET cc_start: 0.8660 (pmm) cc_final: 0.8451 (pmm) REVERT: B 168 MET cc_start: 0.7915 (tpp) cc_final: 0.7418 (tpp) REVERT: B 276 MET cc_start: 0.7831 (tpt) cc_final: 0.7101 (tpt) REVERT: B 288 MET cc_start: 0.8757 (tpt) cc_final: 0.8476 (mmm) REVERT: B 314 ASN cc_start: 0.9114 (t0) cc_final: 0.8454 (t0) REVERT: B 336 ASP cc_start: 0.8363 (m-30) cc_final: 0.7492 (t70) REVERT: B 379 GLU cc_start: 0.8158 (pp20) cc_final: 0.7897 (pp20) REVERT: B 485 LYS cc_start: 0.7485 (tttt) cc_final: 0.6875 (tttp) REVERT: B 509 MET cc_start: 0.7962 (ppp) cc_final: 0.7735 (tmm) REVERT: B 638 ILE cc_start: 0.9420 (mm) cc_final: 0.9147 (mm) REVERT: B 876 MET cc_start: 0.8950 (ptt) cc_final: 0.8705 (ttp) REVERT: B 948 PHE cc_start: 0.8358 (p90) cc_final: 0.7929 (p90) REVERT: C 41 ASP cc_start: 0.6752 (p0) cc_final: 0.6473 (p0) REVERT: C 136 MET cc_start: 0.8971 (tmm) cc_final: 0.8727 (tmm) REVERT: C 157 TYR cc_start: 0.9114 (m-80) cc_final: 0.8448 (m-80) REVERT: C 347 MET cc_start: 0.8098 (mpp) cc_final: 0.7688 (mpp) REVERT: C 412 LEU cc_start: 0.8777 (mt) cc_final: 0.8545 (mt) REVERT: C 474 MET cc_start: 0.9208 (mmm) cc_final: 0.8373 (mmm) REVERT: C 487 MET cc_start: 0.8458 (mmm) cc_final: 0.7966 (mtp) REVERT: C 538 GLN cc_start: 0.8631 (mm-40) cc_final: 0.8187 (mm110) REVERT: D 217 ASP cc_start: 0.8447 (m-30) cc_final: 0.7753 (t0) REVERT: D 468 GLN cc_start: 0.8055 (mm-40) cc_final: 0.7720 (tp40) REVERT: D 509 MET cc_start: 0.8272 (pmm) cc_final: 0.8070 (pmm) REVERT: D 618 LEU cc_start: 0.9419 (tp) cc_final: 0.9193 (pp) REVERT: D 771 TYR cc_start: 0.8639 (p90) cc_final: 0.8131 (p90) REVERT: D 835 TYR cc_start: 0.8104 (m-80) cc_final: 0.7676 (m-10) REVERT: D 941 TYR cc_start: 0.8346 (t80) cc_final: 0.7841 (t80) outliers start: 1 outliers final: 1 residues processed: 167 average time/residue: 0.1279 time to fit residues: 36.0690 Evaluate side-chains 132 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 119 optimal weight: 5.9990 chunk 176 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 63 optimal weight: 0.6980 chunk 81 optimal weight: 10.0000 chunk 266 optimal weight: 9.9990 chunk 92 optimal weight: 0.9980 chunk 143 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 155 optimal weight: 0.7980 overall best weight: 2.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 ASN ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN ** B 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 804 GLN ** 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 = 0.3378 r_free = 0.3378 target = 0.059664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.045480 restraints weight = 133629.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.045591 restraints weight = 99502.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.046198 restraints weight = 77469.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.046292 restraints weight = 66060.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.046379 restraints weight = 62357.478| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.8491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 23097 Z= 0.151 Angle : 0.626 12.059 31348 Z= 0.332 Chirality : 0.045 0.163 3263 Planarity : 0.004 0.058 4129 Dihedral : 5.071 34.973 3146 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.94 % Favored : 95.03 % Rotamer: Outliers : 0.04 % Allowed : 0.29 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.16), residues: 2836 helix: 0.32 (0.21), residues: 645 sheet: -0.49 (0.19), residues: 736 loop : -1.09 (0.16), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 457 TYR 0.020 0.001 TYR C 253 PHE 0.023 0.001 PHE B 606 TRP 0.016 0.001 TRP D 535 HIS 0.004 0.001 HIS D 799 Details of bonding type rmsd covalent geometry : bond 0.00329 (23092) covalent geometry : angle 0.62248 (31340) SS BOND : bond 0.01270 ( 4) SS BOND : angle 4.47316 ( 8) hydrogen bonds : bond 0.03661 ( 899) hydrogen bonds : angle 5.05007 ( 2475) Misc. bond : bond 0.00071 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5672 Ramachandran restraints generated. 2836 Oldfield, 0 Emsley, 2836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 0.831 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: A 126 MET cc_start: 0.9061 (mtm) cc_final: 0.8632 (ttp) REVERT: A 136 MET cc_start: 0.9621 (mtm) cc_final: 0.9246 (mtm) REVERT: A 242 MET cc_start: 0.9133 (mpp) cc_final: 0.8721 (mpp) REVERT: A 474 MET cc_start: 0.9418 (mmt) cc_final: 0.8585 (mmt) REVERT: B 276 MET cc_start: 0.7343 (tpt) cc_final: 0.6790 (tpt) REVERT: B 336 ASP cc_start: 0.8389 (m-30) cc_final: 0.7399 (t70) REVERT: B 379 GLU cc_start: 0.8101 (pp20) cc_final: 0.7826 (pp20) REVERT: B 485 LYS cc_start: 0.7415 (tttt) cc_final: 0.6731 (tttp) REVERT: B 509 MET cc_start: 0.8014 (ppp) cc_final: 0.7766 (tmm) REVERT: B 741 MET cc_start: 0.8638 (ttm) cc_final: 0.8396 (ttm) REVERT: B 948 PHE cc_start: 0.8192 (p90) cc_final: 0.7771 (p90) REVERT: C 41 ASP cc_start: 0.6697 (p0) cc_final: 0.6389 (p0) REVERT: C 136 MET cc_start: 0.8775 (tmm) cc_final: 0.8521 (tmm) REVERT: C 157 TYR cc_start: 0.8955 (m-80) cc_final: 0.8403 (m-80) REVERT: C 347 MET cc_start: 0.7851 (mpp) cc_final: 0.7495 (mpp) REVERT: C 412 LEU cc_start: 0.8643 (mt) cc_final: 0.8411 (mt) REVERT: C 474 MET cc_start: 0.9073 (mmm) cc_final: 0.8256 (mmm) REVERT: C 538 GLN cc_start: 0.8431 (mm-40) cc_final: 0.8130 (mm110) REVERT: D 217 ASP cc_start: 0.8451 (m-30) cc_final: 0.7724 (t0) REVERT: D 451 TYR cc_start: 0.7921 (t80) cc_final: 0.7072 (t80) REVERT: D 480 GLN cc_start: 0.7299 (mm-40) cc_final: 0.7047 (mm-40) REVERT: D 509 MET cc_start: 0.8210 (pmm) cc_final: 0.7930 (pmm) REVERT: D 534 MET cc_start: 0.8415 (mmt) cc_final: 0.7217 (mmt) REVERT: D 618 LEU cc_start: 0.9309 (tp) cc_final: 0.9019 (pp) REVERT: D 771 TYR cc_start: 0.8344 (p90) cc_final: 0.7933 (p90) REVERT: D 775 ILE cc_start: 0.5894 (mt) cc_final: 0.5362 (mp) REVERT: D 801 TYR cc_start: 0.7466 (t80) cc_final: 0.7184 (t80) REVERT: D 835 TYR cc_start: 0.7991 (m-80) cc_final: 0.7711 (m-10) REVERT: D 941 TYR cc_start: 0.8359 (t80) cc_final: 0.7904 (t80) outliers start: 1 outliers final: 1 residues processed: 175 average time/residue: 0.1319 time to fit residues: 38.8487 Evaluate side-chains 137 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 224 optimal weight: 6.9990 chunk 198 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 112 optimal weight: 8.9990 chunk 276 optimal weight: 6.9990 chunk 47 optimal weight: 20.0000 chunk 118 optimal weight: 20.0000 chunk 181 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 216 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 ASN ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN B 632 ASN ** B 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 804 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.057470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.043363 restraints weight = 138180.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.043701 restraints weight = 96904.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.044117 restraints weight = 78205.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.044259 restraints weight = 68099.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.044545 restraints weight = 59884.027| |-----------------------------------------------------------------------------| r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.8992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 23097 Z= 0.254 Angle : 0.731 12.283 31348 Z= 0.390 Chirality : 0.047 0.169 3263 Planarity : 0.005 0.068 4129 Dihedral : 5.556 34.584 3146 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.44 % Favored : 92.52 % Rotamer: Outliers : 0.04 % Allowed : 0.51 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.21 (0.16), residues: 2836 helix: 0.04 (0.20), residues: 645 sheet: -0.59 (0.18), residues: 731 loop : -1.26 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 600 TYR 0.028 0.002 TYR B 522 PHE 0.023 0.002 PHE D 526 TRP 0.017 0.002 TRP D 295 HIS 0.007 0.001 HIS D 799 Details of bonding type rmsd covalent geometry : bond 0.00544 (23092) covalent geometry : angle 0.72771 (31340) SS BOND : bond 0.01154 ( 4) SS BOND : angle 4.49786 ( 8) hydrogen bonds : bond 0.04293 ( 899) hydrogen bonds : angle 5.35893 ( 2475) Misc. bond : bond 0.00153 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3017.41 seconds wall clock time: 53 minutes 45.21 seconds (3225.21 seconds total)