Starting phenix.real_space_refine on Fri Aug 7 09:46:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lj2_63131/08_2026/9lj2_63131.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lj2_63131/08_2026/9lj2_63131.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lj2_63131/08_2026/9lj2_63131.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lj2_63131/08_2026/9lj2_63131.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lj2_63131/08_2026/9lj2_63131.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lj2_63131/08_2026/9lj2_63131.map" } resolution = 2.98 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 298 5.49 5 Mg 2 5.21 5 S 38 5.16 5 C 12448 2.51 5 N 3821 2.21 5 O 4524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21131 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 708 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3002 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3025 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 4921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4921 Classifications: {'peptide': 598} Link IDs: {'PCIS': 3, 'PTRANS': 20, 'TRANS': 574} Chain breaks: 4 Chain: "N" Number of atoms: 4066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 4066 Classifications: {'peptide': 495} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 477} Chain breaks: 4 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.68, per 1000 atoms: 0.17 Number of scatterers: 21131 At special positions: 0 Unit cell: (114.745, 117.992, 194.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 38 16.00 P 298 15.00 Mg 2 11.99 O 4524 8.00 N 3821 7.00 C 12448 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 618.4 milliseconds 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3536 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 15 sheets defined 60.6% alpha, 4.1% beta 137 base pairs and 267 stacking pairs defined. Time for finding SS restraints: 2.41 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 86 through 114 removed outlier: 3.533A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.741A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.249A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.584A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.598A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.548A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.652A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 130 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 removed outlier: 4.016A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.780A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.562A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 76 Processing helix chain 'K' and resid 82 through 90 removed outlier: 4.049A pdb=" N LYS K 88 " --> pdb=" O GLU K 84 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG K 89 " --> pdb=" O SER K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 116 Processing helix chain 'K' and resid 119 through 129 removed outlier: 3.705A pdb=" N ILE K 123 " --> pdb=" O PHE K 119 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER K 125 " --> pdb=" O HIS K 121 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 143 removed outlier: 3.654A pdb=" N ARG K 134 " --> pdb=" O ASP K 130 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL K 136 " --> pdb=" O LYS K 132 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 212 Processing helix chain 'K' and resid 226 through 241 Processing helix chain 'K' and resid 253 through 255 No H-bonds generated for 'chain 'K' and resid 253 through 255' Processing helix chain 'K' and resid 256 through 268 Processing helix chain 'K' and resid 279 through 290 Processing helix chain 'K' and resid 302 through 309 removed outlier: 3.867A pdb=" N ILE K 307 " --> pdb=" O TYR K 303 " (cutoff:3.500A) Processing helix chain 'K' and resid 310 through 315 removed outlier: 3.676A pdb=" N LYS K 315 " --> pdb=" O SER K 311 " (cutoff:3.500A) Processing helix chain 'K' and resid 325 through 330 removed outlier: 4.037A pdb=" N ARG K 328 " --> pdb=" O GLU K 325 " (cutoff:3.500A) Processing helix chain 'K' and resid 334 through 340 Processing helix chain 'K' and resid 360 through 371 removed outlier: 3.935A pdb=" N LEU K 370 " --> pdb=" O LEU K 366 " (cutoff:3.500A) Processing helix chain 'K' and resid 377 through 385 removed outlier: 3.829A pdb=" N PHE K 381 " --> pdb=" O ASP K 377 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE K 385 " --> pdb=" O PHE K 381 " (cutoff:3.500A) Processing helix chain 'K' and resid 392 through 397 Processing helix chain 'K' and resid 405 through 409 removed outlier: 4.050A pdb=" N LEU K 409 " --> pdb=" O GLN K 406 " (cutoff:3.500A) Processing helix chain 'K' and resid 413 through 417 removed outlier: 3.880A pdb=" N VAL K 417 " --> pdb=" O LYS K 414 " (cutoff:3.500A) Processing helix chain 'K' and resid 434 through 446 Processing helix chain 'K' and resid 467 through 478 removed outlier: 3.639A pdb=" N ARG K 473 " --> pdb=" O MET K 469 " (cutoff:3.500A) Processing helix chain 'K' and resid 479 through 482 Processing helix chain 'K' and resid 497 through 500 removed outlier: 3.578A pdb=" N ASN K 500 " --> pdb=" O LEU K 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 497 through 500' Processing helix chain 'K' and resid 501 through 518 Processing helix chain 'K' and resid 527 through 541 removed outlier: 3.693A pdb=" N ILE K 533 " --> pdb=" O ARG K 529 " (cutoff:3.500A) Processing helix chain 'K' and resid 553 through 565 Processing helix chain 'K' and resid 601 through 609 removed outlier: 3.777A pdb=" N ASP K 605 " --> pdb=" O ASN K 601 " (cutoff:3.500A) Processing helix chain 'K' and resid 609 through 614 removed outlier: 3.778A pdb=" N HIS K 613 " --> pdb=" O MET K 609 " (cutoff:3.500A) Processing helix chain 'K' and resid 631 through 651 removed outlier: 3.795A pdb=" N LYS K 635 " --> pdb=" O SER K 631 " (cutoff:3.500A) Processing helix chain 'K' and resid 707 through 728 removed outlier: 3.701A pdb=" N LEU K 711 " --> pdb=" O ASP K 707 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR K 728 " --> pdb=" O ALA K 724 " (cutoff:3.500A) Processing helix chain 'K' and resid 730 through 735 Processing helix chain 'N' and resid 102 through 115 removed outlier: 3.648A pdb=" N PHE N 109 " --> pdb=" O THR N 105 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU N 110 " --> pdb=" O THR N 106 " (cutoff:3.500A) Processing helix chain 'N' and resid 121 through 126 Processing helix chain 'N' and resid 133 through 139 removed outlier: 3.731A pdb=" N VAL N 139 " --> pdb=" O GLN N 135 " (cutoff:3.500A) Processing helix chain 'N' and resid 140 through 143 Processing helix chain 'N' and resid 197 through 214 removed outlier: 3.850A pdb=" N ILE N 201 " --> pdb=" O ARG N 197 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN N 202 " --> pdb=" O PRO N 198 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLY N 203 " --> pdb=" O TYR N 199 " (cutoff:3.500A) Processing helix chain 'N' and resid 226 through 241 removed outlier: 4.095A pdb=" N PHE N 234 " --> pdb=" O GLN N 230 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU N 235 " --> pdb=" O THR N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 253 through 255 No H-bonds generated for 'chain 'N' and resid 253 through 255' Processing helix chain 'N' and resid 256 through 268 removed outlier: 3.650A pdb=" N TRP N 260 " --> pdb=" O THR N 256 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU N 261 " --> pdb=" O LEU N 257 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG N 266 " --> pdb=" O ARG N 262 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TRP N 267 " --> pdb=" O GLU N 263 " (cutoff:3.500A) Processing helix chain 'N' and resid 279 through 290 removed outlier: 3.545A pdb=" N ARG N 283 " --> pdb=" O ASP N 279 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA N 284 " --> pdb=" O LYS N 280 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN N 288 " --> pdb=" O ALA N 284 " (cutoff:3.500A) Processing helix chain 'N' and resid 302 through 307 removed outlier: 3.618A pdb=" N ILE N 307 " --> pdb=" O TYR N 303 " (cutoff:3.500A) Processing helix chain 'N' and resid 309 through 316 removed outlier: 3.567A pdb=" N LEU N 313 " --> pdb=" O GLU N 309 " (cutoff:3.500A) Processing helix chain 'N' and resid 326 through 329 Processing helix chain 'N' and resid 334 through 341 removed outlier: 3.518A pdb=" N ARG N 341 " --> pdb=" O SER N 337 " (cutoff:3.500A) Processing helix chain 'N' and resid 360 through 371 removed outlier: 3.769A pdb=" N TRP N 364 " --> pdb=" O LEU N 360 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA N 365 " --> pdb=" O HIS N 361 " (cutoff:3.500A) Processing helix chain 'N' and resid 385 through 391 removed outlier: 3.859A pdb=" N THR N 390 " --> pdb=" O SER N 386 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLU N 391 " --> pdb=" O SER N 387 " (cutoff:3.500A) Processing helix chain 'N' and resid 396 through 405 removed outlier: 3.695A pdb=" N THR N 403 " --> pdb=" O LYS N 399 " (cutoff:3.500A) Processing helix chain 'N' and resid 434 through 446 Processing helix chain 'N' and resid 467 through 478 Processing helix chain 'N' and resid 479 through 483 removed outlier: 3.695A pdb=" N ASP N 483 " --> pdb=" O TYR N 480 " (cutoff:3.500A) Processing helix chain 'N' and resid 494 through 500 removed outlier: 4.060A pdb=" N VAL N 498 " --> pdb=" O ASP N 494 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN N 500 " --> pdb=" O HIS N 496 " (cutoff:3.500A) Processing helix chain 'N' and resid 501 through 516 removed outlier: 3.647A pdb=" N LYS N 509 " --> pdb=" O GLN N 505 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS N 515 " --> pdb=" O LEU N 511 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU N 516 " --> pdb=" O LYS N 512 " (cutoff:3.500A) Processing helix chain 'N' and resid 528 through 541 removed outlier: 3.594A pdb=" N ASP N 532 " --> pdb=" O SER N 528 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE N 533 " --> pdb=" O ARG N 529 " (cutoff:3.500A) Processing helix chain 'N' and resid 553 through 565 Processing helix chain 'N' and resid 601 through 613 removed outlier: 3.507A pdb=" N ASP N 605 " --> pdb=" O ASN N 601 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ALA N 608 " --> pdb=" O ALA N 604 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA N 612 " --> pdb=" O ALA N 608 " (cutoff:3.500A) Processing helix chain 'N' and resid 631 through 651 removed outlier: 4.199A pdb=" N LYS N 635 " --> pdb=" O SER N 631 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU N 638 " --> pdb=" O GLU N 634 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP N 647 " --> pdb=" O LYS N 643 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN N 648 " --> pdb=" O LEU N 644 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.032A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 removed outlier: 3.518A pdb=" N TYR B 98 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.129A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.629A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.040A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.861A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'K' and resid 248 through 251 removed outlier: 5.973A pdb=" N LEU K 249 " --> pdb=" O ILE K 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'K' and resid 273 through 275 Processing sheet with id=AB3, first strand: chain 'K' and resid 429 through 431 removed outlier: 6.953A pdb=" N VAL K 521 " --> pdb=" O PHE K 574 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N LEU K 576 " --> pdb=" O VAL K 521 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE K 523 " --> pdb=" O LEU K 576 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 320 through 324 removed outlier: 6.030A pdb=" N ILE N 321 " --> pdb=" O LEU N 349 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ILE N 351 " --> pdb=" O ILE N 321 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE N 323 " --> pdb=" O ILE N 351 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY N 217 " --> pdb=" O ARG N 348 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU N 350 " --> pdb=" O GLY N 217 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ILE N 218 " --> pdb=" O LEU N 410 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 425 through 426 removed outlier: 6.325A pdb=" N LYS N 425 " --> pdb=" O VAL N 623 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ARG N 625 " --> pdb=" O LYS N 425 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL N 521 " --> pdb=" O PHE N 574 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N LEU N 576 " --> pdb=" O VAL N 521 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE N 523 " --> pdb=" O LEU N 576 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N CYS N 546 " --> pdb=" O LEU N 575 " (cutoff:3.500A) removed outlier: 9.144A pdb=" N THR N 577 " --> pdb=" O CYS N 546 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 430 through 431 731 hydrogen bonds defined for protein. 2136 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 342 hydrogen bonds 672 hydrogen bond angles 0 basepair planarities 137 basepair parallelities 267 stacking parallelities Total time for adding SS restraints: 4.66 Time building geometry restraints manager: 2.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4790 1.33 - 1.45: 5736 1.45 - 1.57: 10933 1.57 - 1.69: 593 1.69 - 1.81: 64 Bond restraints: 22116 Sorted by residual: bond pdb=" C3' DT I 142 " pdb=" C2' DT I 142 " ideal model delta sigma weight residual 1.516 1.548 -0.032 8.00e-03 1.56e+04 1.57e+01 bond pdb=" CA ASP N 483 " pdb=" C ASP N 483 " ideal model delta sigma weight residual 1.532 1.498 0.035 9.60e-03 1.09e+04 1.31e+01 bond pdb=" CB PRO N 567 " pdb=" CG PRO N 567 " ideal model delta sigma weight residual 1.492 1.668 -0.176 5.00e-02 4.00e+02 1.24e+01 bond pdb=" C1' DC J 110 " pdb=" N1 DC J 110 " ideal model delta sigma weight residual 1.468 1.517 -0.049 1.40e-02 5.10e+03 1.23e+01 bond pdb=" CA LEU K 421 " pdb=" C LEU K 421 " ideal model delta sigma weight residual 1.523 1.482 0.041 1.19e-02 7.06e+03 1.20e+01 ... (remaining 22111 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 30641 2.61 - 5.22: 452 5.22 - 7.83: 32 7.83 - 10.44: 3 10.44 - 13.05: 1 Bond angle restraints: 31129 Sorted by residual: angle pdb=" CA PRO N 567 " pdb=" N PRO N 567 " pdb=" CD PRO N 567 " ideal model delta sigma weight residual 112.00 98.95 13.05 1.40e+00 5.10e-01 8.69e+01 angle pdb=" N GLU K 418 " pdb=" CA GLU K 418 " pdb=" C GLU K 418 " ideal model delta sigma weight residual 114.62 108.50 6.12 1.14e+00 7.69e-01 2.88e+01 angle pdb=" O4' DA I 60 " pdb=" C4' DA I 60 " pdb=" C3' DA I 60 " ideal model delta sigma weight residual 106.00 102.81 3.19 6.00e-01 2.78e+00 2.83e+01 angle pdb=" O4' DT I 68 " pdb=" C4' DT I 68 " pdb=" C3' DT I 68 " ideal model delta sigma weight residual 106.00 103.04 2.96 6.00e-01 2.78e+00 2.44e+01 angle pdb=" O4' DT J 50 " pdb=" C4' DT J 50 " pdb=" C3' DT J 50 " ideal model delta sigma weight residual 106.00 103.21 2.79 6.00e-01 2.78e+00 2.17e+01 ... (remaining 31124 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.33: 11134 35.33 - 70.66: 1473 70.66 - 105.99: 23 105.99 - 141.32: 16 141.32 - 176.65: 6 Dihedral angle restraints: 12652 sinusoidal: 7205 harmonic: 5447 Sorted by residual: dihedral pdb=" O2A ADP K1202 " pdb=" O3A ADP K1202 " pdb=" PA ADP K1202 " pdb=" PB ADP K1202 " ideal model delta sinusoidal sigma weight residual 300.00 123.35 176.65 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP K1202 " pdb=" O5' ADP K1202 " pdb=" PA ADP K1202 " pdb=" O2A ADP K1202 " ideal model delta sinusoidal sigma weight residual -60.00 83.29 -143.29 1 2.00e+01 2.50e-03 4.32e+01 dihedral pdb=" C4' ADP K1202 " pdb=" C5' ADP K1202 " pdb=" O5' ADP K1202 " pdb=" PA ADP K1202 " ideal model delta sinusoidal sigma weight residual -180.00 -71.47 -108.53 1 2.00e+01 2.50e-03 3.16e+01 ... (remaining 12649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2239 0.039 - 0.078: 894 0.078 - 0.116: 308 0.116 - 0.155: 56 0.155 - 0.194: 12 Chirality restraints: 3509 Sorted by residual: chirality pdb=" CA PRO N 567 " pdb=" N PRO N 567 " pdb=" C PRO N 567 " pdb=" CB PRO N 567 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.19 2.00e-01 2.50e+01 9.40e-01 chirality pdb=" CG LEU N 576 " pdb=" CB LEU N 576 " pdb=" CD1 LEU N 576 " pdb=" CD2 LEU N 576 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.00e-01 chirality pdb=" CA ASP E 81 " pdb=" N ASP E 81 " pdb=" C ASP E 81 " pdb=" CB ASP E 81 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.64e-01 ... (remaining 3506 not shown) Planarity restraints: 2931 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA N 566 " 0.089 5.00e-02 4.00e+02 1.24e-01 2.47e+01 pdb=" N PRO N 567 " -0.214 5.00e-02 4.00e+02 pdb=" CA PRO N 567 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO N 567 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA K 566 " -0.040 5.00e-02 4.00e+02 6.05e-02 5.86e+00 pdb=" N PRO K 567 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO K 567 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO K 567 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS K 72 " -0.036 5.00e-02 4.00e+02 5.46e-02 4.76e+00 pdb=" N PRO K 73 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO K 73 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO K 73 " -0.031 5.00e-02 4.00e+02 ... (remaining 2928 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 370 2.62 - 3.19: 18745 3.19 - 3.76: 36812 3.76 - 4.33: 49438 4.33 - 4.90: 73321 Nonbonded interactions: 178686 Sorted by model distance: nonbonded pdb="MG MG K1201 " pdb=" O2B ADP K1202 " model vdw 2.044 2.170 nonbonded pdb=" NZ LYS B 59 " pdb=" OE2 GLU B 63 " model vdw 2.083 3.120 nonbonded pdb=" O2 DC I 92 " pdb=" N2 DG J 56 " model vdw 2.119 2.496 nonbonded pdb=" OG SER K 434 " pdb=" OE1 GLN K 437 " model vdw 2.120 3.040 nonbonded pdb="MG MG N1201 " pdb=" O3B ADP N1202 " model vdw 2.155 2.170 ... (remaining 178681 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' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 15 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } ncs_group { reference = (chain 'I' and (resid 1 through 55 or resid 57 through 64 or resid 67 or resid 6 \ 9 through 74 or resid 76 through 77 or resid 79 or resid 83 through 88 or resid \ 90 through 91 or resid 93 through 147)) selection = (chain 'J' and (resid 1 through 55 or resid 57 through 61 or resid 63 through 65 \ or resid 68 or resid 71 through 72 or resid 74 through 79 or resid 81 or resid \ 84 through 91 or resid 93 through 147)) } 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 individual isotropic 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: 0.010 Normalize map: mean=0, sd=1: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.330 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 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 : 0.006 0.176 22116 Z= 0.461 Angle : 0.828 13.049 31129 Z= 0.632 Chirality : 0.047 0.194 3509 Planarity : 0.005 0.124 2931 Dihedral : 24.540 176.649 9116 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 0.18 % Allowed : 0.49 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.20), residues: 1825 helix: 0.80 (0.17), residues: 1001 sheet: -2.56 (0.51), residues: 103 loop : -1.96 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 42 TYR 0.015 0.002 TYR K 543 PHE 0.018 0.002 PHE K 574 TRP 0.020 0.002 TRP N 260 HIS 0.005 0.001 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00603 / 0.46 (22116) covalent geometry : angle 0.82807 / 0.63 (31129) hydrogen bonds : bond 0.14049 / 9.60 ( 1073) hydrogen bonds : angle 5.30456 / 3.85 ( 2808) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 238 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 92 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8126 (mm-30) REVERT: E 106 ASP cc_start: 0.7891 (m-30) cc_final: 0.7425 (m-30) REVERT: E 120 MET cc_start: 0.7563 (mtt) cc_final: 0.7217 (mtt) REVERT: G 104 GLN cc_start: 0.8512 (mm110) cc_final: 0.8281 (mm110) REVERT: H 90 GLU cc_start: 0.8250 (mp0) cc_final: 0.7835 (mp0) REVERT: K 183 PHE cc_start: 0.8833 (m-10) cc_final: 0.8311 (m-10) REVERT: K 722 LEU cc_start: 0.7881 (mm) cc_final: 0.7619 (mm) REVERT: N 645 ARG cc_start: 0.9160 (ttp80) cc_final: 0.8913 (ttp80) outliers start: 3 outliers final: 1 residues processed: 241 average time/residue: 0.6119 time to fit residues: 165.0406 Evaluate side-chains 162 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 122 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN D 44 GLN G 104 GLN ** K 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 HIS N 121 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.092458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.065266 restraints weight = 61910.862| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.68 r_work: 0.3040 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 22116 Z= 0.219 Angle : 0.766 10.301 31129 Z= 0.410 Chirality : 0.048 0.333 3509 Planarity : 0.005 0.051 2931 Dihedral : 28.805 173.762 5297 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 2.21 % Allowed : 9.83 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.20), residues: 1825 helix: 0.89 (0.16), residues: 1022 sheet: -2.50 (0.45), residues: 113 loop : -1.81 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 92 TYR 0.018 0.002 TYR N 499 PHE 0.016 0.002 PHE K 408 TRP 0.023 0.002 TRP N 260 HIS 0.014 0.001 HIS K 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.22 (22116) covalent geometry : angle 0.76587 / 0.41 (31129) hydrogen bonds : bond 0.06558 / 4.42 ( 1073) hydrogen bonds : angle 4.34453 / 3.14 ( 2808) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 182 time to evaluate : 0.549 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8948 (pm20) cc_final: 0.8737 (pm20) REVERT: B 59 LYS cc_start: 0.9162 (tttp) cc_final: 0.8800 (tttm) REVERT: C 90 ASP cc_start: 0.8629 (t0) cc_final: 0.8293 (t0) REVERT: D 105 LYS cc_start: 0.8973 (mtpm) cc_final: 0.8735 (mttp) REVERT: E 90 MET cc_start: 0.9072 (mmm) cc_final: 0.8838 (mmp) REVERT: E 106 ASP cc_start: 0.8375 (m-30) cc_final: 0.8076 (m-30) REVERT: E 120 MET cc_start: 0.8360 (mtt) cc_final: 0.8023 (mtt) REVERT: F 93 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.7032 (mp10) REVERT: H 90 GLU cc_start: 0.8823 (mp0) cc_final: 0.8363 (mp0) REVERT: K 183 PHE cc_start: 0.8811 (m-10) cc_final: 0.8602 (m-10) REVERT: K 722 LEU cc_start: 0.7805 (mm) cc_final: 0.7554 (mm) REVERT: N 606 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8308 (tm) outliers start: 36 outliers final: 15 residues processed: 204 average time/residue: 0.6651 time to fit residues: 152.4666 Evaluate side-chains 178 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 279 ASP Chi-restraints excluded: chain K residue 361 HIS Chi-restraints excluded: chain K residue 363 LEU Chi-restraints excluded: chain K residue 420 SER Chi-restraints excluded: chain K residue 525 SER Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain N residue 335 MET Chi-restraints excluded: chain N residue 606 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 38 optimal weight: 0.0470 chunk 156 optimal weight: 7.9990 chunk 101 optimal weight: 0.0030 chunk 129 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 135 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 145 optimal weight: 0.9990 overall best weight: 0.5088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 505 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.094121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.067137 restraints weight = 62607.662| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.73 r_work: 0.3080 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22116 Z= 0.147 Angle : 0.688 9.240 31129 Z= 0.376 Chirality : 0.045 0.299 3509 Planarity : 0.004 0.061 2931 Dihedral : 28.605 170.907 5295 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.09 % Allowed : 13.89 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.20), residues: 1825 helix: 1.07 (0.17), residues: 1028 sheet: -2.19 (0.47), residues: 113 loop : -1.82 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG N 266 TYR 0.022 0.001 TYR N 499 PHE 0.027 0.002 PHE N 122 TRP 0.033 0.002 TRP N 267 HIS 0.007 0.001 HIS N 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.15 (22116) covalent geometry : angle 0.68842 / 0.38 (31129) hydrogen bonds : bond 0.05650 / 3.81 ( 1073) hydrogen bonds : angle 4.00945 / 2.91 ( 2808) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 197 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8938 (pm20) cc_final: 0.8679 (pm20) REVERT: A 94 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8613 (mm-30) REVERT: B 59 LYS cc_start: 0.9144 (tttp) cc_final: 0.8771 (tttm) REVERT: D 33 SER cc_start: 0.8527 (t) cc_final: 0.8310 (t) REVERT: D 39 TYR cc_start: 0.8693 (t80) cc_final: 0.8216 (t80) REVERT: D 105 LYS cc_start: 0.8746 (mtpm) cc_final: 0.8499 (mttp) REVERT: E 90 MET cc_start: 0.8989 (mmm) cc_final: 0.8738 (mmp) REVERT: E 106 ASP cc_start: 0.8341 (m-30) cc_final: 0.7982 (m-30) REVERT: E 120 MET cc_start: 0.8193 (mtt) cc_final: 0.7845 (mtt) REVERT: F 93 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7030 (mp10) REVERT: H 53 SER cc_start: 0.9392 (t) cc_final: 0.9173 (p) REVERT: H 90 GLU cc_start: 0.8832 (mp0) cc_final: 0.8422 (mp0) REVERT: K 183 PHE cc_start: 0.8720 (m-10) cc_final: 0.8514 (m-10) REVERT: K 362 GLU cc_start: 0.8066 (tt0) cc_final: 0.7773 (pt0) REVERT: K 525 SER cc_start: 0.9008 (OUTLIER) cc_final: 0.8454 (t) REVERT: K 722 LEU cc_start: 0.7740 (mm) cc_final: 0.7490 (mm) REVERT: N 645 ARG cc_start: 0.8933 (ttp80) cc_final: 0.8664 (ttp80) outliers start: 34 outliers final: 15 residues processed: 216 average time/residue: 0.5797 time to fit residues: 141.6867 Evaluate side-chains 189 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 172 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 279 ASP Chi-restraints excluded: chain K residue 363 LEU Chi-restraints excluded: chain K residue 406 GLN Chi-restraints excluded: chain K residue 499 TYR Chi-restraints excluded: chain K residue 525 SER Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain N residue 298 VAL Chi-restraints excluded: chain N residue 335 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 105 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 81 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 55 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 chunk 147 optimal weight: 7.9990 chunk 202 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN E 76 GLN ** K 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 347 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.094110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.067192 restraints weight = 62355.543| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.72 r_work: 0.3085 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22116 Z= 0.150 Angle : 0.668 9.339 31129 Z= 0.364 Chirality : 0.044 0.293 3509 Planarity : 0.004 0.055 2931 Dihedral : 28.545 167.143 5295 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 2.52 % Allowed : 16.59 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.20), residues: 1825 helix: 1.16 (0.17), residues: 1031 sheet: -2.00 (0.46), residues: 123 loop : -1.76 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 76 TYR 0.018 0.001 TYR N 499 PHE 0.027 0.001 PHE N 122 TRP 0.017 0.002 TRP N 364 HIS 0.007 0.001 HIS N 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.15 (22116) covalent geometry : angle 0.66775 / 0.36 (31129) hydrogen bonds : bond 0.05401 / 3.64 ( 1073) hydrogen bonds : angle 3.89749 / 2.83 ( 2808) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 185 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8940 (pm20) cc_final: 0.8624 (pm20) REVERT: A 65 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8793 (tm) REVERT: B 59 LYS cc_start: 0.9105 (tttp) cc_final: 0.8719 (tttm) REVERT: D 33 SER cc_start: 0.8489 (t) cc_final: 0.8278 (t) REVERT: D 39 TYR cc_start: 0.8722 (t80) cc_final: 0.8227 (t80) REVERT: D 105 LYS cc_start: 0.8728 (mtpm) cc_final: 0.8477 (mttp) REVERT: E 68 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.7963 (tm-30) REVERT: E 106 ASP cc_start: 0.8372 (m-30) cc_final: 0.8006 (m-30) REVERT: E 120 MET cc_start: 0.8169 (mtt) cc_final: 0.7813 (mtt) REVERT: F 93 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.7002 (mp10) REVERT: G 91 GLU cc_start: 0.8356 (pm20) cc_final: 0.7452 (pm20) REVERT: H 53 SER cc_start: 0.9402 (t) cc_final: 0.9173 (p) REVERT: H 90 GLU cc_start: 0.8884 (mp0) cc_final: 0.8440 (mp0) REVERT: K 183 PHE cc_start: 0.8766 (m-10) cc_final: 0.8546 (m-10) REVERT: K 362 GLU cc_start: 0.8035 (tt0) cc_final: 0.7730 (pt0) REVERT: K 426 GLU cc_start: 0.8262 (mp0) cc_final: 0.7982 (mm-30) REVERT: K 525 SER cc_start: 0.9032 (OUTLIER) cc_final: 0.8455 (t) REVERT: K 609 MET cc_start: 0.8630 (pp-130) cc_final: 0.8185 (pp-130) REVERT: K 722 LEU cc_start: 0.7782 (mm) cc_final: 0.7543 (mm) REVERT: N 221 ASP cc_start: 0.6571 (m-30) cc_final: 0.6286 (m-30) REVERT: N 370 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8199 (mp) REVERT: N 606 LEU cc_start: 0.8623 (mt) cc_final: 0.8236 (tt) REVERT: N 645 ARG cc_start: 0.8942 (ttp80) cc_final: 0.8649 (ttp80) outliers start: 41 outliers final: 12 residues processed: 212 average time/residue: 0.5945 time to fit residues: 142.8060 Evaluate side-chains 186 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 406 GLN Chi-restraints excluded: chain K residue 499 TYR Chi-restraints excluded: chain K residue 525 SER Chi-restraints excluded: chain K residue 533 ILE Chi-restraints excluded: chain N residue 298 VAL Chi-restraints excluded: chain N residue 370 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 30 optimal weight: 2.9990 chunk 158 optimal weight: 9.9990 chunk 14 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 38 optimal weight: 0.0570 chunk 170 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 86 optimal weight: 20.0000 chunk 46 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 193 optimal weight: 6.9990 overall best weight: 1.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN D 92 GLN ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.093755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.066738 restraints weight = 62098.853| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.70 r_work: 0.3063 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22116 Z= 0.163 Angle : 0.675 10.335 31129 Z= 0.364 Chirality : 0.044 0.283 3509 Planarity : 0.004 0.055 2931 Dihedral : 28.537 167.626 5295 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 2.46 % Allowed : 17.95 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.21), residues: 1825 helix: 1.17 (0.17), residues: 1045 sheet: -2.18 (0.44), residues: 129 loop : -1.65 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 76 TYR 0.030 0.001 TYR N 499 PHE 0.029 0.002 PHE N 624 TRP 0.021 0.002 TRP N 267 HIS 0.006 0.001 HIS N 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.16 (22116) covalent geometry : angle 0.67541 / 0.36 (31129) hydrogen bonds : bond 0.05417 / 3.65 ( 1073) hydrogen bonds : angle 3.81835 / 2.78 ( 2808) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 170 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8846 (tm) REVERT: B 59 LYS cc_start: 0.9179 (tttp) cc_final: 0.8826 (tttm) REVERT: D 33 SER cc_start: 0.8488 (t) cc_final: 0.8286 (t) REVERT: D 105 LYS cc_start: 0.8827 (mtpm) cc_final: 0.8602 (mttp) REVERT: E 68 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8007 (tm-30) REVERT: E 106 ASP cc_start: 0.8327 (m-30) cc_final: 0.7963 (m-30) REVERT: E 115 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8894 (mtpt) REVERT: E 120 MET cc_start: 0.8175 (mtt) cc_final: 0.7826 (mtt) REVERT: F 93 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.7058 (mp10) REVERT: H 53 SER cc_start: 0.9384 (t) cc_final: 0.9167 (p) REVERT: H 90 GLU cc_start: 0.8887 (mp0) cc_final: 0.8489 (mp0) REVERT: K 183 PHE cc_start: 0.8815 (m-10) cc_final: 0.8603 (m-10) REVERT: K 525 SER cc_start: 0.9091 (OUTLIER) cc_final: 0.8451 (t) REVERT: K 722 LEU cc_start: 0.7775 (mm) cc_final: 0.7548 (mm) REVERT: N 370 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8215 (mp) REVERT: N 606 LEU cc_start: 0.8577 (mt) cc_final: 0.8370 (tm) REVERT: N 645 ARG cc_start: 0.9030 (ttp80) cc_final: 0.8708 (ttp80) outliers start: 40 outliers final: 15 residues processed: 199 average time/residue: 0.6106 time to fit residues: 137.3112 Evaluate side-chains 182 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 210 LEU Chi-restraints excluded: chain K residue 406 GLN Chi-restraints excluded: chain K residue 499 TYR Chi-restraints excluded: chain K residue 504 LEU Chi-restraints excluded: chain K residue 525 SER Chi-restraints excluded: chain K residue 533 ILE Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain N residue 298 VAL Chi-restraints excluded: chain N residue 370 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 63 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 182 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 154 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN E 76 GLN K 111 HIS ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 500 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.093187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.066028 restraints weight = 62127.078| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.68 r_work: 0.3058 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22116 Z= 0.183 Angle : 0.691 13.175 31129 Z= 0.371 Chirality : 0.045 0.280 3509 Planarity : 0.004 0.054 2931 Dihedral : 28.555 168.276 5295 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 2.89 % Allowed : 18.87 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.21), residues: 1825 helix: 1.25 (0.17), residues: 1039 sheet: -2.20 (0.43), residues: 129 loop : -1.57 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 266 TYR 0.020 0.001 TYR N 499 PHE 0.028 0.002 PHE N 122 TRP 0.044 0.002 TRP N 267 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 (22116) covalent geometry : angle 0.69126 / 0.37 (31129) hydrogen bonds : bond 0.05535 / 3.72 ( 1073) hydrogen bonds : angle 3.81818 / 2.77 ( 2808) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 173 time to evaluate : 0.677 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8849 (tm) REVERT: B 59 LYS cc_start: 0.9162 (tttp) cc_final: 0.8845 (tttm) REVERT: D 33 SER cc_start: 0.8508 (t) cc_final: 0.8288 (t) REVERT: D 105 LYS cc_start: 0.8861 (mtpm) cc_final: 0.8636 (mttp) REVERT: E 68 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8005 (tm-30) REVERT: E 106 ASP cc_start: 0.8359 (m-30) cc_final: 0.7991 (m-30) REVERT: E 115 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8901 (mtpt) REVERT: E 120 MET cc_start: 0.8157 (mtt) cc_final: 0.7793 (mtt) REVERT: F 93 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.7089 (mp10) REVERT: H 53 SER cc_start: 0.9381 (t) cc_final: 0.9149 (p) REVERT: H 90 GLU cc_start: 0.8906 (mp0) cc_final: 0.8497 (mp0) REVERT: K 183 PHE cc_start: 0.8835 (m-10) cc_final: 0.8631 (m-10) REVERT: K 470 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8391 (tpp) REVERT: K 525 SER cc_start: 0.9120 (OUTLIER) cc_final: 0.8463 (t) REVERT: K 722 LEU cc_start: 0.7797 (mm) cc_final: 0.7567 (mm) REVERT: N 221 ASP cc_start: 0.6578 (m-30) cc_final: 0.6060 (m-30) REVERT: N 289 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.9021 (mttt) REVERT: N 370 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8234 (mp) REVERT: N 645 ARG cc_start: 0.9008 (ttp80) cc_final: 0.8726 (ttp80) REVERT: N 649 LEU cc_start: 0.9130 (tt) cc_final: 0.8847 (tm) outliers start: 47 outliers final: 18 residues processed: 206 average time/residue: 0.5673 time to fit residues: 132.1516 Evaluate side-chains 190 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 210 LEU Chi-restraints excluded: chain K residue 287 ILE Chi-restraints excluded: chain K residue 406 GLN Chi-restraints excluded: chain K residue 470 MET Chi-restraints excluded: chain K residue 499 TYR Chi-restraints excluded: chain K residue 504 LEU Chi-restraints excluded: chain K residue 525 SER Chi-restraints excluded: chain K residue 533 ILE Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain N residue 267 TRP Chi-restraints excluded: chain N residue 289 LYS Chi-restraints excluded: chain N residue 298 VAL Chi-restraints excluded: chain N residue 370 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 137 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 125 optimal weight: 0.0970 chunk 34 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 131 optimal weight: 9.9990 chunk 163 optimal weight: 7.9990 chunk 183 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN E 85 GLN ** K 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 437 GLN N 230 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.091801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.064413 restraints weight = 62268.920| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.67 r_work: 0.3017 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 22116 Z= 0.267 Angle : 0.754 14.008 31129 Z= 0.398 Chirality : 0.048 0.293 3509 Planarity : 0.004 0.053 2931 Dihedral : 28.677 169.089 5295 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 2.83 % Allowed : 20.10 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.20), residues: 1825 helix: 1.07 (0.16), residues: 1050 sheet: -2.29 (0.45), residues: 122 loop : -1.71 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 108 TYR 0.034 0.002 TYR N 499 PHE 0.024 0.002 PHE N 234 TRP 0.051 0.003 TRP K 384 HIS 0.019 0.002 HIS K 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.27 (22116) covalent geometry : angle 0.75353 / 0.40 (31129) hydrogen bonds : bond 0.06276 / 4.23 ( 1073) hydrogen bonds : angle 3.95644 / 2.85 ( 2808) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 165 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8849 (tm) REVERT: D 33 SER cc_start: 0.8654 (t) cc_final: 0.8419 (t) REVERT: D 105 LYS cc_start: 0.8973 (mtpm) cc_final: 0.8745 (mttp) REVERT: E 68 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.7982 (tm-30) REVERT: E 106 ASP cc_start: 0.8391 (m-30) cc_final: 0.8029 (m-30) REVERT: E 120 MET cc_start: 0.8264 (mtt) cc_final: 0.7863 (mtt) REVERT: F 93 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.7187 (mp10) REVERT: G 36 LYS cc_start: 0.9066 (mmtm) cc_final: 0.8825 (mmpt) REVERT: G 64 GLU cc_start: 0.8784 (tt0) cc_final: 0.8256 (tm-30) REVERT: G 91 GLU cc_start: 0.8686 (mp0) cc_final: 0.8396 (pm20) REVERT: G 92 GLU cc_start: 0.8245 (mp0) cc_final: 0.7063 (mp0) REVERT: H 90 GLU cc_start: 0.8941 (mp0) cc_final: 0.8494 (mp0) REVERT: K 123 ILE cc_start: 0.7489 (mp) cc_final: 0.7237 (mp) REVERT: K 470 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8450 (tpp) REVERT: K 722 LEU cc_start: 0.7991 (mm) cc_final: 0.7768 (mm) REVERT: N 289 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.9040 (mttt) REVERT: N 645 ARG cc_start: 0.9051 (ttp80) cc_final: 0.8775 (ttp80) REVERT: N 649 LEU cc_start: 0.9095 (tt) cc_final: 0.8843 (tm) outliers start: 46 outliers final: 22 residues processed: 199 average time/residue: 0.6290 time to fit residues: 141.3781 Evaluate side-chains 182 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 210 LEU Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 402 HIS Chi-restraints excluded: chain K residue 406 GLN Chi-restraints excluded: chain K residue 420 SER Chi-restraints excluded: chain K residue 470 MET Chi-restraints excluded: chain K residue 499 TYR Chi-restraints excluded: chain K residue 504 LEU Chi-restraints excluded: chain K residue 525 SER Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain N residue 267 TRP Chi-restraints excluded: chain N residue 289 LYS Chi-restraints excluded: chain N residue 298 VAL Chi-restraints excluded: chain N residue 349 LEU Chi-restraints excluded: chain N residue 510 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 20 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 chunk 165 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 195 optimal weight: 0.9990 chunk 151 optimal weight: 0.9980 chunk 191 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 207 optimal weight: 8.9990 chunk 33 optimal weight: 0.6980 chunk 141 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN B 93 GLN H 46 HIS ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 230 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.093701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.066711 restraints weight = 61957.424| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.68 r_work: 0.3075 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22116 Z= 0.144 Angle : 0.689 11.391 31129 Z= 0.368 Chirality : 0.045 0.268 3509 Planarity : 0.004 0.054 2931 Dihedral : 28.495 169.034 5295 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.40 % Allowed : 20.84 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.21), residues: 1825 helix: 1.23 (0.17), residues: 1054 sheet: -2.15 (0.44), residues: 124 loop : -1.70 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 89 TYR 0.029 0.001 TYR N 499 PHE 0.032 0.002 PHE N 122 TRP 0.049 0.003 TRP K 384 HIS 0.009 0.001 HIS K 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.14 (22116) covalent geometry : angle 0.68854 / 0.37 (31129) hydrogen bonds : bond 0.05296 / 3.54 ( 1073) hydrogen bonds : angle 3.73385 / 2.70 ( 2808) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 173 time to evaluate : 0.652 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8813 (tm) REVERT: A 94 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8669 (tp30) REVERT: B 59 LYS cc_start: 0.9143 (tttp) cc_final: 0.8814 (tttm) REVERT: D 33 SER cc_start: 0.8491 (t) cc_final: 0.8262 (t) REVERT: D 39 TYR cc_start: 0.8724 (t80) cc_final: 0.8245 (t80) REVERT: D 105 LYS cc_start: 0.8838 (mtpm) cc_final: 0.8623 (mttp) REVERT: E 68 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7924 (tm-30) REVERT: E 106 ASP cc_start: 0.8339 (m-30) cc_final: 0.8031 (m-30) REVERT: E 115 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8893 (mtpt) REVERT: F 93 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.7090 (mp10) REVERT: G 36 LYS cc_start: 0.9086 (mmtm) cc_final: 0.8845 (mmpt) REVERT: G 91 GLU cc_start: 0.8631 (mp0) cc_final: 0.8361 (pm20) REVERT: G 92 GLU cc_start: 0.8321 (mp0) cc_final: 0.7462 (mp0) REVERT: H 53 SER cc_start: 0.9371 (t) cc_final: 0.9142 (p) REVERT: H 90 GLU cc_start: 0.8940 (mp0) cc_final: 0.8497 (mp0) REVERT: H 102 GLU cc_start: 0.7966 (tp30) cc_final: 0.7728 (tp30) REVERT: K 722 LEU cc_start: 0.7956 (mm) cc_final: 0.7738 (mm) REVERT: N 289 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8980 (mttt) REVERT: N 433 MET cc_start: 0.8004 (ttt) cc_final: 0.7724 (tmm) REVERT: N 470 MET cc_start: 0.8396 (ttp) cc_final: 0.8096 (ttp) REVERT: N 527 MET cc_start: 0.8168 (mtp) cc_final: 0.7567 (ttm) REVERT: N 645 ARG cc_start: 0.8964 (ttp80) cc_final: 0.8695 (ttp80) outliers start: 39 outliers final: 14 residues processed: 201 average time/residue: 0.5850 time to fit residues: 132.6639 Evaluate side-chains 177 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 287 ILE Chi-restraints excluded: chain K residue 406 GLN Chi-restraints excluded: chain K residue 499 TYR Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain N residue 267 TRP Chi-restraints excluded: chain N residue 289 LYS Chi-restraints excluded: chain N residue 298 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 67 optimal weight: 3.9990 chunk 23 optimal weight: 0.2980 chunk 152 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 101 optimal weight: 0.6980 chunk 167 optimal weight: 8.9990 chunk 128 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 190 optimal weight: 0.0070 overall best weight: 0.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN E 85 GLN H 46 HIS ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 230 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.094723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.067764 restraints weight = 61617.629| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.71 r_work: 0.3098 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 22116 Z= 0.138 Angle : 0.677 12.952 31129 Z= 0.362 Chirality : 0.044 0.265 3509 Planarity : 0.004 0.054 2931 Dihedral : 28.332 168.632 5295 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.60 % Allowed : 22.50 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.21), residues: 1825 helix: 1.33 (0.17), residues: 1048 sheet: -2.13 (0.44), residues: 121 loop : -1.59 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 76 TYR 0.025 0.001 TYR N 499 PHE 0.020 0.001 PHE N 234 TRP 0.036 0.002 TRP N 267 HIS 0.005 0.001 HIS K 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 (22116) covalent geometry : angle 0.67699 / 0.36 (31129) hydrogen bonds : bond 0.05024 / 3.37 ( 1073) hydrogen bonds : angle 3.63730 / 2.65 ( 2808) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8801 (tm) REVERT: B 59 LYS cc_start: 0.9138 (tttp) cc_final: 0.8812 (tttm) REVERT: D 33 SER cc_start: 0.8388 (t) cc_final: 0.8177 (t) REVERT: D 105 LYS cc_start: 0.8727 (mtpm) cc_final: 0.8506 (mttp) REVERT: E 68 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7925 (tt0) REVERT: E 106 ASP cc_start: 0.8321 (m-30) cc_final: 0.7995 (m-30) REVERT: E 115 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8857 (mtpt) REVERT: E 120 MET cc_start: 0.8100 (mtt) cc_final: 0.7793 (mtt) REVERT: F 93 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.7079 (mp10) REVERT: G 36 LYS cc_start: 0.9114 (mmtm) cc_final: 0.8869 (mmpt) REVERT: G 91 GLU cc_start: 0.8574 (mp0) cc_final: 0.8323 (pm20) REVERT: G 92 GLU cc_start: 0.8349 (mp0) cc_final: 0.7481 (mp0) REVERT: H 90 GLU cc_start: 0.8921 (mp0) cc_final: 0.8488 (mp0) REVERT: K 279 ASP cc_start: 0.8059 (p0) cc_final: 0.7655 (p0) REVERT: K 722 LEU cc_start: 0.7963 (mm) cc_final: 0.7745 (mm) REVERT: N 433 MET cc_start: 0.7999 (ttt) cc_final: 0.7763 (tmm) REVERT: N 527 MET cc_start: 0.8185 (mtp) cc_final: 0.7594 (ttm) REVERT: N 606 LEU cc_start: 0.8656 (mt) cc_final: 0.8359 (tm) REVERT: N 645 ARG cc_start: 0.8971 (ttp80) cc_final: 0.8712 (ttp80) outliers start: 26 outliers final: 17 residues processed: 195 average time/residue: 0.6511 time to fit residues: 143.3702 Evaluate side-chains 185 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 287 ILE Chi-restraints excluded: chain K residue 406 GLN Chi-restraints excluded: chain K residue 499 TYR Chi-restraints excluded: chain N residue 267 TRP Chi-restraints excluded: chain N residue 289 LYS Chi-restraints excluded: chain N residue 298 VAL Chi-restraints excluded: chain N residue 510 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 6 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 124 optimal weight: 5.9990 chunk 182 optimal weight: 8.9990 chunk 52 optimal weight: 0.6980 chunk 127 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN H 46 HIS ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.093949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.066806 restraints weight = 62251.324| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.73 r_work: 0.3075 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 22116 Z= 0.172 Angle : 0.706 14.918 31129 Z= 0.374 Chirality : 0.045 0.314 3509 Planarity : 0.004 0.053 2931 Dihedral : 28.370 168.821 5295 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.79 % Favored : 93.15 % Rotamer: Outliers : 1.66 % Allowed : 22.50 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.21), residues: 1825 helix: 1.29 (0.17), residues: 1044 sheet: -2.29 (0.43), residues: 126 loop : -1.59 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 23 TYR 0.027 0.001 TYR N 499 PHE 0.034 0.002 PHE N 122 TRP 0.035 0.002 TRP N 267 HIS 0.005 0.001 HIS K 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 (22116) covalent geometry : angle 0.70634 / 0.37 (31129) hydrogen bonds : bond 0.05214 / 3.49 ( 1073) hydrogen bonds : angle 3.66458 / 2.66 ( 2808) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8830 (tm) REVERT: B 59 LYS cc_start: 0.9135 (tttp) cc_final: 0.8801 (tttm) REVERT: D 33 SER cc_start: 0.8454 (t) cc_final: 0.8234 (t) REVERT: D 105 LYS cc_start: 0.8850 (mtpm) cc_final: 0.8631 (mttp) REVERT: E 68 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8009 (tt0) REVERT: E 106 ASP cc_start: 0.8349 (m-30) cc_final: 0.8019 (m-30) REVERT: E 115 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8914 (mtpt) REVERT: E 120 MET cc_start: 0.8173 (mtt) cc_final: 0.7858 (mtt) REVERT: F 93 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.7134 (mp10) REVERT: G 36 LYS cc_start: 0.9148 (mmtm) cc_final: 0.8897 (mmpt) REVERT: G 64 GLU cc_start: 0.8791 (tt0) cc_final: 0.8261 (tm-30) REVERT: H 90 GLU cc_start: 0.8933 (mp0) cc_final: 0.8489 (mp0) REVERT: K 279 ASP cc_start: 0.8045 (p0) cc_final: 0.7641 (p0) REVERT: K 722 LEU cc_start: 0.7968 (mm) cc_final: 0.7744 (mm) REVERT: N 221 ASP cc_start: 0.5606 (m-30) cc_final: 0.5184 (m-30) REVERT: N 527 MET cc_start: 0.8209 (mtp) cc_final: 0.7645 (ttm) REVERT: N 645 ARG cc_start: 0.8986 (ttp80) cc_final: 0.8721 (ttp80) outliers start: 27 outliers final: 14 residues processed: 182 average time/residue: 0.6059 time to fit residues: 124.4194 Evaluate side-chains 177 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 406 GLN Chi-restraints excluded: chain K residue 499 TYR Chi-restraints excluded: chain N residue 289 LYS Chi-restraints excluded: chain N residue 298 VAL Chi-restraints excluded: chain N residue 510 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 185 optimal weight: 8.9990 chunk 106 optimal weight: 0.0470 chunk 123 optimal weight: 0.4980 chunk 201 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 158 optimal weight: 8.9990 overall best weight: 1.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN B 93 GLN H 46 HIS ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 230 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.094237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.067182 restraints weight = 62397.410| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.69 r_work: 0.3094 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22116 Z= 0.152 Angle : 0.690 14.010 31129 Z= 0.367 Chirality : 0.044 0.285 3509 Planarity : 0.004 0.054 2931 Dihedral : 28.333 169.406 5295 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 1.66 % Allowed : 22.56 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.21), residues: 1825 helix: 1.34 (0.17), residues: 1042 sheet: -2.06 (0.45), residues: 121 loop : -1.57 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 23 TYR 0.027 0.001 TYR N 499 PHE 0.020 0.002 PHE N 234 TRP 0.095 0.003 TRP N 267 HIS 0.004 0.001 HIS K 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.15 (22116) covalent geometry : angle 0.68971 / 0.37 (31129) hydrogen bonds : bond 0.05080 / 3.40 ( 1073) hydrogen bonds : angle 3.61149 / 2.63 ( 2808) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5785.88 seconds wall clock time: 99 minutes 24.19 seconds (5964.19 seconds total)