Starting phenix.real_space_refine on Sat Oct 11 16:38:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vjh_43281/10_2025/8vjh_43281.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vjh_43281/10_2025/8vjh_43281.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vjh_43281/10_2025/8vjh_43281.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vjh_43281/10_2025/8vjh_43281.map" model { file = "/net/cci-nas-00/data/ceres_data/8vjh_43281/10_2025/8vjh_43281.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vjh_43281/10_2025/8vjh_43281.cif" } resolution = 4.2 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= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 1 7.16 5 S 66 5.16 5 C 9861 2.51 5 N 2860 2.21 5 O 3179 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15967 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 769, 4654 Classifications: {'peptide': 769} Incomplete info: {'backbone_only': 331} Link IDs: {'PTRANS': 42, 'TRANS': 726} Unresolved chain link angles: 26 Unresolved non-hydrogen bonds: 1464 Unresolved non-hydrogen angles: 2145 Unresolved non-hydrogen dihedrals: 956 Unresolved non-hydrogen chiralities: 428 Planarities with less than four sites: {'TYR:plan': 18, 'GLU:plan': 21, 'ASN:plan1': 15, 'ARG:plan': 19, 'ASP:plan': 29, 'GLN:plan1': 14, 'PHE:plan': 10, 'TRP:plan': 9, 'HIS:plan': 5} Unresolved non-hydrogen planarities: 745 Chain: "B" Number of atoms: 4412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4412 Classifications: {'peptide': 557} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 525} Chain: "D" Number of atoms: 2055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2055 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 252} Chain: "J" Number of atoms: 2147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2147 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 8, 'TRANS': 267} Chain: "K" Number of atoms: 2139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2139 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 8, 'TRANS': 266} Chain: "Q" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 243 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 28} Chain: "U" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 316 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'TRANS': 38} Chain breaks: 1 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10243 SG CYS D 155 55.749 56.905 105.259 1.00115.21 S ATOM 10905 SG CYS D 244 53.687 55.245 101.530 1.00111.87 S Time building chain proxies: 3.87, per 1000 atoms: 0.24 Number of scatterers: 15967 At special positions: 0 Unit cell: (145.14, 110.7, 238.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 1 26.01 S 66 16.00 O 3179 8.00 N 2860 7.00 C 9861 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: 1.36 Conformation dependent library (CDL) restraints added in 885.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3398 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 31 sheets defined 13.2% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 4 through 8 removed outlier: 3.959A pdb=" N VAL A 8 " --> pdb=" O SER A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 84 through 92 removed outlier: 3.934A pdb=" N LYS A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 140 removed outlier: 3.621A pdb=" N LYS A 140 " --> pdb=" O TYR A 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 137 through 140' Processing helix chain 'A' and resid 161 through 171 Processing helix chain 'A' and resid 180 through 184 Processing helix chain 'A' and resid 185 through 199 removed outlier: 3.744A pdb=" N THR A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN A 198 " --> pdb=" O ASP A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 225 Processing helix chain 'A' and resid 297 through 305 removed outlier: 3.706A pdb=" N ASN A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY A 305 " --> pdb=" O ILE A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 336 removed outlier: 3.527A pdb=" N THR A 336 " --> pdb=" O ARG A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 438 Processing helix chain 'A' and resid 439 through 444 removed outlier: 4.058A pdb=" N ASN A 444 " --> pdb=" O ASP A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 515 removed outlier: 4.251A pdb=" N ASP A 514 " --> pdb=" O ASP A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 677 Processing helix chain 'A' and resid 723 through 728 Processing helix chain 'B' and resid 15 through 21 Processing helix chain 'B' and resid 140 through 145 Processing helix chain 'B' and resid 153 through 158 removed outlier: 3.643A pdb=" N LEU B 156 " --> pdb=" O ASP B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 169 removed outlier: 3.614A pdb=" N ASP B 169 " --> pdb=" O ASN B 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 166 through 169' Processing helix chain 'B' and resid 211 through 224 Processing helix chain 'B' and resid 233 through 236 Processing helix chain 'B' and resid 409 through 423 Processing helix chain 'B' and resid 458 through 463 Processing helix chain 'B' and resid 467 through 470 Processing helix chain 'D' and resid 3 through 8 Processing helix chain 'D' and resid 73 through 78 Processing helix chain 'D' and resid 128 through 132 Processing helix chain 'D' and resid 178 through 183 removed outlier: 3.808A pdb=" N ALA D 182 " --> pdb=" O ALA D 178 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR D 183 " --> pdb=" O ALA D 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 178 through 183' Processing helix chain 'D' and resid 240 through 247 Processing helix chain 'D' and resid 250 through 254 Processing helix chain 'J' and resid 81 through 90 Processing helix chain 'J' and resid 150 through 154 removed outlier: 3.735A pdb=" N ILE J 153 " --> pdb=" O SER J 150 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR J 154 " --> pdb=" O GLY J 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 150 through 154' Processing helix chain 'K' and resid 81 through 90 Processing helix chain 'Q' and resid 1401 through 1406 removed outlier: 3.564A pdb=" N ALA Q1405 " --> pdb=" O LYS Q1401 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1409 through 1421 removed outlier: 4.024A pdb=" N LYS Q1413 " --> pdb=" O PRO Q1409 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1422 through 1431 Processing helix chain 'U' and resid 2 through 7 Processing helix chain 'U' and resid 8 through 10 No H-bonds generated for 'chain 'U' and resid 8 through 10' Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 24 removed outlier: 5.668A pdb=" N PHE A 19 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N PHE A 106 " --> pdb=" O PHE A 19 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLY A 21 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ALA A 104 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE A 23 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 74 " --> pdb=" O THR A 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 45 removed outlier: 5.341A pdb=" N THR A 39 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL A 35 " --> pdb=" O THR A 39 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N THR A 31 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ILE A 45 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU A 29 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ILE A 30 " --> pdb=" O ARG A 125 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ARG A 125 " --> pdb=" O ILE A 30 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU A 32 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N THR U 66 " --> pdb=" O TRP A 120 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N PHE A 122 " --> pdb=" O THR U 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 146 Processing sheet with id=AA4, first strand: chain 'A' and resid 226 through 230 Processing sheet with id=AA5, first strand: chain 'A' and resid 253 through 254 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 253 through 254 current: chain 'A' and resid 340 through 345 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 340 through 345 current: chain 'A' and resid 368 through 379 removed outlier: 5.364A pdb=" N VAL A 391 " --> pdb=" O GLY A 376 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL A 378 " --> pdb=" O LYS A 389 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS A 389 " --> pdb=" O VAL A 378 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 289 through 296 removed outlier: 3.515A pdb=" N GLU A 289 " --> pdb=" O ASN A 284 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 424 through 428 Processing sheet with id=AA8, first strand: chain 'A' and resid 450 through 451 Processing sheet with id=AA9, first strand: chain 'A' and resid 464 through 472 removed outlier: 6.839A pdb=" N TYR A 467 " --> pdb=" O ASN A 484 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ASN A 484 " --> pdb=" O TYR A 467 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N MET A 469 " --> pdb=" O ARG A 482 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 480 through 485 current: chain 'A' and resid 605 through 606 Processing sheet with id=AB1, first strand: chain 'A' and resid 503 through 504 removed outlier: 7.300A pdb=" N VAL A 552 " --> pdb=" O ILE A 548 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ILE A 548 " --> pdb=" O VAL A 552 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N THR A 554 " --> pdb=" O ASP A 546 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N MET A 572 " --> pdb=" O ALA A 525 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 630 through 635 removed outlier: 5.987A pdb=" N ASN A 631 " --> pdb=" O ALA A 669 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ALA A 669 " --> pdb=" O ASN A 631 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 649 through 651 removed outlier: 3.703A pdb=" N SER A 764 " --> pdb=" O SER A 649 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N TYR A 696 " --> pdb=" O GLY A 713 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY A 713 " --> pdb=" O TYR A 696 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG A 709 " --> pdb=" O VAL A 700 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 10 through 12 Processing sheet with id=AB5, first strand: chain 'B' and resid 40 through 50 Processing sheet with id=AB6, first strand: chain 'B' and resid 56 through 61 removed outlier: 3.616A pdb=" N VAL B 58 " --> pdb=" O GLN B 116 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 66 through 69 removed outlier: 6.582A pdb=" N LEU B 67 " --> pdb=" O VAL B 74 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 171 through 176 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 199 through 208 current: chain 'B' and resid 275 through 284 removed outlier: 3.973A pdb=" N GLY B 282 " --> pdb=" O THR B 291 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS B 289 " --> pdb=" O ASP B 284 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 289 through 292 current: chain 'B' and resid 328 through 336 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 328 through 336 current: chain 'B' and resid 541 through 543 Processing sheet with id=AB9, first strand: chain 'B' and resid 179 through 183 Processing sheet with id=AC1, first strand: chain 'B' and resid 399 through 402 Processing sheet with id=AC2, first strand: chain 'B' and resid 451 through 455 removed outlier: 3.579A pdb=" N SER B 489 " --> pdb=" O PHE B 500 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N GLU B 476 " --> pdb=" O ARG B 514 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 18 through 23 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 26 through 31 current: chain 'D' and resid 42 through 46 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 42 through 46 current: chain 'D' and resid 104 through 106 Processing sheet with id=AC4, first strand: chain 'D' and resid 65 through 69 removed outlier: 3.533A pdb=" N THR D 123 " --> pdb=" O ASN D 114 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER D 112 " --> pdb=" O THR D 125 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 164 through 167 removed outlier: 7.642A pdb=" N ILE D 230 " --> pdb=" O ILE D 197 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ILE D 197 " --> pdb=" O ILE D 230 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 170 through 172 removed outlier: 3.583A pdb=" N THR D 175 " --> pdb=" O GLY D 172 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 16 through 20 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 16 through 20 current: chain 'J' and resid 71 through 77 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 71 through 77 current: chain 'J' and resid 202 through 207 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 202 through 207 current: chain 'J' and resid 229 through 245 removed outlier: 4.075A pdb=" N LYS J 235 " --> pdb=" O MET J 261 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP J 241 " --> pdb=" O SER J 255 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N SER J 255 " --> pdb=" O ASP J 241 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 254 through 261 current: chain 'K' and resid 31 through 33 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 31 through 33 current: chain 'K' and resid 59 through 77 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 59 through 77 current: chain 'K' and resid 229 through 240 Processing sheet with id=AC8, first strand: chain 'J' and resid 47 through 49 removed outlier: 7.818A pdb=" N GLU J 47 " --> pdb=" O LEU J 67 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU J 67 " --> pdb=" O GLU J 47 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU J 49 " --> pdb=" O VAL J 65 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL J 65 " --> pdb=" O LEU J 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'J' and resid 105 through 107 removed outlier: 3.936A pdb=" N THR J 160 " --> pdb=" O LYS J 139 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 116 through 118 removed outlier: 3.751A pdb=" N ARG J 176 " --> pdb=" O ASP J 171 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 93 through 97 Processing sheet with id=AD3, first strand: chain 'K' and resid 101 through 108 removed outlier: 5.362A pdb=" N THR K 102 " --> pdb=" O VAL K 198 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL K 198 " --> pdb=" O THR K 102 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 115 through 118 removed outlier: 3.853A pdb=" N ARG K 176 " --> pdb=" O ASP K 171 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP K 171 " --> pdb=" O ARG K 176 " (cutoff:3.500A) 363 hydrogen bonds defined for protein. 951 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.83 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5593 1.34 - 1.46: 3487 1.46 - 1.58: 7078 1.58 - 1.70: 0 1.70 - 1.81: 115 Bond restraints: 16273 Sorted by residual: bond pdb=" CA THR B 378 " pdb=" C THR B 378 " ideal model delta sigma weight residual 1.523 1.489 0.034 1.34e-02 5.57e+03 6.42e+00 bond pdb=" N GLY A 2 " pdb=" CA GLY A 2 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.13e+00 bond pdb=" CA TYR B 379 " pdb=" C TYR B 379 " ideal model delta sigma weight residual 1.523 1.499 0.025 1.24e-02 6.50e+03 3.93e+00 bond pdb=" N MET U 1 " pdb=" CA MET U 1 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.49e+00 bond pdb=" N MET J 1 " pdb=" CA MET J 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.14e+00 ... (remaining 16268 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 21580 1.92 - 3.83: 357 3.83 - 5.75: 25 5.75 - 7.66: 5 7.66 - 9.58: 2 Bond angle restraints: 21969 Sorted by residual: angle pdb=" C PRO A 384 " pdb=" N ASP A 385 " pdb=" CA ASP A 385 " ideal model delta sigma weight residual 121.54 128.12 -6.58 1.91e+00 2.74e-01 1.19e+01 angle pdb=" N ASP J 50 " pdb=" CA ASP J 50 " pdb=" C ASP J 50 " ideal model delta sigma weight residual 107.93 113.30 -5.37 1.65e+00 3.67e-01 1.06e+01 angle pdb=" CB ARG B 255 " pdb=" CG ARG B 255 " pdb=" CD ARG B 255 " ideal model delta sigma weight residual 111.30 118.34 -7.04 2.30e+00 1.89e-01 9.36e+00 angle pdb=" N ASP D 98 " pdb=" CA ASP D 98 " pdb=" C ASP D 98 " ideal model delta sigma weight residual 113.72 109.11 4.61 1.52e+00 4.33e-01 9.19e+00 angle pdb=" C SER B 347 " pdb=" N ASP B 348 " pdb=" CA ASP B 348 " ideal model delta sigma weight residual 121.54 127.12 -5.58 1.91e+00 2.74e-01 8.55e+00 ... (remaining 21964 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 8400 17.57 - 35.15: 626 35.15 - 52.72: 95 52.72 - 70.30: 25 70.30 - 87.87: 8 Dihedral angle restraints: 9154 sinusoidal: 3466 harmonic: 5688 Sorted by residual: dihedral pdb=" CA PRO A 115 " pdb=" C PRO A 115 " pdb=" N TYR A 116 " pdb=" CA TYR A 116 " ideal model delta harmonic sigma weight residual -180.00 -153.59 -26.41 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA MET K 112 " pdb=" C MET K 112 " pdb=" N ARG K 113 " pdb=" CA ARG K 113 " ideal model delta harmonic sigma weight residual 180.00 154.46 25.54 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA VAL J 213 " pdb=" C VAL J 213 " pdb=" N TYR J 214 " pdb=" CA TYR J 214 " ideal model delta harmonic sigma weight residual -180.00 -155.83 -24.17 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 9151 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1476 0.034 - 0.069: 484 0.069 - 0.103: 158 0.103 - 0.138: 111 0.138 - 0.172: 10 Chirality restraints: 2239 Sorted by residual: chirality pdb=" CA ILE B 372 " pdb=" N ILE B 372 " pdb=" C ILE B 372 " pdb=" CB ILE B 372 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.39e-01 chirality pdb=" CA ILE K 156 " pdb=" N ILE K 156 " pdb=" C ILE K 156 " pdb=" CB ILE K 156 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.95e-01 chirality pdb=" CA ILE B 101 " pdb=" N ILE B 101 " pdb=" C ILE B 101 " pdb=" CB ILE B 101 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.08e-01 ... (remaining 2236 not shown) Planarity restraints: 3015 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU K 180 " -0.045 5.00e-02 4.00e+02 6.74e-02 7.27e+00 pdb=" N PRO K 181 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO K 181 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO K 181 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 392 " -0.036 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO B 393 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 393 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 393 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 379 " 0.022 2.00e-02 2.50e+03 1.33e-02 3.54e+00 pdb=" CG TYR B 379 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR B 379 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR B 379 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 379 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 379 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 379 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 379 " 0.005 2.00e-02 2.50e+03 ... (remaining 3012 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 343 2.61 - 3.18: 15503 3.18 - 3.75: 23949 3.75 - 4.33: 33173 4.33 - 4.90: 53050 Nonbonded interactions: 126018 Sorted by model distance: nonbonded pdb=" OH TYR J 244 " pdb=" OE1 GLN J 252 " model vdw 2.036 3.040 nonbonded pdb=" OD1 ASP K 123 " pdb=" N ASP K 124 " model vdw 2.111 3.120 nonbonded pdb=" O GLY B 270 " pdb=" OG1 THR B 271 " model vdw 2.175 3.040 nonbonded pdb=" OE1 GLU D 20 " pdb=" NH2 ARG D 93 " model vdw 2.197 3.120 nonbonded pdb=" OG1 THR B 54 " pdb=" OD1 ASP B 120 " model vdw 2.202 3.040 ... (remaining 126013 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 'J' and resid 2 through 276) selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 17.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 15.880 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16273 Z= 0.131 Angle : 0.596 9.580 21969 Z= 0.327 Chirality : 0.045 0.172 2239 Planarity : 0.004 0.069 3015 Dihedral : 12.743 87.869 5756 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 0.32 % Allowed : 0.19 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -2.73 (0.17), residues: 2203 helix: -0.25 (0.37), residues: 197 sheet: -1.55 (0.20), residues: 608 loop : -2.27 (0.15), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 176 TYR 0.029 0.001 TYR B 379 PHE 0.030 0.001 PHE B 294 TRP 0.019 0.001 TRP B 177 HIS 0.004 0.001 HIS B 234 Details of bonding type rmsd covalent geometry : bond 0.00261 (16273) covalent geometry : angle 0.59648 (21969) hydrogen bonds : bond 0.23876 ( 363) hydrogen bonds : angle 10.59596 ( 951) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 412 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.5460 (tpt) cc_final: 0.5143 (mmm) REVERT: A 173 TYR cc_start: 0.8269 (t80) cc_final: 0.8060 (t80) REVERT: A 196 LEU cc_start: 0.9446 (mt) cc_final: 0.9173 (mt) REVERT: A 203 LEU cc_start: 0.8787 (tp) cc_final: 0.8490 (tp) REVERT: B 13 PHE cc_start: 0.7647 (t80) cc_final: 0.7249 (t80) REVERT: B 194 ILE cc_start: 0.8230 (mm) cc_final: 0.7997 (mm) REVERT: B 524 LEU cc_start: 0.8805 (tp) cc_final: 0.8542 (tt) REVERT: B 545 LEU cc_start: 0.8652 (mp) cc_final: 0.8428 (mp) REVERT: B 550 PHE cc_start: 0.8213 (p90) cc_final: 0.7660 (p90) REVERT: D 7 GLU cc_start: 0.9085 (tp30) cc_final: 0.8782 (tp30) REVERT: D 118 ASN cc_start: 0.8664 (t0) cc_final: 0.8187 (p0) REVERT: J 1 MET cc_start: 0.2617 (mtt) cc_final: 0.2252 (mtm) REVERT: J 229 LYS cc_start: 0.7305 (ptpt) cc_final: 0.7019 (pttt) REVERT: K 16 VAL cc_start: 0.9382 (t) cc_final: 0.9022 (p) REVERT: K 112 MET cc_start: 0.7726 (pmm) cc_final: 0.7286 (ppp) REVERT: K 192 ILE cc_start: 0.9284 (mm) cc_final: 0.9060 (tp) REVERT: K 209 LYS cc_start: 0.6635 (tptt) cc_final: 0.5982 (mmtt) REVERT: K 222 ASP cc_start: 0.8306 (t0) cc_final: 0.7999 (t0) REVERT: K 261 MET cc_start: 0.7210 (ptp) cc_final: 0.6951 (ttt) REVERT: Q 1421 ARG cc_start: 0.9020 (mtm-85) cc_final: 0.8387 (mtm-85) REVERT: Q 1422 ASN cc_start: 0.8890 (m-40) cc_final: 0.7953 (p0) REVERT: Q 1427 LYS cc_start: 0.6060 (mmtt) cc_final: 0.5721 (mttt) REVERT: U 7 MET cc_start: 0.8798 (mmm) cc_final: 0.8436 (mmm) REVERT: U 67 LYS cc_start: 0.6341 (mtpt) cc_final: 0.5620 (ttpt) outliers start: 5 outliers final: 0 residues processed: 416 average time/residue: 0.1391 time to fit residues: 84.1582 Evaluate side-chains 237 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 40.0000 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 9.9990 chunk 212 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 GLN B 14 ASN ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 HIS B 225 GLN ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 503 GLN K 36 ASN K 125 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.076357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.069005 restraints weight = 96470.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.071035 restraints weight = 62926.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.071774 restraints weight = 37692.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.072432 restraints weight = 27038.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.072915 restraints weight = 21430.031| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 16273 Z= 0.280 Angle : 0.785 10.993 21969 Z= 0.415 Chirality : 0.052 0.202 2239 Planarity : 0.006 0.054 3015 Dihedral : 6.148 39.957 2397 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.44 % Favored : 90.51 % Rotamer: Outliers : 0.19 % Allowed : 7.12 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -2.86 (0.17), residues: 2203 helix: -0.86 (0.33), residues: 221 sheet: -1.69 (0.19), residues: 660 loop : -2.27 (0.16), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 206 TYR 0.029 0.003 TYR B 379 PHE 0.028 0.003 PHE J 108 TRP 0.022 0.002 TRP D 142 HIS 0.007 0.002 HIS B 358 Details of bonding type rmsd covalent geometry : bond 0.00595 (16273) covalent geometry : angle 0.78478 (21969) hydrogen bonds : bond 0.04480 ( 363) hydrogen bonds : angle 7.82399 ( 951) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 302 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 TYR cc_start: 0.8452 (t80) cc_final: 0.8103 (t80) REVERT: A 196 LEU cc_start: 0.9527 (mt) cc_final: 0.9216 (mt) REVERT: A 203 LEU cc_start: 0.8846 (tp) cc_final: 0.8533 (tp) REVERT: B 93 ASP cc_start: 0.8957 (m-30) cc_final: 0.8460 (t0) REVERT: B 119 ARG cc_start: 0.8611 (tmm160) cc_final: 0.8193 (tmm160) REVERT: B 236 MET cc_start: 0.6960 (ptt) cc_final: 0.6605 (ptp) REVERT: B 524 LEU cc_start: 0.9083 (tp) cc_final: 0.8768 (tt) REVERT: B 550 PHE cc_start: 0.8642 (p90) cc_final: 0.7761 (p90) REVERT: D 11 ASP cc_start: 0.8264 (p0) cc_final: 0.7949 (p0) REVERT: D 118 ASN cc_start: 0.8847 (t0) cc_final: 0.8386 (p0) REVERT: D 230 ILE cc_start: 0.8370 (mt) cc_final: 0.8056 (tt) REVERT: J 1 MET cc_start: 0.3084 (mtt) cc_final: 0.2734 (mtt) REVERT: J 39 GLU cc_start: 0.8563 (mp0) cc_final: 0.8351 (mp0) REVERT: J 61 MET cc_start: 0.7729 (tmm) cc_final: 0.7458 (tmm) REVERT: J 229 LYS cc_start: 0.7174 (ptpt) cc_final: 0.6876 (pttt) REVERT: K 112 MET cc_start: 0.8126 (pmm) cc_final: 0.7545 (ppp) REVERT: K 192 ILE cc_start: 0.9408 (mm) cc_final: 0.9144 (tp) REVERT: K 209 LYS cc_start: 0.6519 (tptt) cc_final: 0.5326 (mmtt) REVERT: K 212 MET cc_start: 0.8774 (ttt) cc_final: 0.8346 (ttt) REVERT: Q 1406 MET cc_start: 0.9008 (tpp) cc_final: 0.8754 (tpp) REVERT: Q 1421 ARG cc_start: 0.9030 (mtm-85) cc_final: 0.8099 (mmp-170) REVERT: Q 1427 LYS cc_start: 0.6327 (mmtt) cc_final: 0.5882 (mttt) REVERT: U 67 LYS cc_start: 0.6711 (mtpt) cc_final: 0.5520 (ttpt) outliers start: 3 outliers final: 1 residues processed: 305 average time/residue: 0.1301 time to fit residues: 59.3556 Evaluate side-chains 213 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 212 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 77 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 146 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 178 optimal weight: 6.9990 chunk 82 optimal weight: 0.6980 chunk 136 optimal weight: 9.9990 chunk 135 optimal weight: 3.9990 chunk 190 optimal weight: 0.7980 chunk 26 optimal weight: 0.0570 chunk 23 optimal weight: 4.9990 overall best weight: 1.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 291 GLN A 304 GLN ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.079031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.071512 restraints weight = 93941.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.073335 restraints weight = 61729.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.074322 restraints weight = 38379.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.075397 restraints weight = 26315.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.075601 restraints weight = 19055.708| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16273 Z= 0.134 Angle : 0.648 10.536 21969 Z= 0.341 Chirality : 0.048 0.188 2239 Planarity : 0.005 0.092 3015 Dihedral : 5.714 43.732 2397 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -2.57 (0.17), residues: 2203 helix: -0.34 (0.35), residues: 213 sheet: -1.55 (0.19), residues: 659 loop : -2.09 (0.16), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 533 TYR 0.021 0.002 TYR B 55 PHE 0.028 0.002 PHE J 89 TRP 0.041 0.002 TRP A 207 HIS 0.003 0.001 HIS D 96 Details of bonding type rmsd covalent geometry : bond 0.00298 (16273) covalent geometry : angle 0.64775 (21969) hydrogen bonds : bond 0.03563 ( 363) hydrogen bonds : angle 7.10395 ( 951) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8162 (tmm) cc_final: 0.7558 (tmm) REVERT: A 173 TYR cc_start: 0.8338 (t80) cc_final: 0.8084 (t80) REVERT: A 196 LEU cc_start: 0.9443 (mt) cc_final: 0.9059 (mt) REVERT: A 203 LEU cc_start: 0.8875 (tp) cc_final: 0.8564 (tp) REVERT: B 119 ARG cc_start: 0.8433 (tmm160) cc_final: 0.8109 (tmm160) REVERT: B 333 ARG cc_start: 0.7785 (ttm-80) cc_final: 0.7524 (ttm-80) REVERT: B 524 LEU cc_start: 0.8992 (tp) cc_final: 0.8759 (tt) REVERT: D 11 ASP cc_start: 0.8110 (p0) cc_final: 0.7867 (p0) REVERT: D 18 MET cc_start: 0.8388 (mtm) cc_final: 0.8147 (ttm) REVERT: D 115 GLN cc_start: 0.8178 (mp-120) cc_final: 0.5879 (tt0) REVERT: D 118 ASN cc_start: 0.8787 (t0) cc_final: 0.8299 (p0) REVERT: D 230 ILE cc_start: 0.8361 (mt) cc_final: 0.8020 (tt) REVERT: J 1 MET cc_start: 0.3124 (mtt) cc_final: 0.2764 (mtt) REVERT: J 61 MET cc_start: 0.7752 (tmm) cc_final: 0.7453 (tmm) REVERT: J 229 LYS cc_start: 0.6963 (ptpt) cc_final: 0.6738 (pttt) REVERT: J 259 LYS cc_start: 0.9068 (ptpp) cc_final: 0.8863 (ptmm) REVERT: K 16 VAL cc_start: 0.9162 (t) cc_final: 0.8917 (p) REVERT: K 32 MET cc_start: 0.7579 (tmm) cc_final: 0.7340 (tmm) REVERT: K 112 MET cc_start: 0.7755 (pmm) cc_final: 0.7487 (ppp) REVERT: K 180 GLU cc_start: 0.8322 (tp30) cc_final: 0.8084 (tp30) REVERT: K 192 ILE cc_start: 0.9393 (mm) cc_final: 0.9137 (tp) REVERT: K 209 LYS cc_start: 0.6526 (tptt) cc_final: 0.5241 (mmtt) REVERT: K 212 MET cc_start: 0.8713 (ttt) cc_final: 0.8338 (ttt) REVERT: Q 1406 MET cc_start: 0.8931 (tpp) cc_final: 0.8687 (tpp) REVERT: Q 1421 ARG cc_start: 0.8952 (mtm-85) cc_final: 0.8015 (mmp-170) REVERT: Q 1427 LYS cc_start: 0.6354 (mmtt) cc_final: 0.5862 (mttt) outliers start: 0 outliers final: 0 residues processed: 294 average time/residue: 0.1325 time to fit residues: 57.4169 Evaluate side-chains 217 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 214 optimal weight: 0.6980 chunk 85 optimal weight: 0.4980 chunk 165 optimal weight: 9.9990 chunk 153 optimal weight: 20.0000 chunk 37 optimal weight: 3.9990 chunk 27 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 73 optimal weight: 0.0060 chunk 6 optimal weight: 30.0000 chunk 68 optimal weight: 40.0000 chunk 191 optimal weight: 20.0000 overall best weight: 2.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 GLN ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN B 380 ASN K 8 ASN ** K 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.078576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.070953 restraints weight = 94692.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.073029 restraints weight = 60369.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.073879 restraints weight = 36575.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.074894 restraints weight = 25299.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.074979 restraints weight = 18362.207| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16273 Z= 0.146 Angle : 0.643 10.630 21969 Z= 0.334 Chirality : 0.048 0.182 2239 Planarity : 0.005 0.087 3015 Dihedral : 5.566 42.350 2397 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 0.06 % Allowed : 4.20 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -2.48 (0.17), residues: 2203 helix: -0.28 (0.36), residues: 214 sheet: -1.51 (0.19), residues: 695 loop : -2.01 (0.17), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 206 TYR 0.018 0.001 TYR B 102 PHE 0.019 0.002 PHE J 89 TRP 0.024 0.002 TRP A 207 HIS 0.003 0.001 HIS D 96 Details of bonding type rmsd covalent geometry : bond 0.00330 (16273) covalent geometry : angle 0.64287 (21969) hydrogen bonds : bond 0.03230 ( 363) hydrogen bonds : angle 6.82715 ( 951) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 279 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8221 (tmm) cc_final: 0.7662 (tmm) REVERT: A 160 MET cc_start: 0.7747 (ttp) cc_final: 0.7285 (ttp) REVERT: A 173 TYR cc_start: 0.8461 (t80) cc_final: 0.8191 (t80) REVERT: A 203 LEU cc_start: 0.8920 (tp) cc_final: 0.8573 (tp) REVERT: B 58 VAL cc_start: 0.8945 (t) cc_final: 0.8491 (t) REVERT: B 60 TYR cc_start: 0.6907 (t80) cc_final: 0.6044 (m-80) REVERT: B 93 ASP cc_start: 0.8971 (m-30) cc_final: 0.8365 (t0) REVERT: B 119 ARG cc_start: 0.8570 (tmm160) cc_final: 0.8144 (tmm160) REVERT: B 182 MET cc_start: 0.8488 (pmm) cc_final: 0.8276 (pmm) REVERT: B 333 ARG cc_start: 0.7905 (ttm-80) cc_final: 0.7270 (ttm-80) REVERT: B 524 LEU cc_start: 0.9082 (tp) cc_final: 0.8856 (tt) REVERT: B 550 PHE cc_start: 0.8349 (p90) cc_final: 0.7858 (p90) REVERT: D 11 ASP cc_start: 0.8053 (p0) cc_final: 0.7828 (p0) REVERT: D 45 GLU cc_start: 0.9040 (mp0) cc_final: 0.8720 (mp0) REVERT: D 115 GLN cc_start: 0.8157 (mp-120) cc_final: 0.5875 (tt0) REVERT: D 118 ASN cc_start: 0.8864 (t0) cc_final: 0.8306 (p0) REVERT: D 230 ILE cc_start: 0.8363 (mt) cc_final: 0.7991 (tt) REVERT: J 1 MET cc_start: 0.2994 (mtt) cc_final: 0.2764 (mtt) REVERT: J 61 MET cc_start: 0.7726 (tmm) cc_final: 0.7446 (tmm) REVERT: J 261 MET cc_start: 0.6737 (mtm) cc_final: 0.6471 (mtm) REVERT: K 16 VAL cc_start: 0.9317 (t) cc_final: 0.9063 (p) REVERT: K 18 PHE cc_start: 0.8853 (t80) cc_final: 0.8652 (t80) REVERT: K 61 MET cc_start: 0.8692 (ppp) cc_final: 0.6601 (ppp) REVERT: K 112 MET cc_start: 0.7893 (pmm) cc_final: 0.7604 (ppp) REVERT: K 163 ASN cc_start: 0.8485 (t0) cc_final: 0.8027 (t0) REVERT: K 180 GLU cc_start: 0.8402 (tp30) cc_final: 0.8144 (tp30) REVERT: K 192 ILE cc_start: 0.9320 (mm) cc_final: 0.9034 (tp) REVERT: K 212 MET cc_start: 0.8800 (ttt) cc_final: 0.8427 (ttt) REVERT: Q 1406 MET cc_start: 0.8954 (tpp) cc_final: 0.8693 (tpp) REVERT: Q 1421 ARG cc_start: 0.8909 (mtm-85) cc_final: 0.8284 (mtm110) REVERT: Q 1427 LYS cc_start: 0.6397 (mmtt) cc_final: 0.6006 (mttt) outliers start: 1 outliers final: 0 residues processed: 280 average time/residue: 0.1368 time to fit residues: 56.4007 Evaluate side-chains 211 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 5 optimal weight: 10.0000 chunk 192 optimal weight: 0.0060 chunk 131 optimal weight: 9.9990 chunk 198 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 15 optimal weight: 20.0000 chunk 174 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 chunk 179 optimal weight: 20.0000 chunk 77 optimal weight: 4.9990 overall best weight: 4.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN J 7 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.077245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.069656 restraints weight = 94848.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.071643 restraints weight = 60084.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.072512 restraints weight = 37540.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.073599 restraints weight = 25504.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.073779 restraints weight = 18182.747| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16273 Z= 0.189 Angle : 0.666 10.508 21969 Z= 0.348 Chirality : 0.048 0.252 2239 Planarity : 0.005 0.061 3015 Dihedral : 5.593 40.914 2397 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -2.51 (0.17), residues: 2203 helix: -0.36 (0.35), residues: 220 sheet: -1.46 (0.19), residues: 679 loop : -2.06 (0.16), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 192 TYR 0.015 0.002 TYR A 116 PHE 0.016 0.002 PHE U 61 TRP 0.054 0.002 TRP A 207 HIS 0.005 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00421 (16273) covalent geometry : angle 0.66614 (21969) hydrogen bonds : bond 0.03276 ( 363) hydrogen bonds : angle 6.75039 ( 951) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8254 (tmm) cc_final: 0.7711 (tmm) REVERT: A 173 TYR cc_start: 0.8530 (t80) cc_final: 0.8236 (t80) REVERT: A 203 LEU cc_start: 0.8893 (tp) cc_final: 0.8542 (tp) REVERT: A 277 GLU cc_start: 0.7902 (mp0) cc_final: 0.7578 (tp30) REVERT: B 44 MET cc_start: 0.6797 (pmm) cc_final: 0.6456 (pmm) REVERT: B 119 ARG cc_start: 0.8596 (tmm160) cc_final: 0.8146 (tmm160) REVERT: B 333 ARG cc_start: 0.7946 (ttm-80) cc_final: 0.7257 (ttm-80) REVERT: B 362 LEU cc_start: 0.7613 (tp) cc_final: 0.6655 (tp) REVERT: D 11 ASP cc_start: 0.8065 (p0) cc_final: 0.7772 (p0) REVERT: D 45 GLU cc_start: 0.9123 (mp0) cc_final: 0.8750 (mp0) REVERT: D 47 MET cc_start: 0.6861 (tpp) cc_final: 0.6638 (tpp) REVERT: D 118 ASN cc_start: 0.8876 (t0) cc_final: 0.8268 (p0) REVERT: D 195 GLU cc_start: 0.7252 (mm-30) cc_final: 0.6978 (mm-30) REVERT: J 235 LYS cc_start: 0.8196 (ptmm) cc_final: 0.7716 (pttp) REVERT: J 261 MET cc_start: 0.6957 (mtm) cc_final: 0.5554 (mtm) REVERT: J 263 LEU cc_start: 0.8533 (tp) cc_final: 0.8229 (tp) REVERT: K 18 PHE cc_start: 0.8931 (t80) cc_final: 0.8703 (t80) REVERT: K 32 MET cc_start: 0.7872 (tmm) cc_final: 0.7231 (tmm) REVERT: K 61 MET cc_start: 0.8573 (ppp) cc_final: 0.8218 (ppp) REVERT: K 106 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7986 (mt-10) REVERT: K 163 ASN cc_start: 0.8521 (t0) cc_final: 0.7819 (t0) REVERT: K 180 GLU cc_start: 0.8484 (tp30) cc_final: 0.8218 (tp30) REVERT: K 192 ILE cc_start: 0.9395 (mm) cc_final: 0.8982 (tp) REVERT: K 212 MET cc_start: 0.8873 (ttt) cc_final: 0.8445 (ttt) REVERT: Q 1421 ARG cc_start: 0.8893 (mtm-85) cc_final: 0.8226 (mtm110) REVERT: Q 1427 LYS cc_start: 0.6386 (mmtt) cc_final: 0.5994 (mttt) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.1297 time to fit residues: 52.0727 Evaluate side-chains 207 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 21 optimal weight: 2.9990 chunk 120 optimal weight: 8.9990 chunk 211 optimal weight: 0.6980 chunk 77 optimal weight: 8.9990 chunk 124 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 chunk 178 optimal weight: 7.9990 chunk 141 optimal weight: 0.9990 chunk 122 optimal weight: 7.9990 chunk 206 optimal weight: 9.9990 chunk 135 optimal weight: 1.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 191 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.077965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.070484 restraints weight = 93369.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.072410 restraints weight = 61832.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.073343 restraints weight = 38030.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.074375 restraints weight = 26858.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.074605 restraints weight = 18239.490| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 16273 Z= 0.149 Angle : 0.648 11.331 21969 Z= 0.334 Chirality : 0.048 0.232 2239 Planarity : 0.005 0.117 3015 Dihedral : 5.458 44.079 2397 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -2.45 (0.17), residues: 2203 helix: -0.32 (0.36), residues: 218 sheet: -1.36 (0.19), residues: 687 loop : -2.06 (0.16), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 20 TYR 0.016 0.002 TYR A 116 PHE 0.016 0.002 PHE U 61 TRP 0.068 0.002 TRP A 207 HIS 0.003 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00340 (16273) covalent geometry : angle 0.64838 (21969) hydrogen bonds : bond 0.03040 ( 363) hydrogen bonds : angle 6.56172 ( 951) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 MET cc_start: 0.7731 (ttp) cc_final: 0.7343 (ttp) REVERT: A 203 LEU cc_start: 0.8838 (tp) cc_final: 0.8515 (tp) REVERT: A 277 GLU cc_start: 0.7920 (mp0) cc_final: 0.7483 (tp30) REVERT: A 297 ASN cc_start: 0.7980 (t0) cc_final: 0.7472 (t0) REVERT: B 48 MET cc_start: 0.7696 (mtm) cc_final: 0.6543 (mtm) REVERT: B 119 ARG cc_start: 0.8469 (tmm160) cc_final: 0.7954 (tmm160) REVERT: B 182 MET cc_start: 0.8718 (pmm) cc_final: 0.8407 (pmm) REVERT: B 333 ARG cc_start: 0.7882 (ttm-80) cc_final: 0.7256 (ttm-80) REVERT: B 362 LEU cc_start: 0.7565 (tp) cc_final: 0.6654 (tp) REVERT: D 11 ASP cc_start: 0.7964 (p0) cc_final: 0.7612 (p0) REVERT: D 45 GLU cc_start: 0.9150 (mp0) cc_final: 0.8707 (mp0) REVERT: D 115 GLN cc_start: 0.8257 (mp-120) cc_final: 0.5994 (tt0) REVERT: D 118 ASN cc_start: 0.8866 (t0) cc_final: 0.8405 (t0) REVERT: J 68 GLU cc_start: 0.7111 (mm-30) cc_final: 0.6667 (tp30) REVERT: J 235 LYS cc_start: 0.7976 (ptmm) cc_final: 0.7649 (pttp) REVERT: J 261 MET cc_start: 0.6689 (mtm) cc_final: 0.5505 (mtm) REVERT: J 263 LEU cc_start: 0.8467 (tp) cc_final: 0.8189 (tp) REVERT: K 16 VAL cc_start: 0.9376 (t) cc_final: 0.9094 (p) REVERT: K 18 PHE cc_start: 0.8793 (t80) cc_final: 0.8528 (t80) REVERT: K 153 ILE cc_start: 0.7576 (pt) cc_final: 0.7340 (pt) REVERT: K 163 ASN cc_start: 0.8565 (t0) cc_final: 0.7811 (t0) REVERT: K 180 GLU cc_start: 0.8415 (tp30) cc_final: 0.8215 (tp30) REVERT: K 212 MET cc_start: 0.8862 (ttt) cc_final: 0.8468 (ttt) REVERT: Q 1421 ARG cc_start: 0.8905 (mtm-85) cc_final: 0.8214 (mtm110) REVERT: Q 1427 LYS cc_start: 0.6445 (mmtt) cc_final: 0.6065 (mttt) REVERT: U 1 MET cc_start: 0.7343 (ppp) cc_final: 0.6944 (ppp) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.1407 time to fit residues: 55.6540 Evaluate side-chains 201 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 90 optimal weight: 0.3980 chunk 44 optimal weight: 30.0000 chunk 173 optimal weight: 10.0000 chunk 144 optimal weight: 20.0000 chunk 66 optimal weight: 50.0000 chunk 154 optimal weight: 0.0770 chunk 116 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 117 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 overall best weight: 3.6944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN K 125 ASN K 230 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.077448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.069853 restraints weight = 95325.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.071818 restraints weight = 60557.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.072754 restraints weight = 37421.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.073777 restraints weight = 25487.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.073986 restraints weight = 18508.832| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16273 Z= 0.171 Angle : 0.670 11.580 21969 Z= 0.348 Chirality : 0.047 0.188 2239 Planarity : 0.005 0.060 3015 Dihedral : 5.503 42.746 2397 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -2.48 (0.17), residues: 2203 helix: -0.31 (0.35), residues: 215 sheet: -1.41 (0.19), residues: 680 loop : -2.07 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG J 20 TYR 0.038 0.002 TYR A 137 PHE 0.015 0.002 PHE B 254 TRP 0.054 0.002 TRP A 207 HIS 0.004 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00381 (16273) covalent geometry : angle 0.67034 (21969) hydrogen bonds : bond 0.03115 ( 363) hydrogen bonds : angle 6.51094 ( 951) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 MET cc_start: 0.7808 (ttp) cc_final: 0.7395 (ttp) REVERT: A 203 LEU cc_start: 0.8827 (tp) cc_final: 0.8496 (tp) REVERT: A 206 ARG cc_start: 0.7025 (tpt-90) cc_final: 0.6767 (tpt-90) REVERT: A 297 ASN cc_start: 0.7989 (t0) cc_final: 0.7702 (t0) REVERT: B 48 MET cc_start: 0.7654 (mtm) cc_final: 0.6768 (mtm) REVERT: B 119 ARG cc_start: 0.8570 (tmm160) cc_final: 0.7980 (tmm160) REVERT: B 333 ARG cc_start: 0.7997 (ttm-80) cc_final: 0.7674 (ttm-80) REVERT: B 550 PHE cc_start: 0.8740 (p90) cc_final: 0.8169 (p90) REVERT: D 11 ASP cc_start: 0.8054 (p0) cc_final: 0.7726 (p0) REVERT: D 45 GLU cc_start: 0.9210 (mp0) cc_final: 0.8732 (mp0) REVERT: D 118 ASN cc_start: 0.8869 (t0) cc_final: 0.8216 (p0) REVERT: D 195 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6948 (mm-30) REVERT: J 68 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6602 (tp30) REVERT: J 212 MET cc_start: 0.7648 (tpp) cc_final: 0.6784 (ttp) REVERT: J 235 LYS cc_start: 0.7981 (ptmm) cc_final: 0.7766 (pttp) REVERT: J 261 MET cc_start: 0.7504 (mtm) cc_final: 0.6139 (mtm) REVERT: J 263 LEU cc_start: 0.8494 (tp) cc_final: 0.8279 (tp) REVERT: K 18 PHE cc_start: 0.8951 (t80) cc_final: 0.8727 (t80) REVERT: K 61 MET cc_start: 0.9032 (ppp) cc_final: 0.8368 (ppp) REVERT: K 163 ASN cc_start: 0.8477 (t0) cc_final: 0.8128 (t0) REVERT: K 180 GLU cc_start: 0.8511 (tp30) cc_final: 0.8280 (tp30) REVERT: K 212 MET cc_start: 0.8910 (ttt) cc_final: 0.8440 (ttt) REVERT: Q 1421 ARG cc_start: 0.8910 (mtm-85) cc_final: 0.8310 (mtm110) REVERT: Q 1427 LYS cc_start: 0.6387 (mmtt) cc_final: 0.5994 (mttt) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.1288 time to fit residues: 51.0470 Evaluate side-chains 203 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 73 optimal weight: 6.9990 chunk 180 optimal weight: 0.2980 chunk 63 optimal weight: 50.0000 chunk 33 optimal weight: 7.9990 chunk 74 optimal weight: 50.0000 chunk 186 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 110 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 chunk 201 optimal weight: 2.9990 overall best weight: 4.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 GLN ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN K 125 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.076685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.069243 restraints weight = 97286.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.071293 restraints weight = 61177.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.072085 restraints weight = 38197.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.073059 restraints weight = 25877.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.073248 restraints weight = 18934.434| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 16273 Z= 0.203 Angle : 0.710 11.699 21969 Z= 0.368 Chirality : 0.048 0.175 2239 Planarity : 0.005 0.077 3015 Dihedral : 5.719 44.227 2397 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -2.54 (0.17), residues: 2203 helix: -0.47 (0.34), residues: 218 sheet: -1.40 (0.19), residues: 671 loop : -2.13 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 20 TYR 0.034 0.002 TYR A 137 PHE 0.017 0.002 PHE B 381 TRP 0.053 0.002 TRP A 207 HIS 0.005 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00451 (16273) covalent geometry : angle 0.70981 (21969) hydrogen bonds : bond 0.03404 ( 363) hydrogen bonds : angle 6.70059 ( 951) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.9003 (tp) cc_final: 0.8697 (tt) REVERT: A 203 LEU cc_start: 0.8825 (tp) cc_final: 0.8498 (tp) REVERT: A 206 ARG cc_start: 0.7276 (tpt-90) cc_final: 0.6877 (tpt-90) REVERT: A 287 MET cc_start: 0.6333 (tpt) cc_final: 0.6030 (tpp) REVERT: B 44 MET cc_start: 0.7269 (pmm) cc_final: 0.6727 (pmm) REVERT: B 48 MET cc_start: 0.7656 (mtm) cc_final: 0.6706 (mtm) REVERT: B 142 LYS cc_start: 0.9248 (mmmm) cc_final: 0.8882 (mmmm) REVERT: B 177 TRP cc_start: 0.7836 (m-90) cc_final: 0.7541 (m-90) REVERT: B 182 MET cc_start: 0.8746 (pmm) cc_final: 0.8513 (pmm) REVERT: B 333 ARG cc_start: 0.7988 (ttm-80) cc_final: 0.7657 (ttm-80) REVERT: B 362 LEU cc_start: 0.8372 (mt) cc_final: 0.8062 (mt) REVERT: B 550 PHE cc_start: 0.8513 (p90) cc_final: 0.8304 (p90) REVERT: D 11 ASP cc_start: 0.8025 (p0) cc_final: 0.7666 (p0) REVERT: D 45 GLU cc_start: 0.9210 (mp0) cc_final: 0.8738 (mp0) REVERT: D 78 LEU cc_start: 0.8742 (mt) cc_final: 0.8366 (tp) REVERT: D 118 ASN cc_start: 0.8887 (t0) cc_final: 0.8250 (p0) REVERT: D 189 PHE cc_start: 0.8091 (m-80) cc_final: 0.7765 (m-80) REVERT: D 193 PHE cc_start: 0.8401 (p90) cc_final: 0.7958 (p90) REVERT: J 68 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6490 (tp30) REVERT: J 219 MET cc_start: 0.8371 (tpp) cc_final: 0.8072 (tpt) REVERT: J 261 MET cc_start: 0.7311 (mtm) cc_final: 0.6917 (mtm) REVERT: K 61 MET cc_start: 0.8934 (ppp) cc_final: 0.8192 (ppp) REVERT: K 163 ASN cc_start: 0.8459 (t0) cc_final: 0.8126 (t0) REVERT: K 180 GLU cc_start: 0.8457 (tp30) cc_final: 0.8223 (tp30) REVERT: Q 1421 ARG cc_start: 0.8906 (mtm-85) cc_final: 0.8458 (mtm110) REVERT: Q 1427 LYS cc_start: 0.6348 (mmtt) cc_final: 0.5942 (mttt) REVERT: U 75 LYS cc_start: 0.9141 (mmmm) cc_final: 0.8904 (mmmm) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.1392 time to fit residues: 54.2518 Evaluate side-chains 204 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 177 optimal weight: 6.9990 chunk 192 optimal weight: 10.0000 chunk 110 optimal weight: 20.0000 chunk 182 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 184 optimal weight: 10.0000 chunk 89 optimal weight: 0.0570 overall best weight: 4.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 GLN A 351 ASN ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 191 GLN K 125 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.076882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.069666 restraints weight = 96773.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.071453 restraints weight = 62585.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.072255 restraints weight = 41025.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.073147 restraints weight = 28205.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.073418 restraints weight = 21082.297| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 16273 Z= 0.184 Angle : 0.706 12.044 21969 Z= 0.363 Chirality : 0.048 0.307 2239 Planarity : 0.005 0.080 3015 Dihedral : 5.691 44.667 2397 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -2.53 (0.17), residues: 2203 helix: -0.41 (0.35), residues: 217 sheet: -1.37 (0.20), residues: 663 loop : -2.14 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 20 TYR 0.030 0.002 TYR A 137 PHE 0.017 0.002 PHE B 294 TRP 0.051 0.003 TRP D 44 HIS 0.004 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00413 (16273) covalent geometry : angle 0.70551 (21969) hydrogen bonds : bond 0.03369 ( 363) hydrogen bonds : angle 6.61963 ( 951) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 MET cc_start: 0.7667 (ttp) cc_final: 0.7343 (ttp) REVERT: A 203 LEU cc_start: 0.8756 (tp) cc_final: 0.8458 (tp) REVERT: A 206 ARG cc_start: 0.7358 (tpt-90) cc_final: 0.6945 (tpt-90) REVERT: A 287 MET cc_start: 0.6288 (tpt) cc_final: 0.6003 (tpp) REVERT: B 44 MET cc_start: 0.7408 (pmm) cc_final: 0.6922 (pmm) REVERT: B 48 MET cc_start: 0.7747 (mtm) cc_final: 0.6762 (mtm) REVERT: B 142 LYS cc_start: 0.9220 (mmmm) cc_final: 0.8870 (mmmm) REVERT: B 182 MET cc_start: 0.8784 (pmm) cc_final: 0.8541 (pmm) REVERT: B 333 ARG cc_start: 0.7883 (ttm-80) cc_final: 0.7552 (ttm-80) REVERT: B 550 PHE cc_start: 0.8747 (p90) cc_final: 0.8141 (p90) REVERT: D 11 ASP cc_start: 0.7959 (p0) cc_final: 0.7624 (p0) REVERT: D 45 GLU cc_start: 0.9103 (mp0) cc_final: 0.8578 (mp0) REVERT: D 78 LEU cc_start: 0.8754 (mt) cc_final: 0.8536 (mt) REVERT: D 118 ASN cc_start: 0.8846 (t0) cc_final: 0.8188 (p0) REVERT: J 261 MET cc_start: 0.7319 (mtm) cc_final: 0.6856 (mtm) REVERT: K 32 MET cc_start: 0.7576 (tmm) cc_final: 0.7292 (tmm) REVERT: K 61 MET cc_start: 0.9024 (ppp) cc_final: 0.8120 (ppp) REVERT: K 163 ASN cc_start: 0.8403 (t0) cc_final: 0.8075 (t0) REVERT: Q 1421 ARG cc_start: 0.8925 (mtm-85) cc_final: 0.8427 (mtm110) REVERT: Q 1427 LYS cc_start: 0.6344 (mmtt) cc_final: 0.5959 (mttt) REVERT: U 75 LYS cc_start: 0.9088 (mmmm) cc_final: 0.8836 (mmmm) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.1323 time to fit residues: 50.1853 Evaluate side-chains 205 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 127 optimal weight: 5.9990 chunk 213 optimal weight: 0.6980 chunk 194 optimal weight: 20.0000 chunk 142 optimal weight: 5.9990 chunk 217 optimal weight: 7.9990 chunk 41 optimal weight: 20.0000 chunk 144 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 63 optimal weight: 50.0000 chunk 143 optimal weight: 8.9990 chunk 149 optimal weight: 9.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN J 191 GLN K 125 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.076380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.069202 restraints weight = 98248.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.070981 restraints weight = 63730.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.072045 restraints weight = 39426.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.072658 restraints weight = 28245.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.073067 restraints weight = 20966.008| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16273 Z= 0.194 Angle : 0.723 12.413 21969 Z= 0.372 Chirality : 0.048 0.272 2239 Planarity : 0.005 0.053 3015 Dihedral : 5.730 42.269 2397 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -2.59 (0.17), residues: 2203 helix: -0.54 (0.34), residues: 217 sheet: -1.39 (0.20), residues: 639 loop : -2.18 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 191 TYR 0.030 0.002 TYR A 137 PHE 0.019 0.002 PHE B 294 TRP 0.041 0.003 TRP A 207 HIS 0.004 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00435 (16273) covalent geometry : angle 0.72323 (21969) hydrogen bonds : bond 0.03302 ( 363) hydrogen bonds : angle 6.62750 ( 951) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4406 Ramachandran restraints generated. 2203 Oldfield, 0 Emsley, 2203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 MET cc_start: 0.7674 (ttp) cc_final: 0.7312 (ttp) REVERT: A 203 LEU cc_start: 0.8777 (tp) cc_final: 0.8485 (tp) REVERT: A 206 ARG cc_start: 0.7414 (tpt-90) cc_final: 0.7095 (tpt-90) REVERT: B 44 MET cc_start: 0.7315 (pmm) cc_final: 0.6853 (pmm) REVERT: B 48 MET cc_start: 0.7813 (mtm) cc_final: 0.6737 (mtm) REVERT: B 142 LYS cc_start: 0.9229 (mmmm) cc_final: 0.8893 (mmmm) REVERT: B 182 MET cc_start: 0.8784 (pmm) cc_final: 0.8521 (pmm) REVERT: B 333 ARG cc_start: 0.7873 (ttm-80) cc_final: 0.7555 (ttm-80) REVERT: D 11 ASP cc_start: 0.7948 (p0) cc_final: 0.7625 (p0) REVERT: D 45 GLU cc_start: 0.9105 (mp0) cc_final: 0.8625 (mp0) REVERT: D 78 LEU cc_start: 0.8749 (mt) cc_final: 0.8549 (mt) REVERT: D 118 ASN cc_start: 0.8844 (t0) cc_final: 0.8198 (p0) REVERT: D 189 PHE cc_start: 0.7994 (m-80) cc_final: 0.7762 (m-80) REVERT: D 193 PHE cc_start: 0.8269 (p90) cc_final: 0.7815 (p90) REVERT: D 195 GLU cc_start: 0.6725 (mm-30) cc_final: 0.6218 (mm-30) REVERT: J 212 MET cc_start: 0.7528 (tpp) cc_final: 0.6554 (ttp) REVERT: J 261 MET cc_start: 0.7321 (mtm) cc_final: 0.6349 (mtm) REVERT: K 32 MET cc_start: 0.7570 (tmm) cc_final: 0.7334 (tmm) REVERT: K 61 MET cc_start: 0.9093 (ppp) cc_final: 0.8296 (ppp) REVERT: K 163 ASN cc_start: 0.8465 (t0) cc_final: 0.8157 (t0) REVERT: K 180 GLU cc_start: 0.8463 (tp30) cc_final: 0.8150 (tp30) REVERT: Q 1421 ARG cc_start: 0.8913 (mtm-85) cc_final: 0.8438 (mtm110) REVERT: U 75 LYS cc_start: 0.9043 (mmmm) cc_final: 0.8672 (mmmm) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.1366 time to fit residues: 50.9943 Evaluate side-chains 203 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 161 optimal weight: 8.9990 chunk 143 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 135 optimal weight: 0.7980 chunk 54 optimal weight: 50.0000 chunk 214 optimal weight: 0.0070 chunk 61 optimal weight: 40.0000 chunk 91 optimal weight: 5.9990 chunk 35 optimal weight: 0.0970 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN A 402 ASN ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN K 125 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.079234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.071683 restraints weight = 95773.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.073695 restraints weight = 60581.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.074524 restraints weight = 38205.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.075549 restraints weight = 26236.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.075728 restraints weight = 18898.884| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.5009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16273 Z= 0.118 Angle : 0.680 12.523 21969 Z= 0.346 Chirality : 0.047 0.250 2239 Planarity : 0.004 0.055 3015 Dihedral : 5.370 49.480 2397 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -2.40 (0.17), residues: 2203 helix: -0.32 (0.35), residues: 220 sheet: -1.27 (0.20), residues: 671 loop : -2.06 (0.16), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 20 TYR 0.022 0.001 TYR A 137 PHE 0.015 0.001 PHE B 294 TRP 0.043 0.002 TRP A 207 HIS 0.007 0.001 HIS D 96 Details of bonding type rmsd covalent geometry : bond 0.00265 (16273) covalent geometry : angle 0.67999 (21969) hydrogen bonds : bond 0.02997 ( 363) hydrogen bonds : angle 6.36482 ( 951) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2965.29 seconds wall clock time: 52 minutes 12.07 seconds (3132.07 seconds total)