Starting phenix.real_space_refine on Sat Jun 14 10:56:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vjh_43281/06_2025/8vjh_43281.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vjh_43281/06_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_43281/06_2025/8vjh_43281.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vjh_43281/06_2025/8vjh_43281.map" model { file = "/net/cci-nas-00/data/ceres_data/8vjh_43281/06_2025/8vjh_43281.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vjh_43281/06_2025/8vjh_43281.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 14, 'HIS:plan': 5, 'TYR:plan': 18, 'ASN:plan1': 15, 'TRP:plan': 9, 'ASP:plan': 29, 'PHE:plan': 10, 'GLU:plan': 21, 'ARG:plan': 19} 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: 12.91, per 1000 atoms: 0.81 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: 4.56 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 2.09 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: 5.67 Time building geometry restraints manager: 5.35 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: 56.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.710 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 42.950 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.400 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.019 0.001 TRP B 177 HIS 0.004 0.001 HIS B 234 PHE 0.030 0.001 PHE B 294 TYR 0.029 0.001 TYR B 379 ARG 0.011 0.001 ARG J 176 Details of bonding type rmsd hydrogen bonds : bond 0.23876 ( 363) hydrogen bonds : angle 10.59596 ( 951) covalent geometry : bond 0.00261 (16273) covalent geometry : angle 0.59648 (21969) *********************** 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 : 1.748 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: 0.5133 (mmm) REVERT: A 173 TYR cc_start: 0.8269 (t80) cc_final: 0.8018 (t80) REVERT: A 196 LEU cc_start: 0.9446 (mt) cc_final: 0.9176 (mt) REVERT: A 203 LEU cc_start: 0.8787 (tp) cc_final: 0.8506 (tp) REVERT: B 13 PHE cc_start: 0.7647 (t80) cc_final: 0.7247 (t80) REVERT: B 194 ILE cc_start: 0.8230 (mm) cc_final: 0.7998 (mm) REVERT: B 524 LEU cc_start: 0.8805 (tp) cc_final: 0.8540 (tt) REVERT: B 545 LEU cc_start: 0.8652 (mp) cc_final: 0.8429 (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: 0.8778 (tp30) REVERT: D 118 ASN cc_start: 0.8664 (t0) cc_final: 0.8186 (p0) REVERT: J 1 MET cc_start: 0.2617 (mtt) cc_final: 0.2253 (mtm) REVERT: J 229 LYS cc_start: 0.7305 (ptpt) cc_final: 0.7017 (pttt) REVERT: K 16 VAL cc_start: 0.9382 (t) cc_final: 0.9030 (p) REVERT: K 112 MET cc_start: 0.7726 (pmm) cc_final: 0.7285 (ppp) REVERT: K 192 ILE cc_start: 0.9284 (mm) cc_final: 0.9059 (tp) REVERT: K 209 LYS cc_start: 0.6635 (tptt) cc_final: 0.5981 (mmtt) REVERT: K 222 ASP cc_start: 0.8306 (t0) cc_final: 0.8000 (t0) REVERT: K 261 MET cc_start: 0.7210 (ptp) cc_final: 0.6954 (ttt) REVERT: Q 1421 ARG cc_start: 0.9020 (mtm-85) cc_final: 0.8388 (mtm-85) REVERT: Q 1422 ASN cc_start: 0.8890 (m-40) cc_final: 0.7952 (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: 0.8431 (mmm) REVERT: U 67 LYS cc_start: 0.6341 (mtpt) cc_final: 0.5612 (ttpt) outliers start: 5 outliers final: 0 residues processed: 416 average time/residue: 0.2936 time to fit residues: 176.5593 Evaluate side-chains 239 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 6.9990 chunk 165 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 56 optimal weight: 40.0000 chunk 111 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 chunk 170 optimal weight: 9.9990 chunk 66 optimal weight: 40.0000 chunk 103 optimal weight: 0.0370 chunk 127 optimal weight: 9.9990 chunk 197 optimal weight: 3.9990 overall best weight: 6.0066 ------------------------------------------------------------------------------- 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 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.076926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.069304 restraints weight = 96003.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.071340 restraints weight = 61376.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.072197 restraints weight = 37199.328| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 16273 Z= 0.262 Angle : 0.754 11.169 21969 Z= 0.399 Chirality : 0.051 0.212 2239 Planarity : 0.006 0.064 3015 Dihedral : 6.004 43.611 2397 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.17), residues: 2203 helix: -0.72 (0.33), residues: 221 sheet: -1.62 (0.19), residues: 654 loop : -2.22 (0.16), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 142 HIS 0.006 0.002 HIS B 358 PHE 0.025 0.002 PHE J 108 TYR 0.025 0.002 TYR B 55 ARG 0.006 0.001 ARG A 125 Details of bonding type rmsd hydrogen bonds : bond 0.04495 ( 363) hydrogen bonds : angle 7.87810 ( 951) covalent geometry : bond 0.00559 (16273) covalent geometry : angle 0.75422 (21969) *********************** 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 300 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 2.239 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 173 TYR cc_start: 0.8482 (t80) cc_final: 0.8232 (t80) REVERT: A 203 LEU cc_start: 0.8919 (tp) cc_final: 0.8583 (tp) REVERT: A 242 ILE cc_start: 0.7971 (mp) cc_final: 0.7616 (mt) REVERT: A 277 GLU cc_start: 0.7780 (tp30) cc_final: 0.7548 (tp30) REVERT: B 50 LEU cc_start: 0.9157 (mp) cc_final: 0.8861 (mp) REVERT: B 119 ARG cc_start: 0.8663 (tmm160) cc_final: 0.8288 (tmm160) REVERT: B 524 LEU cc_start: 0.9085 (tp) cc_final: 0.8784 (tt) REVERT: B 550 PHE cc_start: 0.8591 (p90) cc_final: 0.7707 (p90) REVERT: D 11 ASP cc_start: 0.8299 (p0) cc_final: 0.8061 (p0) REVERT: D 118 ASN cc_start: 0.8860 (t0) cc_final: 0.8359 (p0) REVERT: D 230 ILE cc_start: 0.8332 (mt) cc_final: 0.8017 (tt) REVERT: J 1 MET cc_start: 0.3015 (mtt) cc_final: 0.2578 (mtm) REVERT: J 39 GLU cc_start: 0.8596 (mp0) cc_final: 0.8365 (mp0) REVERT: J 61 MET cc_start: 0.7709 (tmm) cc_final: 0.7473 (tmm) REVERT: J 173 GLU cc_start: 0.8794 (pp20) cc_final: 0.8486 (pp20) REVERT: J 229 LYS cc_start: 0.7190 (ptpt) cc_final: 0.6924 (pttt) REVERT: K 16 VAL cc_start: 0.9472 (t) cc_final: 0.9108 (p) REVERT: K 112 MET cc_start: 0.8092 (pmm) cc_final: 0.7455 (ppp) REVERT: K 180 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8423 (mm-30) REVERT: K 192 ILE cc_start: 0.9392 (mm) cc_final: 0.9135 (tp) REVERT: K 209 LYS cc_start: 0.6594 (tptt) cc_final: 0.5413 (mmtt) REVERT: K 212 MET cc_start: 0.8784 (ttt) cc_final: 0.8290 (ttt) REVERT: K 254 MET cc_start: 0.8078 (ptt) cc_final: 0.7875 (ptt) REVERT: Q 1406 MET cc_start: 0.9031 (tpp) cc_final: 0.8753 (tpp) REVERT: Q 1421 ARG cc_start: 0.9017 (mtm-85) cc_final: 0.8096 (mmp-170) REVERT: Q 1427 LYS cc_start: 0.6343 (mmtt) cc_final: 0.5873 (mttt) REVERT: U 67 LYS cc_start: 0.6793 (mtpt) cc_final: 0.5769 (ttpt) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.3360 time to fit residues: 153.0031 Evaluate side-chains 215 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 3.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 187 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 160 optimal weight: 3.9990 chunk 131 optimal weight: 8.9990 chunk 134 optimal weight: 10.0000 chunk 149 optimal weight: 0.3980 chunk 174 optimal weight: 0.9980 chunk 190 optimal weight: 8.9990 chunk 217 optimal weight: 5.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 208 ASN A 291 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 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 22 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.078520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.070877 restraints weight = 91541.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.072799 restraints weight = 59908.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.073781 restraints weight = 36802.306| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16273 Z= 0.160 Angle : 0.654 10.535 21969 Z= 0.345 Chirality : 0.048 0.189 2239 Planarity : 0.004 0.052 3015 Dihedral : 5.757 51.333 2397 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.17), residues: 2203 helix: -0.51 (0.35), residues: 217 sheet: -1.56 (0.20), residues: 658 loop : -2.09 (0.16), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 207 HIS 0.004 0.001 HIS A 223 PHE 0.017 0.002 PHE U 61 TYR 0.018 0.002 TYR B 55 ARG 0.010 0.001 ARG K 59 Details of bonding type rmsd hydrogen bonds : bond 0.03693 ( 363) hydrogen bonds : angle 7.21774 ( 951) covalent geometry : bond 0.00344 (16273) covalent geometry : angle 0.65359 (21969) *********************** 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 : 1.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8124 (tmm) cc_final: 0.7548 (tmm) REVERT: A 173 TYR cc_start: 0.8463 (t80) cc_final: 0.8103 (t80) REVERT: A 203 LEU cc_start: 0.8933 (tp) cc_final: 0.8611 (tp) REVERT: A 277 GLU cc_start: 0.7661 (tp30) cc_final: 0.7460 (tp30) REVERT: B 119 ARG cc_start: 0.8582 (tmm160) cc_final: 0.8249 (tmm160) REVERT: B 470 LYS cc_start: 0.8982 (mptt) cc_final: 0.8773 (mptt) REVERT: B 524 LEU cc_start: 0.8974 (tp) cc_final: 0.8722 (tt) REVERT: B 550 PHE cc_start: 0.8569 (p90) cc_final: 0.8084 (p90) REVERT: D 11 ASP cc_start: 0.8292 (p0) cc_final: 0.8044 (p0) REVERT: D 18 MET cc_start: 0.8341 (mtm) cc_final: 0.8074 (mtm) REVERT: D 118 ASN cc_start: 0.8826 (t0) cc_final: 0.8263 (p0) REVERT: D 189 PHE cc_start: 0.8030 (m-80) cc_final: 0.7815 (m-80) REVERT: D 230 ILE cc_start: 0.8337 (mt) cc_final: 0.7983 (tt) REVERT: J 1 MET cc_start: 0.3122 (mtt) cc_final: 0.2751 (mtt) REVERT: J 61 MET cc_start: 0.7770 (tmm) cc_final: 0.7441 (tmm) REVERT: K 16 VAL cc_start: 0.9232 (t) cc_final: 0.8988 (p) REVERT: K 112 MET cc_start: 0.7900 (pmm) cc_final: 0.7450 (ppp) REVERT: K 192 ILE cc_start: 0.9360 (mm) cc_final: 0.9148 (tp) REVERT: K 209 LYS cc_start: 0.6527 (tptt) cc_final: 0.5225 (mmtt) REVERT: K 212 MET cc_start: 0.8725 (ttt) cc_final: 0.8366 (ttt) REVERT: Q 1406 MET cc_start: 0.8987 (tpp) cc_final: 0.8713 (tpp) REVERT: Q 1421 ARG cc_start: 0.8967 (mtm-85) cc_final: 0.8035 (mmp-170) REVERT: Q 1427 LYS cc_start: 0.6281 (mmtt) cc_final: 0.5916 (mttt) outliers start: 0 outliers final: 0 residues processed: 294 average time/residue: 0.2852 time to fit residues: 123.8988 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 : 1.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 52 optimal weight: 9.9990 chunk 46 optimal weight: 0.8980 chunk 212 optimal weight: 10.0000 chunk 85 optimal weight: 0.5980 chunk 148 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 49 optimal weight: 50.0000 chunk 159 optimal weight: 6.9990 chunk 164 optimal weight: 0.0000 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 8 ASN ** K 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.078499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.070852 restraints weight = 92153.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.072804 restraints weight = 61288.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.073766 restraints weight = 37424.640| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16273 Z= 0.147 Angle : 0.636 10.730 21969 Z= 0.332 Chirality : 0.048 0.184 2239 Planarity : 0.004 0.052 3015 Dihedral : 5.546 50.577 2397 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.17), residues: 2203 helix: -0.37 (0.35), residues: 217 sheet: -1.53 (0.20), residues: 651 loop : -2.00 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 207 HIS 0.004 0.001 HIS B 358 PHE 0.026 0.002 PHE J 89 TYR 0.017 0.002 TYR B 102 ARG 0.004 0.001 ARG D 163 Details of bonding type rmsd hydrogen bonds : bond 0.03260 ( 363) hydrogen bonds : angle 6.83107 ( 951) covalent geometry : bond 0.00337 (16273) covalent geometry : angle 0.63577 (21969) *********************** 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 283 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 2.871 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: 0.4988 (mmm) cc_final: 0.4523 (mmm) REVERT: A 90 MET cc_start: 0.8138 (tmm) cc_final: 0.7581 (tmm) REVERT: A 160 MET cc_start: 0.7799 (ttp) cc_final: 0.7354 (ttp) REVERT: A 203 LEU cc_start: 0.8894 (tp) cc_final: 0.8609 (tp) REVERT: A 277 GLU cc_start: 0.7679 (tp30) cc_final: 0.7442 (tp30) REVERT: B 58 VAL cc_start: 0.8969 (t) cc_final: 0.8597 (t) REVERT: B 60 TYR cc_start: 0.6834 (t80) cc_final: 0.5985 (m-80) REVERT: B 93 ASP cc_start: 0.8900 (m-30) cc_final: 0.8293 (t0) REVERT: B 119 ARG cc_start: 0.8487 (tmm160) cc_final: 0.8232 (tmm160) REVERT: B 333 ARG cc_start: 0.7790 (ttm-80) cc_final: 0.7179 (ttm-80) REVERT: B 524 LEU cc_start: 0.8949 (tp) cc_final: 0.8743 (tt) REVERT: D 11 ASP cc_start: 0.8249 (p0) cc_final: 0.7994 (p0) REVERT: D 45 GLU cc_start: 0.9062 (mp0) cc_final: 0.8741 (mp0) REVERT: D 94 ARG cc_start: 0.6638 (mtp180) cc_final: 0.6155 (mtp180) REVERT: D 115 GLN cc_start: 0.8253 (mp-120) cc_final: 0.5927 (tt0) REVERT: D 118 ASN cc_start: 0.8877 (t0) cc_final: 0.8303 (p0) REVERT: D 163 ARG cc_start: 0.8190 (mmm-85) cc_final: 0.7929 (mpt180) REVERT: D 230 ILE cc_start: 0.8356 (mt) cc_final: 0.7997 (tt) REVERT: J 1 MET cc_start: 0.3117 (mtt) cc_final: 0.2882 (mtt) REVERT: J 39 GLU cc_start: 0.8450 (mp0) cc_final: 0.8183 (mp0) REVERT: J 61 MET cc_start: 0.7720 (tmm) cc_final: 0.7440 (tmm) REVERT: K 16 VAL cc_start: 0.9271 (t) cc_final: 0.9014 (p) REVERT: K 18 PHE cc_start: 0.8729 (t80) cc_final: 0.8512 (t80) REVERT: K 32 MET cc_start: 0.7408 (tmm) cc_final: 0.7046 (tmm) REVERT: K 61 MET cc_start: 0.8141 (ppp) cc_final: 0.7727 (ppp) REVERT: K 87 LEU cc_start: 0.8834 (mt) cc_final: 0.8625 (mt) REVERT: K 163 ASN cc_start: 0.8509 (t0) cc_final: 0.8074 (t0) REVERT: K 192 ILE cc_start: 0.9302 (mm) cc_final: 0.9024 (tp) REVERT: K 212 MET cc_start: 0.8762 (ttt) cc_final: 0.8413 (ttt) REVERT: Q 1406 MET cc_start: 0.8937 (tpp) cc_final: 0.8707 (tpp) REVERT: Q 1421 ARG cc_start: 0.8963 (mtm-85) cc_final: 0.8336 (mtm110) REVERT: Q 1427 LYS cc_start: 0.6410 (mmtt) cc_final: 0.6033 (mttt) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.3880 time to fit residues: 161.5289 Evaluate side-chains 215 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 2.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 210 optimal weight: 0.9980 chunk 81 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 179 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 75 optimal weight: 30.0000 chunk 118 optimal weight: 10.0000 chunk 182 optimal weight: 9.9990 chunk 190 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 136 optimal weight: 0.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.079018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.071176 restraints weight = 94416.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.073207 restraints weight = 60136.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.074240 restraints weight = 36869.555| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16273 Z= 0.132 Angle : 0.628 10.850 21969 Z= 0.327 Chirality : 0.048 0.263 2239 Planarity : 0.004 0.053 3015 Dihedral : 5.384 52.473 2397 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.17), residues: 2203 helix: -0.23 (0.36), residues: 219 sheet: -1.47 (0.20), residues: 661 loop : -1.97 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP A 207 HIS 0.003 0.001 HIS B 358 PHE 0.018 0.002 PHE U 61 TYR 0.021 0.001 TYR A 173 ARG 0.003 0.000 ARG B 195 Details of bonding type rmsd hydrogen bonds : bond 0.03130 ( 363) hydrogen bonds : angle 6.53599 ( 951) covalent geometry : bond 0.00298 (16273) covalent geometry : angle 0.62804 (21969) *********************** 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 285 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 1.979 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: A 90 MET cc_start: 0.8121 (tmm) cc_final: 0.7613 (tmm) REVERT: A 126 ARG cc_start: 0.8389 (ttt180) cc_final: 0.7992 (ttt180) REVERT: A 145 MET cc_start: 0.8388 (ptm) cc_final: 0.8064 (ptm) REVERT: A 203 LEU cc_start: 0.8878 (tp) cc_final: 0.8557 (tp) REVERT: A 277 GLU cc_start: 0.7711 (tp30) cc_final: 0.7452 (tp30) REVERT: B 44 MET cc_start: 0.6809 (pmm) cc_final: 0.6493 (pmm) REVERT: B 48 MET cc_start: 0.7787 (mtm) cc_final: 0.7398 (mtm) REVERT: B 50 LEU cc_start: 0.9155 (mp) cc_final: 0.8818 (mp) REVERT: B 93 ASP cc_start: 0.9073 (m-30) cc_final: 0.8403 (t0) REVERT: B 119 ARG cc_start: 0.8611 (tmm160) cc_final: 0.8169 (tmm160) REVERT: B 161 PHE cc_start: 0.8015 (t80) cc_final: 0.7772 (t80) REVERT: B 333 ARG cc_start: 0.7868 (ttm-80) cc_final: 0.7281 (ttm-80) REVERT: D 11 ASP cc_start: 0.8273 (p0) cc_final: 0.8067 (p0) REVERT: D 45 GLU cc_start: 0.9112 (mp0) cc_final: 0.8757 (mp0) REVERT: D 115 GLN cc_start: 0.8220 (mp-120) cc_final: 0.5886 (tt0) REVERT: D 118 ASN cc_start: 0.8875 (t0) cc_final: 0.8244 (p0) REVERT: D 230 ILE cc_start: 0.8293 (mt) cc_final: 0.7903 (tt) REVERT: J 39 GLU cc_start: 0.8536 (mp0) cc_final: 0.8301 (mp0) REVERT: J 61 MET cc_start: 0.7709 (tmm) cc_final: 0.7378 (tmm) REVERT: K 18 PHE cc_start: 0.8838 (t80) cc_final: 0.8624 (t80) REVERT: K 163 ASN cc_start: 0.8502 (t0) cc_final: 0.8046 (t0) REVERT: K 192 ILE cc_start: 0.9395 (mm) cc_final: 0.9031 (tp) REVERT: K 212 MET cc_start: 0.8878 (ttt) cc_final: 0.8458 (ttt) REVERT: Q 1421 ARG cc_start: 0.8926 (mtm-85) cc_final: 0.8291 (mtm110) REVERT: Q 1427 LYS cc_start: 0.6406 (mmtt) cc_final: 0.6018 (mttt) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.2984 time to fit residues: 124.0387 Evaluate side-chains 210 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 1.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 29 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 41 optimal weight: 20.0000 chunk 117 optimal weight: 8.9990 chunk 24 optimal weight: 0.6980 chunk 47 optimal weight: 30.0000 chunk 174 optimal weight: 9.9990 chunk 142 optimal weight: 0.0870 chunk 148 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 136 optimal weight: 4.9990 overall best weight: 2.5564 ------------------------------------------------------------------------------- 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 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN K 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.078665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.070981 restraints weight = 93491.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.073018 restraints weight = 61040.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.074027 restraints weight = 36459.824| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16273 Z= 0.146 Angle : 0.649 11.463 21969 Z= 0.333 Chirality : 0.048 0.216 2239 Planarity : 0.004 0.080 3015 Dihedral : 5.339 50.740 2397 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.17), residues: 2203 helix: -0.39 (0.35), residues: 221 sheet: -1.47 (0.19), residues: 695 loop : -1.96 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP A 207 HIS 0.003 0.001 HIS A 158 PHE 0.021 0.002 PHE J 18 TYR 0.022 0.002 TYR A 173 ARG 0.010 0.001 ARG A 206 Details of bonding type rmsd hydrogen bonds : bond 0.03010 ( 363) hydrogen bonds : angle 6.48545 ( 951) covalent geometry : bond 0.00336 (16273) covalent geometry : angle 0.64916 (21969) *********************** 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 273 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 2.685 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: A 90 MET cc_start: 0.8130 (tmm) cc_final: 0.7622 (tmm) REVERT: A 160 MET cc_start: 0.7935 (ttp) cc_final: 0.7574 (ttp) REVERT: A 203 LEU cc_start: 0.8816 (tp) cc_final: 0.8470 (tp) REVERT: A 206 ARG cc_start: 0.6775 (tpt-90) cc_final: 0.6451 (tpt-90) REVERT: A 277 GLU cc_start: 0.7736 (tp30) cc_final: 0.7432 (tp30) REVERT: B 48 MET cc_start: 0.7730 (mtm) cc_final: 0.7460 (mtm) REVERT: B 119 ARG cc_start: 0.8530 (tmm160) cc_final: 0.8187 (tmm160) REVERT: B 333 ARG cc_start: 0.7852 (ttm-80) cc_final: 0.7278 (ttm-80) REVERT: D 11 ASP cc_start: 0.8154 (p0) cc_final: 0.7888 (p0) REVERT: D 45 GLU cc_start: 0.9117 (mp0) cc_final: 0.8667 (mp0) REVERT: D 115 GLN cc_start: 0.8229 (mp-120) cc_final: 0.5891 (tt0) REVERT: D 118 ASN cc_start: 0.8867 (t0) cc_final: 0.8401 (t0) REVERT: D 230 ILE cc_start: 0.8312 (mt) cc_final: 0.7918 (tt) REVERT: J 61 MET cc_start: 0.7714 (tmm) cc_final: 0.7407 (tmm) REVERT: J 68 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6697 (tp30) REVERT: J 271 TYR cc_start: 0.8460 (m-80) cc_final: 0.8257 (m-10) REVERT: K 61 MET cc_start: 0.9072 (ppp) cc_final: 0.7389 (ppp) REVERT: K 106 GLU cc_start: 0.8229 (mt-10) cc_final: 0.8020 (mt-10) REVERT: K 163 ASN cc_start: 0.8481 (t0) cc_final: 0.8017 (t0) REVERT: K 212 MET cc_start: 0.8877 (ttt) cc_final: 0.8435 (ttt) REVERT: Q 1421 ARG cc_start: 0.8921 (mtm-85) cc_final: 0.8175 (mtm110) REVERT: Q 1427 LYS cc_start: 0.6408 (mmtt) cc_final: 0.6025 (mttt) REVERT: U 1 MET cc_start: 0.7243 (ppp) cc_final: 0.6737 (ppp) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.3188 time to fit residues: 128.9610 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 : 2.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 203 optimal weight: 0.0670 chunk 71 optimal weight: 0.0010 chunk 153 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 124 optimal weight: 20.0000 chunk 110 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 overall best weight: 2.6128 ------------------------------------------------------------------------------- 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 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 ASN J 191 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.078477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.070665 restraints weight = 94442.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.072710 restraints weight = 60338.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.073729 restraints weight = 36294.207| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16273 Z= 0.144 Angle : 0.661 14.364 21969 Z= 0.337 Chirality : 0.047 0.248 2239 Planarity : 0.004 0.060 3015 Dihedral : 5.298 49.780 2397 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.17), residues: 2203 helix: -0.42 (0.35), residues: 223 sheet: -1.32 (0.19), residues: 695 loop : -1.96 (0.16), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 207 HIS 0.004 0.001 HIS A 158 PHE 0.028 0.002 PHE J 89 TYR 0.037 0.002 TYR A 137 ARG 0.005 0.001 ARG A 177 Details of bonding type rmsd hydrogen bonds : bond 0.03075 ( 363) hydrogen bonds : angle 6.39866 ( 951) covalent geometry : bond 0.00327 (16273) covalent geometry : angle 0.66065 (21969) *********************** 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 275 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 2.536 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 20 MET cc_start: 0.7202 (ptm) cc_final: 0.6863 (ptt) REVERT: A 90 MET cc_start: 0.8221 (tmm) cc_final: 0.7690 (tmm) REVERT: A 203 LEU cc_start: 0.8825 (tp) cc_final: 0.8497 (tp) REVERT: B 44 MET cc_start: 0.6803 (pmm) cc_final: 0.6577 (pmm) REVERT: B 48 MET cc_start: 0.7807 (mtm) cc_final: 0.7596 (mtm) REVERT: B 119 ARG cc_start: 0.8555 (tmm160) cc_final: 0.8102 (tmm160) REVERT: B 142 LYS cc_start: 0.9202 (mmmm) cc_final: 0.8806 (mmmm) REVERT: B 333 ARG cc_start: 0.7891 (ttm-80) cc_final: 0.7280 (ttm-80) REVERT: B 362 LEU cc_start: 0.7508 (tp) cc_final: 0.6602 (tp) REVERT: B 550 PHE cc_start: 0.8786 (p90) cc_final: 0.8236 (p90) REVERT: D 11 ASP cc_start: 0.8260 (p0) cc_final: 0.8015 (p0) REVERT: D 45 GLU cc_start: 0.9119 (mp0) cc_final: 0.8670 (mp0) REVERT: D 115 GLN cc_start: 0.8293 (mp-120) cc_final: 0.6015 (tt0) REVERT: D 118 ASN cc_start: 0.8881 (t0) cc_final: 0.8399 (t0) REVERT: D 230 ILE cc_start: 0.8323 (mt) cc_final: 0.7910 (tt) REVERT: J 39 GLU cc_start: 0.8532 (mp0) cc_final: 0.8203 (mp0) REVERT: J 68 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6632 (tp30) REVERT: J 271 TYR cc_start: 0.8410 (m-80) cc_final: 0.8159 (m-10) REVERT: K 61 MET cc_start: 0.8740 (ppp) cc_final: 0.8256 (ppp) REVERT: K 163 ASN cc_start: 0.8518 (t0) cc_final: 0.8047 (t0) REVERT: K 192 ILE cc_start: 0.9405 (mm) cc_final: 0.9063 (tp) REVERT: Q 1421 ARG cc_start: 0.8918 (mtm-85) cc_final: 0.8234 (mtm110) REVERT: Q 1427 LYS cc_start: 0.6427 (mmtt) cc_final: 0.6040 (mttt) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.3362 time to fit residues: 138.1034 Evaluate side-chains 206 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 2.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 113 optimal weight: 0.5980 chunk 192 optimal weight: 8.9990 chunk 198 optimal weight: 8.9990 chunk 75 optimal weight: 50.0000 chunk 176 optimal weight: 9.9990 chunk 166 optimal weight: 5.9990 chunk 142 optimal weight: 0.0570 chunk 154 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 overall best weight: 2.3304 ------------------------------------------------------------------------------- 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 ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN J 191 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.078735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.071036 restraints weight = 93387.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.073116 restraints weight = 59668.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.073964 restraints weight = 36288.412| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16273 Z= 0.136 Angle : 0.650 12.061 21969 Z= 0.332 Chirality : 0.047 0.217 2239 Planarity : 0.004 0.054 3015 Dihedral : 5.222 49.354 2397 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.17), residues: 2203 helix: -0.41 (0.35), residues: 220 sheet: -1.28 (0.19), residues: 688 loop : -1.94 (0.16), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 207 HIS 0.003 0.001 HIS A 158 PHE 0.018 0.002 PHE U 61 TYR 0.028 0.002 TYR A 137 ARG 0.004 0.000 ARG J 27 Details of bonding type rmsd hydrogen bonds : bond 0.03037 ( 363) hydrogen bonds : angle 6.32054 ( 951) covalent geometry : bond 0.00310 (16273) covalent geometry : angle 0.64998 (21969) *********************** 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 271 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 3.838 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 20 MET cc_start: 0.6989 (ptm) cc_final: 0.6698 (ptt) REVERT: A 90 MET cc_start: 0.8259 (tmm) cc_final: 0.7722 (tmm) REVERT: A 160 MET cc_start: 0.7878 (ttp) cc_final: 0.7581 (ttp) REVERT: A 203 LEU cc_start: 0.8831 (tp) cc_final: 0.8504 (tp) REVERT: B 44 MET cc_start: 0.7027 (pmm) cc_final: 0.6768 (pmm) REVERT: B 119 ARG cc_start: 0.8584 (tmm160) cc_final: 0.8061 (tmm160) REVERT: B 142 LYS cc_start: 0.9206 (mmmm) cc_final: 0.8803 (mmmm) REVERT: B 333 ARG cc_start: 0.7860 (ttm-80) cc_final: 0.7499 (ttm-80) REVERT: B 362 LEU cc_start: 0.7529 (tp) cc_final: 0.6655 (tp) REVERT: B 550 PHE cc_start: 0.8779 (p90) cc_final: 0.8151 (p90) REVERT: D 11 ASP cc_start: 0.8335 (p0) cc_final: 0.8077 (p0) REVERT: D 45 GLU cc_start: 0.9164 (mp0) cc_final: 0.8694 (mp0) REVERT: D 115 GLN cc_start: 0.8291 (mp-120) cc_final: 0.6018 (tt0) REVERT: D 118 ASN cc_start: 0.8865 (t0) cc_final: 0.8406 (t0) REVERT: J 271 TYR cc_start: 0.8375 (m-80) cc_final: 0.8140 (m-10) REVERT: K 18 PHE cc_start: 0.8880 (t80) cc_final: 0.8667 (t80) REVERT: K 61 MET cc_start: 0.8736 (ppp) cc_final: 0.8328 (ppp) REVERT: K 163 ASN cc_start: 0.8511 (t0) cc_final: 0.8024 (t0) REVERT: K 180 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8449 (mm-30) REVERT: Q 1421 ARG cc_start: 0.8857 (mtm-85) cc_final: 0.8151 (mtm110) REVERT: Q 1427 LYS cc_start: 0.6403 (mmtt) cc_final: 0.6011 (mttt) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.3407 time to fit residues: 134.2130 Evaluate side-chains 198 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 107 optimal weight: 10.0000 chunk 202 optimal weight: 7.9990 chunk 178 optimal weight: 6.9990 chunk 204 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 162 optimal weight: 4.9990 chunk 141 optimal weight: 9.9990 chunk 212 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 14 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 GLN ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 7 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.076289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.068874 restraints weight = 96014.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.070895 restraints weight = 61478.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.071724 restraints weight = 38702.900| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16273 Z= 0.215 Angle : 0.719 11.976 21969 Z= 0.372 Chirality : 0.048 0.203 2239 Planarity : 0.005 0.055 3015 Dihedral : 5.615 45.114 2397 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.17), residues: 2203 helix: -0.68 (0.33), residues: 221 sheet: -1.39 (0.19), residues: 686 loop : -2.05 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.003 TRP A 207 HIS 0.004 0.001 HIS D 148 PHE 0.020 0.002 PHE B 381 TYR 0.024 0.002 TYR A 137 ARG 0.012 0.001 ARG A 209 Details of bonding type rmsd hydrogen bonds : bond 0.03316 ( 363) hydrogen bonds : angle 6.54800 ( 951) covalent geometry : bond 0.00474 (16273) covalent geometry : angle 0.71919 (21969) *********************** 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 254 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 2.103 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 20 MET cc_start: 0.7521 (ptm) cc_final: 0.7124 (ptt) REVERT: A 203 LEU cc_start: 0.8769 (tp) cc_final: 0.8401 (tp) REVERT: A 277 GLU cc_start: 0.7744 (tp30) cc_final: 0.7266 (tp30) REVERT: A 297 ASN cc_start: 0.8161 (t0) cc_final: 0.7774 (t0) REVERT: B 44 MET cc_start: 0.7215 (pmm) cc_final: 0.6875 (pmm) REVERT: B 48 MET cc_start: 0.7602 (mtm) cc_final: 0.6993 (mtm) REVERT: B 142 LYS cc_start: 0.9229 (mmmm) cc_final: 0.8869 (mmmm) REVERT: B 177 TRP cc_start: 0.7895 (m-90) cc_final: 0.7552 (m-90) REVERT: B 333 ARG cc_start: 0.7982 (ttm-80) cc_final: 0.7607 (ttm-80) REVERT: B 362 LEU cc_start: 0.7542 (tp) cc_final: 0.6640 (tp) REVERT: B 550 PHE cc_start: 0.8848 (p90) cc_final: 0.8313 (p90) REVERT: D 11 ASP cc_start: 0.8317 (p0) cc_final: 0.8037 (p0) REVERT: D 18 MET cc_start: 0.8053 (ttm) cc_final: 0.7800 (ttm) REVERT: D 45 GLU cc_start: 0.9244 (mp0) cc_final: 0.8754 (mp0) REVERT: J 271 TYR cc_start: 0.8480 (m-80) cc_final: 0.8234 (m-10) REVERT: K 61 MET cc_start: 0.8709 (ppp) cc_final: 0.8423 (ppp) REVERT: K 163 ASN cc_start: 0.8632 (t0) cc_final: 0.7937 (t0) REVERT: K 180 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8432 (mm-30) REVERT: Q 1421 ARG cc_start: 0.8929 (mtm-85) cc_final: 0.8388 (mtm110) REVERT: Q 1427 LYS cc_start: 0.6351 (mmtt) cc_final: 0.5951 (mttt) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.3281 time to fit residues: 125.0392 Evaluate side-chains 197 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 2.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 204 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 118 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 173 optimal weight: 0.0030 chunk 61 optimal weight: 20.0000 chunk 7 optimal weight: 8.9990 chunk 88 optimal weight: 7.9990 overall best weight: 4.3998 ------------------------------------------------------------------------------- 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 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN D 73 ASN K 191 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.076502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.069234 restraints weight = 96851.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.071168 restraints weight = 62983.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.071937 restraints weight = 40322.164| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16273 Z= 0.193 Angle : 0.710 12.215 21969 Z= 0.364 Chirality : 0.048 0.191 2239 Planarity : 0.004 0.056 3015 Dihedral : 5.655 47.160 2397 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.17), residues: 2203 helix: -0.67 (0.33), residues: 220 sheet: -1.40 (0.20), residues: 648 loop : -2.09 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.003 TRP A 207 HIS 0.003 0.001 HIS A 296 PHE 0.018 0.002 PHE B 294 TYR 0.026 0.002 TYR A 173 ARG 0.006 0.001 ARG B 195 Details of bonding type rmsd hydrogen bonds : bond 0.03225 ( 363) hydrogen bonds : angle 6.55678 ( 951) covalent geometry : bond 0.00430 (16273) covalent geometry : angle 0.71002 (21969) ********************** 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 255 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 2.048 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 203 LEU cc_start: 0.8778 (tp) cc_final: 0.8447 (tp) REVERT: A 277 GLU cc_start: 0.7767 (tp30) cc_final: 0.7327 (tp30) REVERT: A 297 ASN cc_start: 0.8190 (t0) cc_final: 0.7650 (t0) REVERT: B 44 MET cc_start: 0.7393 (pmm) cc_final: 0.7059 (pmm) REVERT: B 48 MET cc_start: 0.7438 (mtm) cc_final: 0.6856 (mtm) REVERT: B 93 ASP cc_start: 0.9017 (m-30) cc_final: 0.8332 (t0) REVERT: B 142 LYS cc_start: 0.9204 (mmmm) cc_final: 0.8854 (mmmm) REVERT: B 333 ARG cc_start: 0.7928 (ttm-80) cc_final: 0.7587 (ttm-80) REVERT: B 362 LEU cc_start: 0.7557 (tp) cc_final: 0.6709 (tp) REVERT: D 11 ASP cc_start: 0.8235 (p0) cc_final: 0.7956 (p0) REVERT: D 45 GLU cc_start: 0.9217 (mp0) cc_final: 0.8739 (mp0) REVERT: D 118 ASN cc_start: 0.8864 (t0) cc_final: 0.8194 (p0) REVERT: D 189 PHE cc_start: 0.8068 (m-80) cc_final: 0.7825 (m-80) REVERT: J 212 MET cc_start: 0.6943 (tmm) cc_final: 0.6647 (ttp) REVERT: K 180 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8395 (mm-30) REVERT: Q 1421 ARG cc_start: 0.8892 (mtm-85) cc_final: 0.8468 (mtm110) REVERT: Q 1427 LYS cc_start: 0.6317 (mmtt) cc_final: 0.5944 (mttt) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.3401 time to fit residues: 128.5738 Evaluate side-chains 198 residues out of total 1873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 2.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 90 optimal weight: 0.0570 chunk 173 optimal weight: 0.0060 chunk 11 optimal weight: 5.9990 chunk 139 optimal weight: 0.0980 chunk 183 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 169 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 74 optimal weight: 50.0000 chunk 89 optimal weight: 0.9980 chunk 151 optimal weight: 8.9990 overall best weight: 0.6316 ------------------------------------------------------------------------------- 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 ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.079355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.071986 restraints weight = 95062.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.073973 restraints weight = 62910.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.074790 restraints weight = 38593.857| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.4830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16273 Z= 0.116 Angle : 0.676 12.482 21969 Z= 0.341 Chirality : 0.047 0.180 2239 Planarity : 0.004 0.055 3015 Dihedral : 5.282 54.417 2397 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.17), residues: 2203 helix: -0.54 (0.34), residues: 227 sheet: -1.23 (0.20), residues: 662 loop : -1.92 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.002 TRP A 207 HIS 0.006 0.001 HIS D 96 PHE 0.029 0.002 PHE U 61 TYR 0.033 0.002 TYR A 173 ARG 0.007 0.000 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.02944 ( 363) hydrogen bonds : angle 6.21072 ( 951) covalent geometry : bond 0.00265 (16273) covalent geometry : angle 0.67646 (21969) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6981.23 seconds wall clock time: 127 minutes 24.33 seconds (7644.33 seconds total)