Starting phenix.real_space_refine on Mon Jul 28 06:21:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s82_19790/07_2025/8s82_19790.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s82_19790/07_2025/8s82_19790.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8s82_19790/07_2025/8s82_19790.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s82_19790/07_2025/8s82_19790.map" model { file = "/net/cci-nas-00/data/ceres_data/8s82_19790/07_2025/8s82_19790.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s82_19790/07_2025/8s82_19790.cif" } resolution = 2.92 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= 0.021 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 P 40 5.49 5 S 40 5.16 5 C 6306 2.51 5 N 1688 2.21 5 O 2054 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10128 Number of models: 1 Model: "" Number of chains: 4 Chain: "K" Number of atoms: 4616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4616 Classifications: {'peptide': 557} Link IDs: {'CIS': 2, 'PTRANS': 20, 'TRANS': 534} Chain: "L" Number of atoms: 4657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4657 Classifications: {'peptide': 587} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 559} Chain: "D" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 441 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "C" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 414 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Time building chain proxies: 8.47, per 1000 atoms: 0.84 Number of scatterers: 10128 At special positions: 0 Unit cell: (95.265, 109.719, 141.912, 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) S 40 16.00 P 40 15.00 O 2054 8.00 N 1688 7.00 C 6306 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: 2.39 Conformation dependent library (CDL) restraints added in 1.1 seconds 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2202 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 7 sheets defined 36.4% alpha, 19.9% beta 19 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 3.30 Creating SS restraints... Processing helix chain 'K' and resid 12 through 17 removed outlier: 3.608A pdb=" N PHE K 16 " --> pdb=" O SER K 12 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS K 17 " --> pdb=" O GLU K 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 12 through 17' Processing helix chain 'K' and resid 26 through 43 Processing helix chain 'K' and resid 77 through 93 Processing helix chain 'K' and resid 97 through 102 Processing helix chain 'K' and resid 114 through 128 removed outlier: 3.580A pdb=" N PHE K 126 " --> pdb=" O MET K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 150 through 154 removed outlier: 3.573A pdb=" N GLN K 154 " --> pdb=" O GLN K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 156 through 172 Processing helix chain 'K' and resid 190 through 198 removed outlier: 3.570A pdb=" N GLN K 198 " --> pdb=" O SER K 194 " (cutoff:3.500A) Processing helix chain 'K' and resid 225 through 232 removed outlier: 3.687A pdb=" N ARG K 232 " --> pdb=" O SER K 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 267 through 270 removed outlier: 3.806A pdb=" N VAL K 270 " --> pdb=" O LYS K 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 267 through 270' Processing helix chain 'K' and resid 318 through 328 removed outlier: 3.788A pdb=" N ILE K 324 " --> pdb=" O SER K 320 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA K 328 " --> pdb=" O ILE K 324 " (cutoff:3.500A) Processing helix chain 'K' and resid 369 through 384 Processing helix chain 'K' and resid 443 through 461 removed outlier: 4.028A pdb=" N TYR K 460 " --> pdb=" O SER K 456 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE K 461 " --> pdb=" O ILE K 457 " (cutoff:3.500A) Processing helix chain 'K' and resid 468 through 472 Processing helix chain 'K' and resid 474 through 490 Processing helix chain 'K' and resid 500 through 512 removed outlier: 3.589A pdb=" N LYS K 505 " --> pdb=" O PRO K 501 " (cutoff:3.500A) Processing helix chain 'K' and resid 513 through 529 removed outlier: 3.748A pdb=" N LYS K 517 " --> pdb=" O ASP K 513 " (cutoff:3.500A) Processing helix chain 'K' and resid 537 through 555 removed outlier: 3.827A pdb=" N LYS K 541 " --> pdb=" O GLN K 537 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL K 543 " --> pdb=" O LEU K 539 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE K 553 " --> pdb=" O PHE K 549 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP K 555 " --> pdb=" O LYS K 551 " (cutoff:3.500A) Processing helix chain 'L' and resid 12 through 18 removed outlier: 3.766A pdb=" N ASN L 18 " --> pdb=" O SER L 14 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 39 removed outlier: 4.080A pdb=" N LYS L 38 " --> pdb=" O ASN L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 93 Processing helix chain 'L' and resid 104 through 121 removed outlier: 3.724A pdb=" N CYS L 108 " --> pdb=" O SER L 104 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU L 109 " --> pdb=" O MET L 105 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU L 110 " --> pdb=" O ILE L 106 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL L 111 " --> pdb=" O GLN L 107 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE L 120 " --> pdb=" O ILE L 116 " (cutoff:3.500A) Processing helix chain 'L' and resid 142 through 153 removed outlier: 4.147A pdb=" N ASP L 147 " --> pdb=" O ASP L 143 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU L 148 " --> pdb=" O GLU L 144 " (cutoff:3.500A) Processing helix chain 'L' and resid 174 through 182 Processing helix chain 'L' and resid 190 through 199 removed outlier: 3.585A pdb=" N THR L 198 " --> pdb=" O LEU L 194 " (cutoff:3.500A) Processing helix chain 'L' and resid 220 through 225 Processing helix chain 'L' and resid 308 through 310 No H-bonds generated for 'chain 'L' and resid 308 through 310' Processing helix chain 'L' and resid 326 through 334 removed outlier: 3.806A pdb=" N VAL L 334 " --> pdb=" O VAL L 330 " (cutoff:3.500A) Processing helix chain 'L' and resid 353 through 357 removed outlier: 3.587A pdb=" N LEU L 357 " --> pdb=" O ARG L 354 " (cutoff:3.500A) Processing helix chain 'L' and resid 372 through 389 Processing helix chain 'L' and resid 467 through 480 Processing helix chain 'L' and resid 498 through 501 Processing helix chain 'L' and resid 512 through 516 removed outlier: 3.615A pdb=" N GLU L 516 " --> pdb=" O LYS L 513 " (cutoff:3.500A) Processing helix chain 'L' and resid 527 through 545 Processing helix chain 'L' and resid 558 through 564 removed outlier: 3.999A pdb=" N LYS L 564 " --> pdb=" O SER L 560 " (cutoff:3.500A) Processing helix chain 'L' and resid 576 through 583 Processing sheet with id=AA1, first strand: chain 'K' and resid 68 through 75 removed outlier: 6.373A pdb=" N CYS K 53 " --> pdb=" O LEU K 70 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ILE K 51 " --> pdb=" O PRO K 72 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ARG K 74 " --> pdb=" O THR K 49 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N THR K 49 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LYS K 139 " --> pdb=" O ASN K 175 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ALA K 177 " --> pdb=" O LYS K 139 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL K 141 " --> pdb=" O ALA K 177 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N PHE K 179 " --> pdb=" O VAL K 141 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU K 143 " --> pdb=" O PHE K 179 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE K 181 " --> pdb=" O LEU K 143 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N THR K 145 " --> pdb=" O ILE K 181 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE K 221 " --> pdb=" O THR K 178 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N PHE K 180 " --> pdb=" O ILE K 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 239 through 248 removed outlier: 7.718A pdb=" N MET K 240 " --> pdb=" O THR K 261 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N THR K 261 " --> pdb=" O MET K 240 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N GLN K 242 " --> pdb=" O GLY K 259 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLY K 259 " --> pdb=" O GLN K 242 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL K 257 " --> pdb=" O PRO K 244 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ILE K 246 " --> pdb=" O VAL K 255 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL K 255 " --> pdb=" O ILE K 246 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N LYS K 386 " --> pdb=" O PRO K 407 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N TRP K 391 " --> pdb=" O ILE K 338 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ILE K 338 " --> pdb=" O TRP K 391 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LYS K 393 " --> pdb=" O LEU K 336 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LEU K 336 " --> pdb=" O LYS K 393 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ASP K 248 " --> pdb=" O ILE K 338 " (cutoff:3.500A) removed outlier: 12.377A pdb=" N GLY K 340 " --> pdb=" O ASP K 248 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 302 through 307 removed outlier: 3.968A pdb=" N TYR L 281 " --> pdb=" O ILE L 307 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N HIS L 284 " --> pdb=" O GLU K 284 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLU K 284 " --> pdb=" O HIS L 284 " (cutoff:3.500A) removed outlier: 10.188A pdb=" N GLU L 286 " --> pdb=" O ARG K 282 " (cutoff:3.500A) removed outlier: 13.070A pdb=" N ARG K 282 " --> pdb=" O GLU L 286 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU K 274 " --> pdb=" O ALA K 285 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 314 through 315 Processing sheet with id=AA5, first strand: chain 'K' and resid 430 through 431 Processing sheet with id=AA6, first strand: chain 'L' and resid 64 through 71 removed outlier: 6.610A pdb=" N CYS L 47 " --> pdb=" O ILE L 67 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N SER L 69 " --> pdb=" O ILE L 45 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ILE L 45 " --> pdb=" O SER L 69 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU L 71 " --> pdb=" O ASP L 43 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ASP L 43 " --> pdb=" O LEU L 71 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLU L 3 " --> pdb=" O TRP L 44 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N SER L 46 " --> pdb=" O GLU L 3 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N THR L 5 " --> pdb=" O SER L 46 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N TYR L 48 " --> pdb=" O THR L 5 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N PHE L 7 " --> pdb=" O TYR L 48 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ALA L 50 " --> pdb=" O PHE L 7 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL L 9 " --> pdb=" O ALA L 50 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N SER L 4 " --> pdb=" O GLN L 128 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL L 130 " --> pdb=" O SER L 4 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N THR L 6 " --> pdb=" O VAL L 130 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N PHE L 132 " --> pdb=" O THR L 6 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE L 8 " --> pdb=" O PHE L 132 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ILE L 129 " --> pdb=" O ILE L 158 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ILE L 160 " --> pdb=" O ILE L 129 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL L 131 " --> pdb=" O ILE L 160 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 211 through 217 removed outlier: 3.537A pdb=" N PHE L 211 " --> pdb=" O ALA L 245 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ALA L 366 " --> pdb=" O LYS L 428 " (cutoff:3.500A) removed outlier: 9.526A pdb=" N LYS L 428 " --> pdb=" O ALA L 366 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N MET L 407 " --> pdb=" O LEU L 435 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N LYS L 391 " --> pdb=" O PRO L 412 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE L 392 " --> pdb=" O PHE L 346 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N PHE L 346 " --> pdb=" O ILE L 392 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL L 394 " --> pdb=" O ARG L 344 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N LEU L 341 " --> pdb=" O SER L 212 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLU L 214 " --> pdb=" O LEU L 341 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N LEU L 343 " --> pdb=" O GLU L 214 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ARG L 216 " --> pdb=" O LEU L 343 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N GLY L 345 " --> pdb=" O ARG L 216 " (cutoff:3.500A) 365 hydrogen bonds defined for protein. 1032 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 3.49 Time building geometry restraints manager: 2.88 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: 3056 1.34 - 1.46: 1779 1.46 - 1.57: 5428 1.57 - 1.69: 80 1.69 - 1.81: 65 Bond restraints: 10408 Sorted by residual: bond pdb=" N ARG K 289 " pdb=" CA ARG K 289 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.49e+00 bond pdb=" N PHE K 71 " pdb=" CA PHE K 71 " ideal model delta sigma weight residual 1.456 1.468 -0.012 1.04e-02 9.25e+03 1.39e+00 bond pdb=" CA GLY K 466 " pdb=" C GLY K 466 " ideal model delta sigma weight residual 1.520 1.507 0.013 1.10e-02 8.26e+03 1.33e+00 bond pdb=" C THR K 494 " pdb=" O THR K 494 " ideal model delta sigma weight residual 1.234 1.245 -0.011 1.00e-02 1.00e+04 1.19e+00 bond pdb=" CA ILE K 67 " pdb=" CB ILE K 67 " ideal model delta sigma weight residual 1.540 1.526 0.015 1.36e-02 5.41e+03 1.15e+00 ... (remaining 10403 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 13883 1.72 - 3.45: 322 3.45 - 5.17: 23 5.17 - 6.90: 4 6.90 - 8.62: 3 Bond angle restraints: 14235 Sorted by residual: angle pdb=" C LYS K 288 " pdb=" N ARG K 289 " pdb=" CA ARG K 289 " ideal model delta sigma weight residual 121.70 130.32 -8.62 1.80e+00 3.09e-01 2.29e+01 angle pdb=" C VAL L 208 " pdb=" N ARG L 209 " pdb=" CA ARG L 209 " ideal model delta sigma weight residual 121.54 129.76 -8.22 1.91e+00 2.74e-01 1.85e+01 angle pdb=" N GLU L 236 " pdb=" CA GLU L 236 " pdb=" C GLU L 236 " ideal model delta sigma weight residual 114.56 110.08 4.48 1.27e+00 6.20e-01 1.25e+01 angle pdb=" N VAL L 210 " pdb=" CA VAL L 210 " pdb=" C VAL L 210 " ideal model delta sigma weight residual 113.43 109.81 3.62 1.09e+00 8.42e-01 1.10e+01 angle pdb=" N VAL L 11 " pdb=" CA VAL L 11 " pdb=" C VAL L 11 " ideal model delta sigma weight residual 111.88 108.47 3.41 1.06e+00 8.90e-01 1.04e+01 ... (remaining 14230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 5592 17.88 - 35.75: 449 35.75 - 53.63: 176 53.63 - 71.51: 51 71.51 - 89.39: 4 Dihedral angle restraints: 6272 sinusoidal: 2876 harmonic: 3396 Sorted by residual: dihedral pdb=" N ARG K 289 " pdb=" C ARG K 289 " pdb=" CA ARG K 289 " pdb=" CB ARG K 289 " ideal model delta harmonic sigma weight residual 122.80 137.48 -14.68 0 2.50e+00 1.60e-01 3.45e+01 dihedral pdb=" C ARG K 289 " pdb=" N ARG K 289 " pdb=" CA ARG K 289 " pdb=" CB ARG K 289 " ideal model delta harmonic sigma weight residual -122.60 -136.22 13.62 0 2.50e+00 1.60e-01 2.97e+01 dihedral pdb=" CA TYR K 286 " pdb=" C TYR K 286 " pdb=" N SER K 287 " pdb=" CA SER K 287 " ideal model delta harmonic sigma weight residual -180.00 -160.36 -19.64 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 6269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 1582 0.114 - 0.229: 15 0.229 - 0.343: 0 0.343 - 0.457: 0 0.457 - 0.571: 1 Chirality restraints: 1598 Sorted by residual: chirality pdb=" CA ARG K 289 " pdb=" N ARG K 289 " pdb=" C ARG K 289 " pdb=" CB ARG K 289 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.16e+00 chirality pdb=" CA ILE L 364 " pdb=" N ILE L 364 " pdb=" C ILE L 364 " pdb=" CB ILE L 364 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.27e-01 chirality pdb=" CA ILE K 96 " pdb=" N ILE K 96 " pdb=" C ILE K 96 " pdb=" CB ILE K 96 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 1595 not shown) Planarity restraints: 1681 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE L 246 " -0.024 5.00e-02 4.00e+02 3.62e-02 2.09e+00 pdb=" N PRO L 247 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO L 247 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO L 247 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS K 243 " -0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO K 244 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO K 244 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO K 244 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN L 228 " 0.020 5.00e-02 4.00e+02 3.05e-02 1.49e+00 pdb=" N PRO L 229 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO L 229 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO L 229 " 0.017 5.00e-02 4.00e+02 ... (remaining 1678 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 136 2.64 - 3.20: 8896 3.20 - 3.77: 15442 3.77 - 4.33: 21603 4.33 - 4.90: 34919 Nonbonded interactions: 80996 Sorted by model distance: nonbonded pdb=" OH TYR K 467 " pdb=" O PRO L 436 " model vdw 2.070 3.040 nonbonded pdb=" O THR L 358 " pdb=" OG1 THR L 358 " model vdw 2.172 3.040 nonbonded pdb=" O VAL L 179 " pdb=" OG SER L 185 " model vdw 2.191 3.040 nonbonded pdb=" O TYR K 367 " pdb=" OG SER K 370 " model vdw 2.201 3.040 nonbonded pdb=" OE2 GLU L 3 " pdb=" OG1 THR L 505 " model vdw 2.229 3.040 ... (remaining 80991 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.140 Process input model: 30.280 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 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 : 0.004 0.035 10408 Z= 0.172 Angle : 0.633 8.620 14235 Z= 0.388 Chirality : 0.041 0.571 1598 Planarity : 0.004 0.036 1681 Dihedral : 15.567 89.386 4070 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.95 % Favored : 95.88 % Rotamer: Outliers : 6.48 % Allowed : 9.59 % Favored : 83.93 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.18 % 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: -0.53 (0.23), residues: 1140 helix: 1.07 (0.27), residues: 363 sheet: 0.14 (0.39), residues: 161 loop : -1.41 (0.22), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP K 391 HIS 0.003 0.001 HIS L 417 PHE 0.015 0.001 PHE K 71 TYR 0.013 0.001 TYR K 550 ARG 0.002 0.000 ARG L 354 Details of bonding type rmsd hydrogen bonds : bond 0.14974 ( 415) hydrogen bonds : angle 6.04587 ( 1132) covalent geometry : bond 0.00351 (10408) covalent geometry : angle 0.63322 (14235) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 172 time to evaluate : 1.036 Fit side-chains revert: symmetry clash REVERT: K 18 GLU cc_start: 0.8251 (mp0) cc_final: 0.7495 (tm-30) REVERT: K 114 ARG cc_start: 0.7877 (mtm110) cc_final: 0.7547 (mmp80) REVERT: K 152 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6948 (mp0) REVERT: K 154 GLN cc_start: 0.5888 (mm110) cc_final: 0.5672 (mm110) REVERT: K 218 THR cc_start: 0.8621 (p) cc_final: 0.8330 (m) REVERT: K 219 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7638 (tptt) REVERT: K 238 ARG cc_start: 0.7648 (ttp80) cc_final: 0.7330 (ttm-80) REVERT: K 289 ARG cc_start: 0.4528 (OUTLIER) cc_final: 0.1125 (mmm-85) REVERT: K 356 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7729 (mtmt) REVERT: K 446 ASP cc_start: 0.7115 (OUTLIER) cc_final: 0.6908 (t0) REVERT: K 513 ASP cc_start: 0.7837 (t0) cc_final: 0.7144 (m-30) REVERT: L 23 LYS cc_start: 0.8067 (mttt) cc_final: 0.7837 (mtmt) REVERT: L 88 GLN cc_start: 0.8627 (tt0) cc_final: 0.8416 (tt0) REVERT: L 164 LYS cc_start: 0.5800 (OUTLIER) cc_final: 0.5239 (mptm) REVERT: L 184 ASN cc_start: 0.7164 (m-40) cc_final: 0.6263 (t0) REVERT: L 243 VAL cc_start: 0.8114 (OUTLIER) cc_final: 0.7857 (t) REVERT: L 303 ILE cc_start: 0.6521 (OUTLIER) cc_final: 0.6290 (pp) REVERT: L 344 ARG cc_start: 0.5984 (mtm110) cc_final: 0.5677 (mtp85) REVERT: L 401 LYS cc_start: 0.7242 (OUTLIER) cc_final: 0.6479 (ttpt) REVERT: L 445 ASP cc_start: 0.7642 (m-30) cc_final: 0.7428 (m-30) outliers start: 69 outliers final: 28 residues processed: 229 average time/residue: 1.1843 time to fit residues: 291.8268 Evaluate side-chains 150 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 130 ILE Chi-restraints excluded: chain K residue 134 LYS Chi-restraints excluded: chain K residue 152 GLU Chi-restraints excluded: chain K residue 204 ASN Chi-restraints excluded: chain K residue 219 LYS Chi-restraints excluded: chain K residue 254 ILE Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 289 ARG Chi-restraints excluded: chain K residue 356 LYS Chi-restraints excluded: chain K residue 446 ASP Chi-restraints excluded: chain K residue 454 THR Chi-restraints excluded: chain K residue 506 ASP Chi-restraints excluded: chain K residue 544 LYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 164 LYS Chi-restraints excluded: chain L residue 243 VAL Chi-restraints excluded: chain L residue 283 ILE Chi-restraints excluded: chain L residue 292 VAL Chi-restraints excluded: chain L residue 303 ILE Chi-restraints excluded: chain L residue 328 VAL Chi-restraints excluded: chain L residue 333 THR Chi-restraints excluded: chain L residue 354 ARG Chi-restraints excluded: chain L residue 358 THR Chi-restraints excluded: chain L residue 401 LYS Chi-restraints excluded: chain L residue 467 HIS Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 487 GLU Chi-restraints excluded: chain L residue 497 ILE Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 546 ILE Chi-restraints excluded: chain L residue 578 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.5980 chunk 88 optimal weight: 0.0970 chunk 49 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 133 GLN K 204 ASN K 316 ASN K 455 GLN ** L 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 547 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.241183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.199293 restraints weight = 10656.438| |-----------------------------------------------------------------------------| r_work (start): 0.4364 rms_B_bonded: 2.25 r_work: 0.4020 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10408 Z= 0.144 Angle : 0.565 10.560 14235 Z= 0.306 Chirality : 0.041 0.168 1598 Planarity : 0.004 0.049 1681 Dihedral : 17.381 81.038 1767 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.51 % Favored : 96.32 % Rotamer: Outliers : 6.95 % Allowed : 16.54 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.18 % 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: -0.17 (0.24), residues: 1140 helix: 1.49 (0.27), residues: 368 sheet: 0.21 (0.40), residues: 158 loop : -1.26 (0.22), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 44 HIS 0.007 0.001 HIS L 284 PHE 0.015 0.001 PHE L 476 TYR 0.014 0.001 TYR K 276 ARG 0.003 0.000 ARG K 282 Details of bonding type rmsd hydrogen bonds : bond 0.04320 ( 415) hydrogen bonds : angle 4.66555 ( 1132) covalent geometry : bond 0.00318 (10408) covalent geometry : angle 0.56490 (14235) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 117 time to evaluate : 1.121 Fit side-chains revert: symmetry clash REVERT: K 18 GLU cc_start: 0.8246 (mp0) cc_final: 0.7601 (tm-30) REVERT: K 46 ARG cc_start: 0.7750 (tpp-160) cc_final: 0.7284 (mmm-85) REVERT: K 82 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.6502 (ttmm) REVERT: K 114 ARG cc_start: 0.7679 (mtm110) cc_final: 0.7468 (mmp80) REVERT: K 155 ASP cc_start: 0.6898 (t70) cc_final: 0.6650 (t0) REVERT: K 218 THR cc_start: 0.8661 (p) cc_final: 0.8384 (m) REVERT: K 219 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7718 (mptt) REVERT: K 289 ARG cc_start: 0.3833 (OUTLIER) cc_final: 0.0995 (mmm-85) REVERT: K 312 ASP cc_start: 0.7227 (p0) cc_final: 0.6999 (p0) REVERT: K 323 GLN cc_start: 0.7765 (mm110) cc_final: 0.7202 (mm110) REVERT: K 513 ASP cc_start: 0.7736 (t0) cc_final: 0.7019 (m-30) REVERT: K 548 MET cc_start: 0.6076 (mmm) cc_final: 0.5782 (mpt) REVERT: L 88 GLN cc_start: 0.8564 (tt0) cc_final: 0.8359 (tt0) REVERT: L 105 MET cc_start: 0.6240 (tmt) cc_final: 0.5402 (tmm) REVERT: L 156 ARG cc_start: 0.7435 (ptm160) cc_final: 0.6873 (ptp90) REVERT: L 164 LYS cc_start: 0.5841 (OUTLIER) cc_final: 0.5233 (mptt) REVERT: L 195 VAL cc_start: 0.8307 (p) cc_final: 0.8071 (m) REVERT: L 243 VAL cc_start: 0.7978 (OUTLIER) cc_final: 0.7725 (t) REVERT: L 302 TYR cc_start: 0.6042 (OUTLIER) cc_final: 0.5006 (p90) REVERT: L 303 ILE cc_start: 0.6628 (OUTLIER) cc_final: 0.6366 (pp) REVERT: L 401 LYS cc_start: 0.7251 (OUTLIER) cc_final: 0.6526 (ttpt) REVERT: L 521 ASP cc_start: 0.6342 (OUTLIER) cc_final: 0.5946 (t0) outliers start: 74 outliers final: 28 residues processed: 178 average time/residue: 1.0859 time to fit residues: 210.3147 Evaluate side-chains 140 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 103 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 82 LYS Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 130 ILE Chi-restraints excluded: chain K residue 134 LYS Chi-restraints excluded: chain K residue 219 LYS Chi-restraints excluded: chain K residue 254 ILE Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 289 ARG Chi-restraints excluded: chain K residue 506 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 164 LYS Chi-restraints excluded: chain L residue 222 LEU Chi-restraints excluded: chain L residue 243 VAL Chi-restraints excluded: chain L residue 292 VAL Chi-restraints excluded: chain L residue 302 TYR Chi-restraints excluded: chain L residue 303 ILE Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 328 VAL Chi-restraints excluded: chain L residue 333 THR Chi-restraints excluded: chain L residue 401 LYS Chi-restraints excluded: chain L residue 413 VAL Chi-restraints excluded: chain L residue 467 HIS Chi-restraints excluded: chain L residue 487 GLU Chi-restraints excluded: chain L residue 497 ILE Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 503 ASP Chi-restraints excluded: chain L residue 521 ASP Chi-restraints excluded: chain L residue 546 ILE Chi-restraints excluded: chain L residue 578 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 4 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 32 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 455 GLN ** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 535 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 = 0.4682 r_free = 0.4682 target = 0.237118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.193486 restraints weight = 10629.211| |-----------------------------------------------------------------------------| r_work (start): 0.4327 rms_B_bonded: 2.20 r_work: 0.4025 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10408 Z= 0.172 Angle : 0.581 10.445 14235 Z= 0.312 Chirality : 0.042 0.160 1598 Planarity : 0.004 0.051 1681 Dihedral : 17.268 81.168 1740 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.12 % Favored : 95.70 % Rotamer: Outliers : 7.14 % Allowed : 16.82 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.18 % 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: -0.22 (0.24), residues: 1140 helix: 1.41 (0.27), residues: 367 sheet: -0.02 (0.39), residues: 158 loop : -1.19 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP L 44 HIS 0.004 0.001 HIS L 417 PHE 0.017 0.002 PHE L 476 TYR 0.017 0.002 TYR K 403 ARG 0.003 0.000 ARG L 186 Details of bonding type rmsd hydrogen bonds : bond 0.04272 ( 415) hydrogen bonds : angle 4.64307 ( 1132) covalent geometry : bond 0.00398 (10408) covalent geometry : angle 0.58083 (14235) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 108 time to evaluate : 1.821 Fit side-chains revert: symmetry clash REVERT: K 18 GLU cc_start: 0.8294 (mp0) cc_final: 0.7612 (tm-30) REVERT: K 46 ARG cc_start: 0.7732 (tpp-160) cc_final: 0.7279 (mmm-85) REVERT: K 82 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.6565 (ttmm) REVERT: K 155 ASP cc_start: 0.6864 (t70) cc_final: 0.6578 (t0) REVERT: K 218 THR cc_start: 0.8714 (p) cc_final: 0.8427 (m) REVERT: K 219 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7719 (mptt) REVERT: K 289 ARG cc_start: 0.3988 (OUTLIER) cc_final: 0.1256 (mmm-85) REVERT: K 323 GLN cc_start: 0.7843 (mm110) cc_final: 0.7368 (mm110) REVERT: K 446 ASP cc_start: 0.7067 (OUTLIER) cc_final: 0.6801 (t0) REVERT: K 513 ASP cc_start: 0.7760 (t0) cc_final: 0.7117 (m-30) REVERT: K 536 ILE cc_start: 0.7963 (mt) cc_final: 0.7725 (mm) REVERT: L 87 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7839 (mtpp) REVERT: L 88 GLN cc_start: 0.8573 (tt0) cc_final: 0.8349 (tt0) REVERT: L 156 ARG cc_start: 0.7414 (ptm160) cc_final: 0.6566 (ptp-170) REVERT: L 164 LYS cc_start: 0.5815 (OUTLIER) cc_final: 0.5267 (mptt) REVERT: L 184 ASN cc_start: 0.6782 (m-40) cc_final: 0.6191 (t160) REVERT: L 195 VAL cc_start: 0.8381 (p) cc_final: 0.8147 (m) REVERT: L 243 VAL cc_start: 0.8008 (OUTLIER) cc_final: 0.7771 (t) REVERT: L 303 ILE cc_start: 0.6643 (OUTLIER) cc_final: 0.6355 (pp) REVERT: L 401 LYS cc_start: 0.7266 (OUTLIER) cc_final: 0.6501 (ttpt) REVERT: L 521 ASP cc_start: 0.6416 (OUTLIER) cc_final: 0.5935 (t0) outliers start: 76 outliers final: 33 residues processed: 170 average time/residue: 1.1229 time to fit residues: 207.2851 Evaluate side-chains 145 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 102 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 82 LYS Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 130 ILE Chi-restraints excluded: chain K residue 134 LYS Chi-restraints excluded: chain K residue 219 LYS Chi-restraints excluded: chain K residue 254 ILE Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 289 ARG Chi-restraints excluded: chain K residue 344 SER Chi-restraints excluded: chain K residue 446 ASP Chi-restraints excluded: chain K residue 506 ASP Chi-restraints excluded: chain K residue 544 LYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 87 LYS Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 164 LYS Chi-restraints excluded: chain L residue 243 VAL Chi-restraints excluded: chain L residue 292 VAL Chi-restraints excluded: chain L residue 303 ILE Chi-restraints excluded: chain L residue 307 ILE Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 328 VAL Chi-restraints excluded: chain L residue 333 THR Chi-restraints excluded: chain L residue 401 LYS Chi-restraints excluded: chain L residue 413 VAL Chi-restraints excluded: chain L residue 467 HIS Chi-restraints excluded: chain L residue 487 GLU Chi-restraints excluded: chain L residue 497 ILE Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 503 ASP Chi-restraints excluded: chain L residue 521 ASP Chi-restraints excluded: chain L residue 546 ILE Chi-restraints excluded: chain L residue 578 LEU Chi-restraints excluded: chain L residue 579 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 19 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 46 optimal weight: 0.3980 chunk 65 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 77 ASN ** K 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 103 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 = 0.4724 r_free = 0.4724 target = 0.242810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.195256 restraints weight = 10820.719| |-----------------------------------------------------------------------------| r_work (start): 0.4306 rms_B_bonded: 2.59 r_work: 0.3974 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10408 Z= 0.169 Angle : 0.574 10.350 14235 Z= 0.307 Chirality : 0.041 0.156 1598 Planarity : 0.004 0.053 1681 Dihedral : 17.268 81.136 1740 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.12 % Favored : 95.70 % Rotamer: Outliers : 6.95 % Allowed : 17.95 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.18 % 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: -0.27 (0.24), residues: 1140 helix: 1.34 (0.27), residues: 366 sheet: -0.13 (0.38), residues: 164 loop : -1.18 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP L 44 HIS 0.003 0.001 HIS L 417 PHE 0.017 0.002 PHE L 476 TYR 0.016 0.002 TYR K 403 ARG 0.002 0.000 ARG L 532 Details of bonding type rmsd hydrogen bonds : bond 0.04157 ( 415) hydrogen bonds : angle 4.59909 ( 1132) covalent geometry : bond 0.00392 (10408) covalent geometry : angle 0.57381 (14235) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 102 time to evaluate : 1.128 Fit side-chains revert: symmetry clash REVERT: K 46 ARG cc_start: 0.7788 (tpp-160) cc_final: 0.7346 (mmm-85) REVERT: K 82 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.6611 (ttmm) REVERT: K 152 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6693 (mm-30) REVERT: K 155 ASP cc_start: 0.6862 (t70) cc_final: 0.6517 (t0) REVERT: K 218 THR cc_start: 0.8719 (p) cc_final: 0.8452 (m) REVERT: K 219 LYS cc_start: 0.8189 (mtmm) cc_final: 0.7735 (mptt) REVERT: K 238 ARG cc_start: 0.8037 (ttt-90) cc_final: 0.7719 (ttm-80) REVERT: K 289 ARG cc_start: 0.3831 (OUTLIER) cc_final: 0.2650 (mmm-85) REVERT: K 323 GLN cc_start: 0.7887 (mm110) cc_final: 0.7300 (mm110) REVERT: K 446 ASP cc_start: 0.7146 (OUTLIER) cc_final: 0.6855 (t0) REVERT: K 506 ASP cc_start: 0.7308 (OUTLIER) cc_final: 0.6891 (m-30) REVERT: K 513 ASP cc_start: 0.7736 (t0) cc_final: 0.7101 (m-30) REVERT: K 536 ILE cc_start: 0.8152 (mt) cc_final: 0.7886 (mm) REVERT: L 87 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7832 (mtpp) REVERT: L 88 GLN cc_start: 0.8592 (tt0) cc_final: 0.8359 (tt0) REVERT: L 156 ARG cc_start: 0.7415 (ptm160) cc_final: 0.6484 (ptp-170) REVERT: L 164 LYS cc_start: 0.5887 (OUTLIER) cc_final: 0.5283 (mptt) REVERT: L 184 ASN cc_start: 0.6819 (m-40) cc_final: 0.6101 (t160) REVERT: L 195 VAL cc_start: 0.8329 (p) cc_final: 0.8118 (m) REVERT: L 243 VAL cc_start: 0.8051 (OUTLIER) cc_final: 0.7822 (t) REVERT: L 303 ILE cc_start: 0.6545 (OUTLIER) cc_final: 0.6221 (pp) REVERT: L 401 LYS cc_start: 0.7300 (OUTLIER) cc_final: 0.6551 (ttpt) REVERT: L 469 ILE cc_start: 0.3108 (OUTLIER) cc_final: 0.2698 (tp) REVERT: L 521 ASP cc_start: 0.6489 (OUTLIER) cc_final: 0.5993 (t0) outliers start: 74 outliers final: 38 residues processed: 160 average time/residue: 1.0109 time to fit residues: 176.1813 Evaluate side-chains 152 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 102 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 82 LYS Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 130 ILE Chi-restraints excluded: chain K residue 134 LYS Chi-restraints excluded: chain K residue 152 GLU Chi-restraints excluded: chain K residue 254 ILE Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 289 ARG Chi-restraints excluded: chain K residue 344 SER Chi-restraints excluded: chain K residue 446 ASP Chi-restraints excluded: chain K residue 506 ASP Chi-restraints excluded: chain K residue 544 LYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 87 LYS Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 162 CYS Chi-restraints excluded: chain L residue 164 LYS Chi-restraints excluded: chain L residue 222 LEU Chi-restraints excluded: chain L residue 243 VAL Chi-restraints excluded: chain L residue 292 VAL Chi-restraints excluded: chain L residue 303 ILE Chi-restraints excluded: chain L residue 307 ILE Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 328 VAL Chi-restraints excluded: chain L residue 333 THR Chi-restraints excluded: chain L residue 341 LEU Chi-restraints excluded: chain L residue 401 LYS Chi-restraints excluded: chain L residue 413 VAL Chi-restraints excluded: chain L residue 467 HIS Chi-restraints excluded: chain L residue 469 ILE Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 487 GLU Chi-restraints excluded: chain L residue 497 ILE Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 503 ASP Chi-restraints excluded: chain L residue 521 ASP Chi-restraints excluded: chain L residue 546 ILE Chi-restraints excluded: chain L residue 578 LEU Chi-restraints excluded: chain L residue 579 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 89 optimal weight: 0.1980 chunk 75 optimal weight: 2.9990 chunk 62 optimal weight: 0.0770 chunk 56 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 84 optimal weight: 20.0000 chunk 54 optimal weight: 0.8980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.238497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.195764 restraints weight = 10508.912| |-----------------------------------------------------------------------------| r_work (start): 0.4364 rms_B_bonded: 1.99 r_work: 0.4039 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10408 Z= 0.137 Angle : 0.546 10.141 14235 Z= 0.293 Chirality : 0.040 0.153 1598 Planarity : 0.004 0.054 1681 Dihedral : 17.162 81.950 1736 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.86 % Favored : 95.96 % Rotamer: Outliers : 6.58 % Allowed : 18.52 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.18 % 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: -0.16 (0.24), residues: 1140 helix: 1.51 (0.27), residues: 364 sheet: -0.02 (0.39), residues: 159 loop : -1.16 (0.23), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 44 HIS 0.003 0.001 HIS L 417 PHE 0.014 0.001 PHE L 476 TYR 0.014 0.001 TYR L 531 ARG 0.004 0.000 ARG L 550 Details of bonding type rmsd hydrogen bonds : bond 0.03851 ( 415) hydrogen bonds : angle 4.45527 ( 1132) covalent geometry : bond 0.00311 (10408) covalent geometry : angle 0.54594 (14235) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 107 time to evaluate : 1.161 Fit side-chains revert: symmetry clash REVERT: K 18 GLU cc_start: 0.8413 (mp0) cc_final: 0.7632 (tm-30) REVERT: K 46 ARG cc_start: 0.7730 (tpp-160) cc_final: 0.7318 (mmm-85) REVERT: K 82 LYS cc_start: 0.7600 (OUTLIER) cc_final: 0.6566 (ttmm) REVERT: K 155 ASP cc_start: 0.6796 (t70) cc_final: 0.6466 (t0) REVERT: K 218 THR cc_start: 0.8702 (p) cc_final: 0.8468 (m) REVERT: K 219 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7716 (mptt) REVERT: K 238 ARG cc_start: 0.7976 (ttt-90) cc_final: 0.7739 (ttm-80) REVERT: K 289 ARG cc_start: 0.3685 (OUTLIER) cc_final: 0.2513 (mmm-85) REVERT: K 446 ASP cc_start: 0.7076 (OUTLIER) cc_final: 0.6743 (t0) REVERT: K 506 ASP cc_start: 0.7176 (OUTLIER) cc_final: 0.6829 (m-30) REVERT: K 513 ASP cc_start: 0.7703 (t0) cc_final: 0.7059 (m-30) REVERT: K 536 ILE cc_start: 0.8126 (mt) cc_final: 0.7861 (mm) REVERT: K 544 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7792 (tptt) REVERT: L 87 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7712 (mtpp) REVERT: L 88 GLN cc_start: 0.8583 (tt0) cc_final: 0.8360 (tt0) REVERT: L 156 ARG cc_start: 0.7382 (ptm160) cc_final: 0.6673 (ptp-170) REVERT: L 164 LYS cc_start: 0.5944 (OUTLIER) cc_final: 0.5360 (mptt) REVERT: L 243 VAL cc_start: 0.8011 (OUTLIER) cc_final: 0.7797 (t) REVERT: L 303 ILE cc_start: 0.6587 (OUTLIER) cc_final: 0.6264 (pp) REVERT: L 344 ARG cc_start: 0.5933 (mtp-110) cc_final: 0.5340 (tmt-80) REVERT: L 401 LYS cc_start: 0.7281 (OUTLIER) cc_final: 0.6505 (ttpt) REVERT: L 474 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.5881 (tm-30) REVERT: L 521 ASP cc_start: 0.6323 (OUTLIER) cc_final: 0.5883 (t0) outliers start: 70 outliers final: 33 residues processed: 162 average time/residue: 1.1314 time to fit residues: 199.6897 Evaluate side-chains 146 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 100 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 82 LYS Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 130 ILE Chi-restraints excluded: chain K residue 134 LYS Chi-restraints excluded: chain K residue 219 LYS Chi-restraints excluded: chain K residue 254 ILE Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 289 ARG Chi-restraints excluded: chain K residue 446 ASP Chi-restraints excluded: chain K residue 506 ASP Chi-restraints excluded: chain K residue 544 LYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 87 LYS Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 162 CYS Chi-restraints excluded: chain L residue 164 LYS Chi-restraints excluded: chain L residue 243 VAL Chi-restraints excluded: chain L residue 292 VAL Chi-restraints excluded: chain L residue 303 ILE Chi-restraints excluded: chain L residue 307 ILE Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 328 VAL Chi-restraints excluded: chain L residue 333 THR Chi-restraints excluded: chain L residue 341 LEU Chi-restraints excluded: chain L residue 401 LYS Chi-restraints excluded: chain L residue 413 VAL Chi-restraints excluded: chain L residue 467 HIS Chi-restraints excluded: chain L residue 474 GLU Chi-restraints excluded: chain L residue 480 MET Chi-restraints excluded: chain L residue 487 GLU Chi-restraints excluded: chain L residue 497 ILE Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 521 ASP Chi-restraints excluded: chain L residue 546 ILE Chi-restraints excluded: chain L residue 578 LEU Chi-restraints excluded: chain L residue 579 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 54 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 85 optimal weight: 0.0170 chunk 50 optimal weight: 0.9990 chunk 60 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.238128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.195458 restraints weight = 10651.042| |-----------------------------------------------------------------------------| r_work (start): 0.4337 rms_B_bonded: 2.06 r_work: 0.4015 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10408 Z= 0.144 Angle : 0.564 10.096 14235 Z= 0.300 Chirality : 0.040 0.151 1598 Planarity : 0.004 0.056 1681 Dihedral : 17.147 82.542 1736 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.04 % Favored : 95.79 % Rotamer: Outliers : 6.02 % Allowed : 19.55 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.18 % 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: -0.18 (0.24), residues: 1140 helix: 1.46 (0.27), residues: 366 sheet: -0.05 (0.40), residues: 159 loop : -1.15 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 44 HIS 0.003 0.001 HIS L 417 PHE 0.015 0.001 PHE L 476 TYR 0.021 0.001 TYR K 272 ARG 0.004 0.000 ARG L 550 Details of bonding type rmsd hydrogen bonds : bond 0.03862 ( 415) hydrogen bonds : angle 4.45544 ( 1132) covalent geometry : bond 0.00332 (10408) covalent geometry : angle 0.56423 (14235) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 101 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: K 46 ARG cc_start: 0.7731 (tpp-160) cc_final: 0.7321 (mmm-85) REVERT: K 82 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.6597 (ttmm) REVERT: K 114 ARG cc_start: 0.6769 (tpm170) cc_final: 0.6557 (tpm170) REVERT: K 152 GLU cc_start: 0.7160 (mm-30) cc_final: 0.6835 (mm-30) REVERT: K 155 ASP cc_start: 0.6850 (t70) cc_final: 0.6481 (t0) REVERT: K 218 THR cc_start: 0.8713 (p) cc_final: 0.8474 (m) REVERT: K 219 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7726 (mptt) REVERT: K 238 ARG cc_start: 0.7969 (ttt-90) cc_final: 0.7758 (ttm-80) REVERT: K 289 ARG cc_start: 0.3726 (OUTLIER) cc_final: 0.2535 (mmm-85) REVERT: K 323 GLN cc_start: 0.7766 (mm110) cc_final: 0.6949 (mm-40) REVERT: K 446 ASP cc_start: 0.7034 (OUTLIER) cc_final: 0.6748 (t0) REVERT: K 506 ASP cc_start: 0.7109 (OUTLIER) cc_final: 0.6804 (m-30) REVERT: K 513 ASP cc_start: 0.7713 (t0) cc_final: 0.7192 (m-30) REVERT: K 536 ILE cc_start: 0.8107 (mt) cc_final: 0.7838 (mm) REVERT: K 544 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7717 (tptt) REVERT: L 87 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7811 (mtpp) REVERT: L 88 GLN cc_start: 0.8560 (tt0) cc_final: 0.8342 (tt0) REVERT: L 156 ARG cc_start: 0.7363 (ptm160) cc_final: 0.6735 (ptp90) REVERT: L 164 LYS cc_start: 0.5996 (OUTLIER) cc_final: 0.5389 (mptm) REVERT: L 186 ARG cc_start: 0.7981 (ptp90) cc_final: 0.7753 (ttp-110) REVERT: L 243 VAL cc_start: 0.8037 (OUTLIER) cc_final: 0.7809 (t) REVERT: L 303 ILE cc_start: 0.6576 (OUTLIER) cc_final: 0.6250 (pp) REVERT: L 344 ARG cc_start: 0.5898 (mtp-110) cc_final: 0.5300 (tmt-80) REVERT: L 401 LYS cc_start: 0.7327 (OUTLIER) cc_final: 0.6563 (ttpt) REVERT: L 474 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.5882 (tm-30) REVERT: L 521 ASP cc_start: 0.6370 (OUTLIER) cc_final: 0.5900 (t0) outliers start: 64 outliers final: 38 residues processed: 150 average time/residue: 1.0705 time to fit residues: 174.3846 Evaluate side-chains 153 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 102 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 82 LYS Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 130 ILE Chi-restraints excluded: chain K residue 134 LYS Chi-restraints excluded: chain K residue 219 LYS Chi-restraints excluded: chain K residue 254 ILE Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 289 ARG Chi-restraints excluded: chain K residue 404 THR Chi-restraints excluded: chain K residue 446 ASP Chi-restraints excluded: chain K residue 506 ASP Chi-restraints excluded: chain K residue 539 LEU Chi-restraints excluded: chain K residue 544 LYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 87 LYS Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 162 CYS Chi-restraints excluded: chain L residue 164 LYS Chi-restraints excluded: chain L residue 243 VAL Chi-restraints excluded: chain L residue 292 VAL Chi-restraints excluded: chain L residue 303 ILE Chi-restraints excluded: chain L residue 307 ILE Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 328 VAL Chi-restraints excluded: chain L residue 333 THR Chi-restraints excluded: chain L residue 341 LEU Chi-restraints excluded: chain L residue 401 LYS Chi-restraints excluded: chain L residue 413 VAL Chi-restraints excluded: chain L residue 467 HIS Chi-restraints excluded: chain L residue 474 GLU Chi-restraints excluded: chain L residue 480 MET Chi-restraints excluded: chain L residue 487 GLU Chi-restraints excluded: chain L residue 497 ILE Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 503 ASP Chi-restraints excluded: chain L residue 521 ASP Chi-restraints excluded: chain L residue 546 ILE Chi-restraints excluded: chain L residue 578 LEU Chi-restraints excluded: chain L residue 579 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 50 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 23 optimal weight: 0.0070 chunk 36 optimal weight: 0.7980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.241477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.198130 restraints weight = 10789.444| |-----------------------------------------------------------------------------| r_work (start): 0.4338 rms_B_bonded: 2.13 r_work: 0.4015 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 10408 Z= 0.143 Angle : 0.561 9.918 14235 Z= 0.297 Chirality : 0.040 0.198 1598 Planarity : 0.004 0.057 1681 Dihedral : 17.125 83.199 1736 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.86 % Favored : 95.96 % Rotamer: Outliers : 6.20 % Allowed : 19.83 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.18 % 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: -0.17 (0.24), residues: 1140 helix: 1.43 (0.27), residues: 366 sheet: -0.09 (0.39), residues: 169 loop : -1.12 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 391 HIS 0.003 0.001 HIS L 417 PHE 0.015 0.001 PHE L 476 TYR 0.019 0.001 TYR K 519 ARG 0.005 0.000 ARG L 550 Details of bonding type rmsd hydrogen bonds : bond 0.03841 ( 415) hydrogen bonds : angle 4.47354 ( 1132) covalent geometry : bond 0.00337 (10408) covalent geometry : angle 0.56055 (14235) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 104 time to evaluate : 1.050 Fit side-chains revert: symmetry clash REVERT: K 18 GLU cc_start: 0.8429 (mp0) cc_final: 0.7609 (tm-30) REVERT: K 46 ARG cc_start: 0.7742 (tpp-160) cc_final: 0.7296 (mmm-85) REVERT: K 82 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.6602 (ttmm) REVERT: K 152 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6718 (mm-30) REVERT: K 218 THR cc_start: 0.8716 (p) cc_final: 0.8479 (m) REVERT: K 219 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7709 (mptt) REVERT: K 289 ARG cc_start: 0.3596 (OUTLIER) cc_final: 0.2268 (mmm-85) REVERT: K 306 LYS cc_start: 0.8217 (mmmt) cc_final: 0.7995 (mmtt) REVERT: K 323 GLN cc_start: 0.7799 (mm110) cc_final: 0.6976 (mm-40) REVERT: K 326 MET cc_start: 0.6725 (mtm) cc_final: 0.6409 (mtt) REVERT: K 506 ASP cc_start: 0.7132 (OUTLIER) cc_final: 0.6865 (m-30) REVERT: K 513 ASP cc_start: 0.7730 (t0) cc_final: 0.7195 (m-30) REVERT: K 536 ILE cc_start: 0.8086 (mt) cc_final: 0.7828 (mm) REVERT: K 544 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7748 (tptt) REVERT: L 88 GLN cc_start: 0.8543 (tt0) cc_final: 0.8312 (tt0) REVERT: L 156 ARG cc_start: 0.7384 (ptm160) cc_final: 0.6754 (ptp90) REVERT: L 164 LYS cc_start: 0.5975 (OUTLIER) cc_final: 0.5334 (mptt) REVERT: L 186 ARG cc_start: 0.7969 (ptp90) cc_final: 0.7716 (ttp-110) REVERT: L 243 VAL cc_start: 0.8047 (OUTLIER) cc_final: 0.7800 (t) REVERT: L 262 GLU cc_start: 0.7333 (pm20) cc_final: 0.6306 (mt-10) REVERT: L 303 ILE cc_start: 0.6612 (OUTLIER) cc_final: 0.6279 (pp) REVERT: L 307 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8231 (tp) REVERT: L 401 LYS cc_start: 0.7343 (OUTLIER) cc_final: 0.6558 (ttpt) REVERT: L 474 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.5883 (tm-30) REVERT: L 521 ASP cc_start: 0.6344 (OUTLIER) cc_final: 0.5898 (t0) outliers start: 66 outliers final: 39 residues processed: 154 average time/residue: 1.2663 time to fit residues: 212.7926 Evaluate side-chains 154 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 102 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 82 LYS Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 130 ILE Chi-restraints excluded: chain K residue 134 LYS Chi-restraints excluded: chain K residue 152 GLU Chi-restraints excluded: chain K residue 219 LYS Chi-restraints excluded: chain K residue 254 ILE Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 272 TYR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 289 ARG Chi-restraints excluded: chain K residue 395 LYS Chi-restraints excluded: chain K residue 404 THR Chi-restraints excluded: chain K residue 446 ASP Chi-restraints excluded: chain K residue 506 ASP Chi-restraints excluded: chain K residue 544 LYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 162 CYS Chi-restraints excluded: chain L residue 164 LYS Chi-restraints excluded: chain L residue 233 MET Chi-restraints excluded: chain L residue 243 VAL Chi-restraints excluded: chain L residue 292 VAL Chi-restraints excluded: chain L residue 303 ILE Chi-restraints excluded: chain L residue 307 ILE Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 328 VAL Chi-restraints excluded: chain L residue 333 THR Chi-restraints excluded: chain L residue 341 LEU Chi-restraints excluded: chain L residue 401 LYS Chi-restraints excluded: chain L residue 413 VAL Chi-restraints excluded: chain L residue 467 HIS Chi-restraints excluded: chain L residue 474 GLU Chi-restraints excluded: chain L residue 480 MET Chi-restraints excluded: chain L residue 487 GLU Chi-restraints excluded: chain L residue 497 ILE Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 503 ASP Chi-restraints excluded: chain L residue 521 ASP Chi-restraints excluded: chain L residue 546 ILE Chi-restraints excluded: chain L residue 578 LEU Chi-restraints excluded: chain L residue 579 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 74 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 chunk 116 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 64 optimal weight: 9.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 77 ASN L 406 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.238827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.195558 restraints weight = 10873.868| |-----------------------------------------------------------------------------| r_work (start): 0.4328 rms_B_bonded: 2.24 r_work: 0.3986 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.122 10408 Z= 0.180 Angle : 0.589 10.135 14235 Z= 0.311 Chirality : 0.042 0.203 1598 Planarity : 0.004 0.057 1681 Dihedral : 17.219 83.574 1736 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.21 % Favored : 95.61 % Rotamer: Outliers : 6.95 % Allowed : 19.27 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.18 % 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: -0.28 (0.24), residues: 1140 helix: 1.31 (0.27), residues: 365 sheet: -0.19 (0.39), residues: 168 loop : -1.15 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 391 HIS 0.003 0.001 HIS L 417 PHE 0.018 0.002 PHE L 476 TYR 0.017 0.002 TYR K 550 ARG 0.003 0.000 ARG L 524 Details of bonding type rmsd hydrogen bonds : bond 0.04164 ( 415) hydrogen bonds : angle 4.67321 ( 1132) covalent geometry : bond 0.00433 (10408) covalent geometry : angle 0.58854 (14235) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 103 time to evaluate : 1.184 Fit side-chains revert: symmetry clash REVERT: K 46 ARG cc_start: 0.7800 (tpp-160) cc_final: 0.7412 (mmm160) REVERT: K 82 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.6704 (ttmm) REVERT: K 114 ARG cc_start: 0.6996 (OUTLIER) cc_final: 0.6690 (tpm170) REVERT: K 218 THR cc_start: 0.8728 (p) cc_final: 0.8505 (m) REVERT: K 219 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7744 (mptt) REVERT: K 289 ARG cc_start: 0.3622 (OUTLIER) cc_final: 0.2171 (mmm-85) REVERT: K 323 GLN cc_start: 0.7867 (mm110) cc_final: 0.7034 (mm-40) REVERT: K 506 ASP cc_start: 0.7128 (OUTLIER) cc_final: 0.6856 (m-30) REVERT: K 513 ASP cc_start: 0.7736 (t0) cc_final: 0.7215 (m-30) REVERT: K 536 ILE cc_start: 0.8135 (mt) cc_final: 0.7896 (mm) REVERT: K 544 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7842 (tptt) REVERT: L 88 GLN cc_start: 0.8589 (tt0) cc_final: 0.8383 (tt0) REVERT: L 141 ILE cc_start: 0.4847 (OUTLIER) cc_final: 0.4437 (mp) REVERT: L 164 LYS cc_start: 0.6003 (OUTLIER) cc_final: 0.5377 (mptt) REVERT: L 243 VAL cc_start: 0.8132 (OUTLIER) cc_final: 0.7896 (t) REVERT: L 303 ILE cc_start: 0.6620 (OUTLIER) cc_final: 0.6296 (pp) REVERT: L 330 VAL cc_start: 0.8153 (OUTLIER) cc_final: 0.7904 (t) REVERT: L 401 LYS cc_start: 0.7322 (OUTLIER) cc_final: 0.6763 (ttpt) REVERT: L 469 ILE cc_start: 0.3224 (OUTLIER) cc_final: 0.2802 (tp) REVERT: L 474 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.5848 (tm-30) REVERT: L 521 ASP cc_start: 0.6491 (OUTLIER) cc_final: 0.5901 (t0) outliers start: 74 outliers final: 40 residues processed: 159 average time/residue: 1.0827 time to fit residues: 187.8331 Evaluate side-chains 155 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 100 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 82 LYS Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 114 ARG Chi-restraints excluded: chain K residue 130 ILE Chi-restraints excluded: chain K residue 134 LYS Chi-restraints excluded: chain K residue 219 LYS Chi-restraints excluded: chain K residue 254 ILE Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 289 ARG Chi-restraints excluded: chain K residue 395 LYS Chi-restraints excluded: chain K residue 404 THR Chi-restraints excluded: chain K residue 446 ASP Chi-restraints excluded: chain K residue 506 ASP Chi-restraints excluded: chain K residue 539 LEU Chi-restraints excluded: chain K residue 544 LYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain L residue 162 CYS Chi-restraints excluded: chain L residue 164 LYS Chi-restraints excluded: chain L residue 233 MET Chi-restraints excluded: chain L residue 243 VAL Chi-restraints excluded: chain L residue 292 VAL Chi-restraints excluded: chain L residue 303 ILE Chi-restraints excluded: chain L residue 307 ILE Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 328 VAL Chi-restraints excluded: chain L residue 330 VAL Chi-restraints excluded: chain L residue 333 THR Chi-restraints excluded: chain L residue 341 LEU Chi-restraints excluded: chain L residue 401 LYS Chi-restraints excluded: chain L residue 413 VAL Chi-restraints excluded: chain L residue 467 HIS Chi-restraints excluded: chain L residue 469 ILE Chi-restraints excluded: chain L residue 474 GLU Chi-restraints excluded: chain L residue 480 MET Chi-restraints excluded: chain L residue 487 GLU Chi-restraints excluded: chain L residue 497 ILE Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 503 ASP Chi-restraints excluded: chain L residue 521 ASP Chi-restraints excluded: chain L residue 546 ILE Chi-restraints excluded: chain L residue 578 LEU Chi-restraints excluded: chain L residue 579 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 41 optimal weight: 0.7980 chunk 104 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 7 optimal weight: 0.0870 chunk 102 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.241115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.196968 restraints weight = 10772.856| |-----------------------------------------------------------------------------| r_work (start): 0.4340 rms_B_bonded: 2.17 r_work: 0.4045 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 10408 Z= 0.150 Angle : 0.575 9.918 14235 Z= 0.305 Chirality : 0.041 0.178 1598 Planarity : 0.004 0.058 1681 Dihedral : 17.184 84.099 1736 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.77 % Favored : 96.05 % Rotamer: Outliers : 6.20 % Allowed : 20.58 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.18 % 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: -0.23 (0.24), residues: 1140 helix: 1.36 (0.27), residues: 365 sheet: -0.17 (0.39), residues: 168 loop : -1.12 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 391 HIS 0.003 0.001 HIS L 417 PHE 0.015 0.001 PHE L 476 TYR 0.021 0.001 TYR K 272 ARG 0.005 0.000 ARG L 186 Details of bonding type rmsd hydrogen bonds : bond 0.03914 ( 415) hydrogen bonds : angle 4.57002 ( 1132) covalent geometry : bond 0.00353 (10408) covalent geometry : angle 0.57538 (14235) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 100 time to evaluate : 1.064 Fit side-chains revert: symmetry clash REVERT: K 46 ARG cc_start: 0.7766 (tpp-160) cc_final: 0.7376 (mmm160) REVERT: K 82 LYS cc_start: 0.7679 (OUTLIER) cc_final: 0.6621 (ttmm) REVERT: K 218 THR cc_start: 0.8718 (p) cc_final: 0.8485 (m) REVERT: K 219 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7744 (tptt) REVERT: K 289 ARG cc_start: 0.3574 (OUTLIER) cc_final: 0.2042 (mmm-85) REVERT: K 323 GLN cc_start: 0.7817 (mm110) cc_final: 0.7094 (mm110) REVERT: K 506 ASP cc_start: 0.7126 (OUTLIER) cc_final: 0.6876 (m-30) REVERT: K 513 ASP cc_start: 0.7723 (t0) cc_final: 0.7197 (m-30) REVERT: K 536 ILE cc_start: 0.8128 (mt) cc_final: 0.7871 (mm) REVERT: K 544 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7826 (tptt) REVERT: L 141 ILE cc_start: 0.4919 (OUTLIER) cc_final: 0.4514 (mp) REVERT: L 156 ARG cc_start: 0.7393 (ptm160) cc_final: 0.6740 (ptp90) REVERT: L 164 LYS cc_start: 0.6053 (OUTLIER) cc_final: 0.5446 (mptt) REVERT: L 243 VAL cc_start: 0.8078 (OUTLIER) cc_final: 0.7821 (t) REVERT: L 262 GLU cc_start: 0.7258 (pm20) cc_final: 0.6220 (mt-10) REVERT: L 297 GLN cc_start: 0.0543 (OUTLIER) cc_final: 0.0319 (mm-40) REVERT: L 303 ILE cc_start: 0.6672 (OUTLIER) cc_final: 0.6368 (pp) REVERT: L 307 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8179 (tp) REVERT: L 330 VAL cc_start: 0.8103 (OUTLIER) cc_final: 0.7862 (t) REVERT: L 344 ARG cc_start: 0.5943 (mtp-110) cc_final: 0.5469 (tmt-80) REVERT: L 390 ARG cc_start: 0.7211 (OUTLIER) cc_final: 0.6853 (mtt-85) REVERT: L 401 LYS cc_start: 0.7329 (OUTLIER) cc_final: 0.6751 (ttpt) REVERT: L 469 ILE cc_start: 0.3159 (OUTLIER) cc_final: 0.2748 (tp) REVERT: L 474 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.5857 (tm-30) outliers start: 66 outliers final: 39 residues processed: 151 average time/residue: 1.0484 time to fit residues: 173.3191 Evaluate side-chains 151 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 96 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 82 LYS Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 130 ILE Chi-restraints excluded: chain K residue 134 LYS Chi-restraints excluded: chain K residue 219 LYS Chi-restraints excluded: chain K residue 254 ILE Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 272 TYR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 289 ARG Chi-restraints excluded: chain K residue 395 LYS Chi-restraints excluded: chain K residue 404 THR Chi-restraints excluded: chain K residue 506 ASP Chi-restraints excluded: chain K residue 539 LEU Chi-restraints excluded: chain K residue 544 LYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain L residue 162 CYS Chi-restraints excluded: chain L residue 164 LYS Chi-restraints excluded: chain L residue 233 MET Chi-restraints excluded: chain L residue 243 VAL Chi-restraints excluded: chain L residue 292 VAL Chi-restraints excluded: chain L residue 297 GLN Chi-restraints excluded: chain L residue 303 ILE Chi-restraints excluded: chain L residue 307 ILE Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 328 VAL Chi-restraints excluded: chain L residue 330 VAL Chi-restraints excluded: chain L residue 333 THR Chi-restraints excluded: chain L residue 341 LEU Chi-restraints excluded: chain L residue 390 ARG Chi-restraints excluded: chain L residue 401 LYS Chi-restraints excluded: chain L residue 413 VAL Chi-restraints excluded: chain L residue 467 HIS Chi-restraints excluded: chain L residue 469 ILE Chi-restraints excluded: chain L residue 474 GLU Chi-restraints excluded: chain L residue 480 MET Chi-restraints excluded: chain L residue 487 GLU Chi-restraints excluded: chain L residue 497 ILE Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 503 ASP Chi-restraints excluded: chain L residue 521 ASP Chi-restraints excluded: chain L residue 546 ILE Chi-restraints excluded: chain L residue 578 LEU Chi-restraints excluded: chain L residue 579 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 15 optimal weight: 0.0010 chunk 90 optimal weight: 0.3980 chunk 33 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 98 optimal weight: 0.5980 chunk 77 optimal weight: 0.1980 chunk 108 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 104 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.240554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.196756 restraints weight = 10587.907| |-----------------------------------------------------------------------------| r_work (start): 0.4342 rms_B_bonded: 2.23 r_work: 0.4029 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 10408 Z= 0.128 Angle : 0.561 9.831 14235 Z= 0.299 Chirality : 0.040 0.174 1598 Planarity : 0.004 0.059 1681 Dihedral : 17.140 84.561 1736 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.51 % Favored : 96.40 % Rotamer: Outliers : 5.26 % Allowed : 21.80 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.18 % 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: -0.19 (0.24), residues: 1140 helix: 1.43 (0.27), residues: 367 sheet: -0.13 (0.39), residues: 169 loop : -1.14 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 391 HIS 0.008 0.001 HIS L 93 PHE 0.014 0.001 PHE L 476 TYR 0.039 0.001 TYR K 272 ARG 0.005 0.000 ARG L 186 Details of bonding type rmsd hydrogen bonds : bond 0.03734 ( 415) hydrogen bonds : angle 4.50092 ( 1132) covalent geometry : bond 0.00290 (10408) covalent geometry : angle 0.56076 (14235) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 99 time to evaluate : 1.248 Fit side-chains revert: symmetry clash REVERT: K 18 GLU cc_start: 0.8441 (mp0) cc_final: 0.7604 (tm-30) REVERT: K 46 ARG cc_start: 0.7766 (tpp-160) cc_final: 0.7368 (mmm160) REVERT: K 82 LYS cc_start: 0.7642 (OUTLIER) cc_final: 0.6583 (ttmm) REVERT: K 218 THR cc_start: 0.8694 (p) cc_final: 0.8460 (m) REVERT: K 219 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7767 (tptt) REVERT: K 289 ARG cc_start: 0.3319 (OUTLIER) cc_final: 0.1804 (mmm-85) REVERT: K 291 PHE cc_start: 0.4817 (OUTLIER) cc_final: 0.3997 (p90) REVERT: K 323 GLN cc_start: 0.7802 (mm110) cc_final: 0.6981 (mm-40) REVERT: K 506 ASP cc_start: 0.7074 (OUTLIER) cc_final: 0.6847 (m-30) REVERT: K 513 ASP cc_start: 0.7734 (t0) cc_final: 0.7212 (m-30) REVERT: K 536 ILE cc_start: 0.8145 (mt) cc_final: 0.7878 (mm) REVERT: L 156 ARG cc_start: 0.7367 (ptm160) cc_final: 0.6721 (ptp90) REVERT: L 164 LYS cc_start: 0.6055 (OUTLIER) cc_final: 0.5401 (mptt) REVERT: L 243 VAL cc_start: 0.8000 (OUTLIER) cc_final: 0.7746 (t) REVERT: L 297 GLN cc_start: 0.0368 (OUTLIER) cc_final: 0.0138 (mm-40) REVERT: L 303 ILE cc_start: 0.6592 (OUTLIER) cc_final: 0.6275 (pp) REVERT: L 307 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8149 (tp) REVERT: L 344 ARG cc_start: 0.5876 (mtp-110) cc_final: 0.5455 (tmt-80) REVERT: L 390 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.6879 (mtt-85) REVERT: L 467 HIS cc_start: 0.6418 (OUTLIER) cc_final: 0.6000 (p-80) REVERT: L 469 ILE cc_start: 0.3057 (OUTLIER) cc_final: 0.2616 (tp) REVERT: L 474 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.5817 (tm-30) REVERT: L 521 ASP cc_start: 0.6351 (OUTLIER) cc_final: 0.5750 (t0) outliers start: 56 outliers final: 34 residues processed: 142 average time/residue: 1.4365 time to fit residues: 222.5252 Evaluate side-chains 145 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 96 time to evaluate : 2.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 82 LYS Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 130 ILE Chi-restraints excluded: chain K residue 134 LYS Chi-restraints excluded: chain K residue 219 LYS Chi-restraints excluded: chain K residue 254 ILE Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 289 ARG Chi-restraints excluded: chain K residue 291 PHE Chi-restraints excluded: chain K residue 395 LYS Chi-restraints excluded: chain K residue 506 ASP Chi-restraints excluded: chain K residue 539 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 162 CYS Chi-restraints excluded: chain L residue 164 LYS Chi-restraints excluded: chain L residue 233 MET Chi-restraints excluded: chain L residue 243 VAL Chi-restraints excluded: chain L residue 292 VAL Chi-restraints excluded: chain L residue 297 GLN Chi-restraints excluded: chain L residue 303 ILE Chi-restraints excluded: chain L residue 307 ILE Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 328 VAL Chi-restraints excluded: chain L residue 333 THR Chi-restraints excluded: chain L residue 341 LEU Chi-restraints excluded: chain L residue 390 ARG Chi-restraints excluded: chain L residue 413 VAL Chi-restraints excluded: chain L residue 467 HIS Chi-restraints excluded: chain L residue 469 ILE Chi-restraints excluded: chain L residue 474 GLU Chi-restraints excluded: chain L residue 480 MET Chi-restraints excluded: chain L residue 487 GLU Chi-restraints excluded: chain L residue 497 ILE Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 503 ASP Chi-restraints excluded: chain L residue 521 ASP Chi-restraints excluded: chain L residue 546 ILE Chi-restraints excluded: chain L residue 578 LEU Chi-restraints excluded: chain L residue 579 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 5 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 36 optimal weight: 0.0370 chunk 49 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 71 optimal weight: 0.0060 chunk 79 optimal weight: 1.9990 overall best weight: 0.4474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.243153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.198670 restraints weight = 10590.269| |-----------------------------------------------------------------------------| r_work (start): 0.4340 rms_B_bonded: 2.16 r_work: 0.4033 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 10408 Z= 0.131 Angle : 0.562 9.740 14235 Z= 0.299 Chirality : 0.040 0.170 1598 Planarity : 0.004 0.058 1681 Dihedral : 17.089 85.165 1732 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.77 % Favored : 96.05 % Rotamer: Outliers : 5.17 % Allowed : 21.99 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.18 % 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: -0.16 (0.24), residues: 1140 helix: 1.43 (0.27), residues: 368 sheet: -0.09 (0.39), residues: 169 loop : -1.12 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 391 HIS 0.007 0.001 HIS L 93 PHE 0.015 0.001 PHE L 476 TYR 0.013 0.001 TYR L 531 ARG 0.005 0.000 ARG L 186 Details of bonding type rmsd hydrogen bonds : bond 0.03727 ( 415) hydrogen bonds : angle 4.47004 ( 1132) covalent geometry : bond 0.00300 (10408) covalent geometry : angle 0.56204 (14235) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8392.16 seconds wall clock time: 149 minutes 36.10 seconds (8976.10 seconds total)