Starting phenix.real_space_refine on Wed Jul 30 07:24:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s8p_19811/07_2025/8s8p_19811.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s8p_19811/07_2025/8s8p_19811.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8s8p_19811/07_2025/8s8p_19811.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s8p_19811/07_2025/8s8p_19811.map" model { file = "/net/cci-nas-00/data/ceres_data/8s8p_19811/07_2025/8s8p_19811.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s8p_19811/07_2025/8s8p_19811.cif" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 40 5.49 5 S 43 5.16 5 C 7564 2.51 5 N 2057 2.21 5 O 2430 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 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: 12134 Number of models: 1 Model: "" Number of chains: 5 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} 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: "K" Number of atoms: 4617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4617 Classifications: {'peptide': 557} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 20, 'TRANS': 535} Chain: "L" Number of atoms: 4658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4658 Classifications: {'peptide': 587} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 559} Chain: "R" Number of atoms: 2004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 2004 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'CIS': 6, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 219} Time building chain proxies: 10.02, per 1000 atoms: 0.83 Number of scatterers: 12134 At special positions: 0 Unit cell: (103.806, 96.579, 159.651, 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 43 16.00 P 40 15.00 O 2430 8.00 N 2057 7.00 C 7564 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: 2.91 Conformation dependent library (CDL) restraints added in 1.4 seconds 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2668 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 11 sheets defined 37.9% alpha, 15.9% beta 19 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 3.97 Creating SS restraints... Processing helix chain 'K' and resid 39 through 44 Processing helix chain 'K' and resid 53 through 73 removed outlier: 3.966A pdb=" N ILE K 71 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 94 removed outlier: 3.689A pdb=" N GLY K 93 " --> pdb=" O ALA K 90 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE K 94 " --> pdb=" O LYS K 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 90 through 94' Processing helix chain 'K' and resid 104 through 120 removed outlier: 3.518A pdb=" N MET K 108 " --> pdb=" O ASN K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 124 through 130 Processing helix chain 'K' and resid 141 through 153 removed outlier: 3.652A pdb=" N PHE K 153 " --> pdb=" O MET K 149 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 181 Processing helix chain 'K' and resid 183 through 199 Processing helix chain 'K' and resid 217 through 225 Processing helix chain 'K' and resid 252 through 259 Processing helix chain 'K' and resid 345 through 354 Processing helix chain 'K' and resid 396 through 409 removed outlier: 3.795A pdb=" N THR K 400 " --> pdb=" O GLY K 396 " (cutoff:3.500A) Processing helix chain 'K' and resid 470 through 488 removed outlier: 3.912A pdb=" N TYR K 487 " --> pdb=" O SER K 483 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE K 488 " --> pdb=" O ILE K 484 " (cutoff:3.500A) Processing helix chain 'K' and resid 495 through 499 Processing helix chain 'K' and resid 501 through 516 Processing helix chain 'K' and resid 527 through 539 Processing helix chain 'K' and resid 539 through 558 removed outlier: 3.636A pdb=" N ARG K 543 " --> pdb=" O ASP K 539 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS K 544 " --> pdb=" O ASP K 540 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU K 556 " --> pdb=" O ILE K 552 " (cutoff:3.500A) Processing helix chain 'K' and resid 564 through 584 removed outlier: 3.711A pdb=" N LYS K 568 " --> pdb=" O GLN K 564 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE K 580 " --> pdb=" O PHE K 576 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASN K 581 " --> pdb=" O TYR K 577 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASP K 582 " --> pdb=" O LYS K 578 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 19 Processing helix chain 'L' and resid 20 through 38 removed outlier: 3.580A pdb=" N LYS L 38 " --> pdb=" O LEU L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 94 Processing helix chain 'L' and resid 106 through 121 removed outlier: 3.557A pdb=" N LEU L 110 " --> pdb=" O MET L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 154 Processing helix chain 'L' and resid 175 through 183 removed outlier: 4.243A pdb=" N LEU L 179 " --> pdb=" O ASN L 175 " (cutoff:3.500A) Processing helix chain 'L' and resid 191 through 200 Processing helix chain 'L' and resid 327 through 334 removed outlier: 3.534A pdb=" N ASP L 332 " --> pdb=" O SER L 328 " (cutoff:3.500A) Processing helix chain 'L' and resid 354 through 358 removed outlier: 3.605A pdb=" N LEU L 358 " --> pdb=" O ARG L 355 " (cutoff:3.500A) Processing helix chain 'L' and resid 373 through 391 removed outlier: 3.632A pdb=" N LEU L 377 " --> pdb=" O CYS L 373 " (cutoff:3.500A) Processing helix chain 'L' and resid 467 through 481 removed outlier: 3.881A pdb=" N ASP L 471 " --> pdb=" O GLY L 467 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU L 472 " --> pdb=" O HIS L 468 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET L 481 " --> pdb=" O PHE L 477 " (cutoff:3.500A) Processing helix chain 'L' and resid 497 through 501 Processing helix chain 'L' and resid 513 through 517 removed outlier: 3.775A pdb=" N GLN L 516 " --> pdb=" O ASN L 513 " (cutoff:3.500A) Processing helix chain 'L' and resid 529 through 547 Processing helix chain 'L' and resid 559 through 566 removed outlier: 4.183A pdb=" N LYS L 565 " --> pdb=" O SER L 561 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE L 566 " --> pdb=" O LEU L 562 " (cutoff:3.500A) Processing helix chain 'L' and resid 576 through 584 Processing helix chain 'R' and resid 365 through 378 Processing helix chain 'R' and resid 379 through 382 removed outlier: 3.706A pdb=" N ARG R 382 " --> pdb=" O PRO R 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 379 through 382' Processing helix chain 'R' and resid 385 through 395 removed outlier: 3.530A pdb=" N ASP R 389 " --> pdb=" O HIS R 385 " (cutoff:3.500A) Processing helix chain 'R' and resid 399 through 410 Processing helix chain 'R' and resid 411 through 415 removed outlier: 3.891A pdb=" N LEU R 415 " --> pdb=" O SER R 412 " (cutoff:3.500A) Processing helix chain 'R' and resid 450 through 471 Processing helix chain 'R' and resid 521 through 534 removed outlier: 3.795A pdb=" N PHE R 525 " --> pdb=" O ILE R 521 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE R 526 " --> pdb=" O ALA R 522 " (cutoff:3.500A) Processing helix chain 'R' and resid 537 through 553 removed outlier: 3.618A pdb=" N TRP R 541 " --> pdb=" O THR R 537 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU R 550 " --> pdb=" O ARG R 546 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ALA R 551 " --> pdb=" O LYS R 547 " (cutoff:3.500A) Processing helix chain 'R' and resid 553 through 567 Processing sheet with id=AA1, first strand: chain 'K' and resid 95 through 102 removed outlier: 6.846A pdb=" N CYS K 80 " --> pdb=" O LEU K 97 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ILE K 78 " --> pdb=" O PRO K 99 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ARG K 101 " --> pdb=" O THR K 76 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N THR K 76 " --> pdb=" O ARG K 101 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU K 30 " --> pdb=" O ALA K 77 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N GLY K 79 " --> pdb=" O GLU K 30 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE K 32 " --> pdb=" O GLY K 79 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N TYR K 81 " --> pdb=" O ILE K 32 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE K 34 " --> pdb=" O TYR K 81 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N TYR K 83 " --> pdb=" O PHE K 34 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ILE K 36 " --> pdb=" O TYR K 83 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLY K 31 " --> pdb=" O ARG K 167 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N PHE K 169 " --> pdb=" O GLY K 31 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU K 33 " --> pdb=" O PHE K 169 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N PHE K 171 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N CYS K 35 " --> pdb=" O PHE K 171 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LYS K 166 " --> pdb=" O ASN K 202 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ALA K 204 " --> pdb=" O LYS K 166 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL K 168 " --> pdb=" O ALA K 204 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N PHE K 206 " --> pdb=" O VAL K 168 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU K 170 " --> pdb=" O PHE K 206 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE K 208 " --> pdb=" O LEU K 170 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N THR K 172 " --> pdb=" O ILE K 208 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE K 248 " --> pdb=" O THR K 205 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N PHE K 207 " --> pdb=" O ILE K 248 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 266 through 269 removed outlier: 6.606A pdb=" N GLY K 286 " --> pdb=" O MET K 267 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLN K 269 " --> pdb=" O VAL K 284 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL K 284 " --> pdb=" O GLN K 269 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER K 385 " --> pdb=" O LEU K 446 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR K 447 " --> pdb=" O THR K 431 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LEU K 429 " --> pdb=" O VAL K 449 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N LYS K 413 " --> pdb=" O PRO K 434 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TRP K 418 " --> pdb=" O ILE K 365 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ILE K 365 " --> pdb=" O TRP K 418 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N LYS K 420 " --> pdb=" O LEU K 363 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LEU K 363 " --> pdb=" O LYS K 420 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ASP K 275 " --> pdb=" O ILE K 365 " (cutoff:3.500A) removed outlier: 11.921A pdb=" N GLY K 367 " --> pdb=" O ASP K 275 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N PHE K 280 " --> pdb=" O LEU K 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 308 through 311 removed outlier: 3.789A pdb=" N GLN K 310 " --> pdb=" O TYR K 303 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 313 through 319 removed outlier: 4.201A pdb=" N TYR L 282 " --> pdb=" O ILE L 308 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN L 286 " --> pdb=" O ILE L 304 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE L 304 " --> pdb=" O ASN L 286 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 341 through 342 removed outlier: 3.750A pdb=" N VAL L 274 " --> pdb=" O VAL L 262 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ARG L 272 " --> pdb=" O VAL L 264 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 394 through 395 Processing sheet with id=AA7, first strand: chain 'L' and resid 65 through 72 removed outlier: 6.635A pdb=" N CYS L 48 " --> pdb=" O ILE L 68 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N SER L 70 " --> pdb=" O ILE L 46 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ILE L 46 " --> pdb=" O SER L 70 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU L 72 " --> pdb=" O ASP L 44 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ASP L 44 " --> pdb=" O LEU L 72 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLU L 4 " --> pdb=" O TRP L 45 " (cutoff:3.500A) removed outlier: 9.144A pdb=" N SER L 47 " --> pdb=" O GLU L 4 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR L 6 " --> pdb=" O SER L 47 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N TYR L 49 " --> pdb=" O THR L 6 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N PHE L 8 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ALA L 51 " --> pdb=" O PHE L 8 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL L 10 " --> pdb=" O ALA L 51 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N SER L 5 " --> pdb=" O GLN L 129 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N VAL L 131 " --> pdb=" O SER L 5 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N THR L 7 " --> pdb=" O VAL L 131 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N PHE L 133 " --> pdb=" O THR L 7 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE L 9 " --> pdb=" O PHE L 133 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LYS L 128 " --> pdb=" O ARG L 157 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ILE L 159 " --> pdb=" O LYS L 128 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE L 130 " --> pdb=" O ILE L 159 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ILE L 161 " --> pdb=" O ILE L 130 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL L 132 " --> pdb=" O ILE L 161 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 248 through 250 removed outlier: 6.389A pdb=" N SER L 362 " --> pdb=" O ALA L 249 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ALA L 367 " --> pdb=" O LYS L 429 " (cutoff:3.500A) removed outlier: 9.892A pdb=" N LYS L 429 " --> pdb=" O ALA L 367 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N MET L 408 " --> pdb=" O LEU L 436 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N LYS L 392 " --> pdb=" O PRO L 413 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY L 346 " --> pdb=" O VAL L 395 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ARG L 397 " --> pdb=" O LEU L 344 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N LEU L 344 " --> pdb=" O ARG L 397 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL L 399 " --> pdb=" O LEU L 342 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N LEU L 342 " --> pdb=" O VAL L 399 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N LEU L 342 " --> pdb=" O SER L 213 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLU L 215 " --> pdb=" O LEU L 342 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LEU L 344 " --> pdb=" O GLU L 215 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ARG L 217 " --> pdb=" O LEU L 344 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N GLY L 346 " --> pdb=" O ARG L 217 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 317 through 319 Processing sheet with id=AB1, first strand: chain 'R' and resid 418 through 419 Processing sheet with id=AB2, first strand: chain 'R' and resid 478 through 479 removed outlier: 3.585A pdb=" N THR R 496 " --> pdb=" O ARG R 478 " (cutoff:3.500A) 429 hydrogen bonds defined for protein. 1200 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 4.11 Time building geometry restraints manager: 3.40 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: 3489 1.34 - 1.45: 2062 1.45 - 1.57: 6763 1.57 - 1.69: 80 1.69 - 1.81: 71 Bond restraints: 12465 Sorted by residual: bond pdb=" C ASP R 498 " pdb=" N PRO R 499 " ideal model delta sigma weight residual 1.334 1.371 -0.037 2.34e-02 1.83e+03 2.47e+00 bond pdb=" CG1 ILE K 407 " pdb=" CD1 ILE K 407 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.84e+00 bond pdb=" C3' DC C 16 " pdb=" O3' DC C 16 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.65e+00 bond pdb=" N LYS R 597 " pdb=" CA LYS R 597 " ideal model delta sigma weight residual 1.458 1.479 -0.021 1.90e-02 2.77e+03 1.24e+00 bond pdb=" O4' DT D 21 " pdb=" C1' DT D 21 " ideal model delta sigma weight residual 1.414 1.393 0.021 2.00e-02 2.50e+03 1.14e+00 ... (remaining 12460 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 16720 1.89 - 3.78: 270 3.78 - 5.67: 22 5.67 - 7.55: 5 7.55 - 9.44: 1 Bond angle restraints: 17018 Sorted by residual: angle pdb=" C GLU L 464 " pdb=" CA GLU L 464 " pdb=" CB GLU L 464 " ideal model delta sigma weight residual 116.34 110.54 5.80 1.40e+00 5.10e-01 1.72e+01 angle pdb=" C ALA R 596 " pdb=" N LYS R 597 " pdb=" CA LYS R 597 " ideal model delta sigma weight residual 121.70 128.93 -7.23 1.80e+00 3.09e-01 1.62e+01 angle pdb=" C VAL K 388 " pdb=" CA VAL K 388 " pdb=" CB VAL K 388 " ideal model delta sigma weight residual 109.33 112.93 -3.60 9.80e-01 1.04e+00 1.35e+01 angle pdb=" C ARG K 409 " pdb=" N LYS K 410 " pdb=" CA LYS K 410 " ideal model delta sigma weight residual 121.54 128.05 -6.51 1.91e+00 2.74e-01 1.16e+01 angle pdb=" N VAL K 388 " pdb=" CA VAL K 388 " pdb=" C VAL K 388 " ideal model delta sigma weight residual 109.19 106.55 2.64 8.20e-01 1.49e+00 1.04e+01 ... (remaining 17013 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.87: 7085 34.87 - 69.75: 423 69.75 - 104.62: 24 104.62 - 139.49: 0 139.49 - 174.37: 1 Dihedral angle restraints: 7533 sinusoidal: 3417 harmonic: 4116 Sorted by residual: dihedral pdb=" CA PHE R 363 " pdb=" C PHE R 363 " pdb=" N THR R 364 " pdb=" CA THR R 364 " ideal model delta harmonic sigma weight residual 180.00 156.46 23.54 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA THR R 364 " pdb=" C THR R 364 " pdb=" N ASP R 365 " pdb=" CA ASP R 365 " ideal model delta harmonic sigma weight residual -180.00 -156.84 -23.16 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" C4' DC C 16 " pdb=" C3' DC C 16 " pdb=" O3' DC C 16 " pdb=" P DA C 17 " ideal model delta sinusoidal sigma weight residual 220.00 45.63 174.37 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 7530 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1154 0.028 - 0.057: 467 0.057 - 0.085: 155 0.085 - 0.113: 85 0.113 - 0.142: 23 Chirality restraints: 1884 Sorted by residual: chirality pdb=" CA PHE R 363 " pdb=" N PHE R 363 " pdb=" C PHE R 363 " pdb=" CB PHE R 363 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.01e-01 chirality pdb=" CA ILE L 188 " pdb=" N ILE L 188 " pdb=" C ILE L 188 " pdb=" CB ILE L 188 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA VAL K 388 " pdb=" N VAL K 388 " pdb=" C VAL K 388 " pdb=" CB VAL K 388 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 1881 not shown) Planarity restraints: 2055 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU L 558 " -0.034 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO L 559 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO L 559 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO L 559 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL K 388 " -0.030 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO K 389 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO K 389 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO K 389 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE L 489 " 0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO L 490 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO L 490 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO L 490 " 0.022 5.00e-02 4.00e+02 ... (remaining 2052 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 419 2.71 - 3.26: 11661 3.26 - 3.80: 19419 3.80 - 4.35: 25064 4.35 - 4.90: 41126 Nonbonded interactions: 97689 Sorted by model distance: nonbonded pdb=" OE1 GLU K 37 " pdb=" OG1 THR K 172 " model vdw 2.162 3.040 nonbonded pdb=" O ARG R 382 " pdb=" OH TYR R 388 " model vdw 2.192 3.040 nonbonded pdb=" OH TYR K 494 " pdb=" O PRO L 437 " model vdw 2.207 3.040 nonbonded pdb=" O PRO R 487 " pdb=" OG1 THR R 488 " model vdw 2.253 3.040 nonbonded pdb=" O ILE L 68 " pdb=" NH1 ARG L 86 " model vdw 2.267 3.120 ... (remaining 97684 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: 13.280 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: 0.670 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 35.140 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12465 Z= 0.126 Angle : 0.573 9.443 17018 Z= 0.323 Chirality : 0.039 0.142 1884 Planarity : 0.004 0.052 2055 Dihedral : 19.608 174.366 4865 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.71 % Favored : 95.14 % Rotamer: Outliers : 0.31 % Allowed : 21.52 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.53 % 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: -0.64 (0.22), residues: 1380 helix: 1.26 (0.24), residues: 465 sheet: -1.16 (0.38), residues: 170 loop : -1.38 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 418 HIS 0.003 0.001 HIS L 418 PHE 0.009 0.001 PHE K 98 TYR 0.014 0.001 TYR K 394 ARG 0.007 0.000 ARG K 543 Details of bonding type rmsd hydrogen bonds : bond 0.16772 ( 479) hydrogen bonds : angle 6.50329 ( 1300) covalent geometry : bond 0.00257 (12465) covalent geometry : angle 0.57291 (17018) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 129 time to evaluate : 1.589 Fit side-chains revert: symmetry clash REVERT: K 213 LYS cc_start: 0.7622 (tttm) cc_final: 0.7082 (tmtt) REVERT: R 412 SER cc_start: 0.7887 (p) cc_final: 0.7584 (p) outliers start: 4 outliers final: 3 residues processed: 132 average time/residue: 0.2561 time to fit residues: 48.1747 Evaluate side-chains 120 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 117 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 29 HIS Chi-restraints excluded: chain K residue 273 ILE Chi-restraints excluded: chain L residue 111 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 42 optimal weight: 0.0970 chunk 67 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 128 optimal weight: 0.0370 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 225 GLN ** R 405 HIS ** 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 = 0.4511 r_free = 0.4511 target = 0.219496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.173581 restraints weight = 13672.798| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 2.58 r_work: 0.3754 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12465 Z= 0.130 Angle : 0.551 7.242 17018 Z= 0.297 Chirality : 0.041 0.163 1884 Planarity : 0.004 0.052 2055 Dihedral : 16.467 174.647 1978 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.13 % Allowed : 19.64 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.53 % 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: -0.57 (0.22), residues: 1380 helix: 1.39 (0.24), residues: 473 sheet: -1.18 (0.38), residues: 176 loop : -1.41 (0.21), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 418 HIS 0.004 0.001 HIS K 512 PHE 0.011 0.001 PHE K 98 TYR 0.013 0.001 TYR K 83 ARG 0.004 0.000 ARG K 534 Details of bonding type rmsd hydrogen bonds : bond 0.03622 ( 479) hydrogen bonds : angle 5.05821 ( 1300) covalent geometry : bond 0.00290 (12465) covalent geometry : angle 0.55123 (17018) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 133 time to evaluate : 1.399 Fit side-chains revert: symmetry clash REVERT: K 176 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7997 (mmtp) REVERT: K 213 LYS cc_start: 0.7676 (tttm) cc_final: 0.7091 (tmtt) REVERT: K 251 LYS cc_start: 0.8665 (mmmt) cc_final: 0.8453 (mmmt) REVERT: L 142 ILE cc_start: 0.3948 (OUTLIER) cc_final: 0.3578 (mt) REVERT: L 181 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7831 (pt0) REVERT: L 324 VAL cc_start: 0.7278 (OUTLIER) cc_final: 0.7054 (m) outliers start: 40 outliers final: 20 residues processed: 158 average time/residue: 0.2734 time to fit residues: 61.8192 Evaluate side-chains 140 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 29 HIS Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain K residue 176 LYS Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain K residue 281 ILE Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 353 MET Chi-restraints excluded: chain K residue 485 MET Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 181 GLU Chi-restraints excluded: chain L residue 236 ASP Chi-restraints excluded: chain L residue 245 GLU Chi-restraints excluded: chain L residue 314 THR Chi-restraints excluded: chain L residue 324 VAL Chi-restraints excluded: chain L residue 331 VAL Chi-restraints excluded: chain L residue 403 ASP Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 505 THR Chi-restraints excluded: chain R residue 440 VAL Chi-restraints excluded: chain R residue 514 THR Chi-restraints excluded: chain R residue 578 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 78 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 77 optimal weight: 0.0030 chunk 6 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 0.0870 chunk 24 optimal weight: 0.0020 chunk 8 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 225 GLN L 333 GLN L 513 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.217438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.173546 restraints weight = 13782.743| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 2.54 r_work: 0.3748 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12465 Z= 0.137 Angle : 0.542 7.577 17018 Z= 0.290 Chirality : 0.041 0.156 1884 Planarity : 0.004 0.045 2055 Dihedral : 16.510 175.786 1976 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.90 % Allowed : 20.66 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.53 % 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: -0.56 (0.22), residues: 1380 helix: 1.39 (0.24), residues: 479 sheet: -1.13 (0.38), residues: 176 loop : -1.43 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 418 HIS 0.004 0.001 HIS K 512 PHE 0.020 0.001 PHE K 197 TYR 0.012 0.001 TYR K 83 ARG 0.005 0.000 ARG K 543 Details of bonding type rmsd hydrogen bonds : bond 0.03548 ( 479) hydrogen bonds : angle 4.83781 ( 1300) covalent geometry : bond 0.00313 (12465) covalent geometry : angle 0.54249 (17018) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 131 time to evaluate : 1.914 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 197 PHE cc_start: 0.7846 (t80) cc_final: 0.7441 (m-80) REVERT: K 213 LYS cc_start: 0.7687 (tttm) cc_final: 0.7135 (tmtt) REVERT: K 216 ASP cc_start: 0.7188 (m-30) cc_final: 0.6942 (t0) REVERT: L 142 ILE cc_start: 0.3903 (OUTLIER) cc_final: 0.3584 (mt) REVERT: L 181 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7859 (pt0) REVERT: L 324 VAL cc_start: 0.7340 (OUTLIER) cc_final: 0.7065 (m) outliers start: 37 outliers final: 21 residues processed: 158 average time/residue: 0.2742 time to fit residues: 63.0991 Evaluate side-chains 146 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 2.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain K residue 255 SER Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 371 SER Chi-restraints excluded: chain K residue 485 MET Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 181 GLU Chi-restraints excluded: chain L residue 236 ASP Chi-restraints excluded: chain L residue 245 GLU Chi-restraints excluded: chain L residue 269 LYS Chi-restraints excluded: chain L residue 313 VAL Chi-restraints excluded: chain L residue 314 THR Chi-restraints excluded: chain L residue 324 VAL Chi-restraints excluded: chain L residue 333 GLN Chi-restraints excluded: chain L residue 403 ASP Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain R residue 373 ASP Chi-restraints excluded: chain R residue 440 VAL Chi-restraints excluded: chain R residue 514 THR Chi-restraints excluded: chain R residue 537 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 13 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 108 optimal weight: 0.1980 chunk 57 optimal weight: 1.9990 chunk 129 optimal weight: 0.0010 chunk 58 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 333 GLN ** R 405 HIS ** 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 = 0.4510 r_free = 0.4510 target = 0.219426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.174021 restraints weight = 13664.332| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 2.59 r_work: 0.3755 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12465 Z= 0.123 Angle : 0.526 7.250 17018 Z= 0.283 Chirality : 0.040 0.152 1884 Planarity : 0.004 0.044 2055 Dihedral : 16.477 176.928 1974 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.21 % Allowed : 20.66 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.53 % 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: -0.48 (0.22), residues: 1380 helix: 1.47 (0.24), residues: 479 sheet: -1.09 (0.38), residues: 176 loop : -1.39 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 418 HIS 0.004 0.001 HIS K 512 PHE 0.012 0.001 PHE K 197 TYR 0.014 0.001 TYR K 83 ARG 0.003 0.000 ARG L 272 Details of bonding type rmsd hydrogen bonds : bond 0.03266 ( 479) hydrogen bonds : angle 4.72702 ( 1300) covalent geometry : bond 0.00274 (12465) covalent geometry : angle 0.52563 (17018) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 136 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 197 PHE cc_start: 0.7836 (t80) cc_final: 0.7476 (m-80) REVERT: K 213 LYS cc_start: 0.7710 (tttm) cc_final: 0.7159 (tmtt) REVERT: L 142 ILE cc_start: 0.3861 (OUTLIER) cc_final: 0.3560 (mt) REVERT: L 324 VAL cc_start: 0.7336 (OUTLIER) cc_final: 0.7075 (m) outliers start: 41 outliers final: 26 residues processed: 169 average time/residue: 0.2979 time to fit residues: 71.5996 Evaluate side-chains 150 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain K residue 255 SER Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain K residue 281 ILE Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 371 SER Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 15 SER Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 236 ASP Chi-restraints excluded: chain L residue 245 GLU Chi-restraints excluded: chain L residue 314 THR Chi-restraints excluded: chain L residue 324 VAL Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 334 THR Chi-restraints excluded: chain L residue 362 SER Chi-restraints excluded: chain L residue 403 ASP Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain R residue 373 ASP Chi-restraints excluded: chain R residue 383 THR Chi-restraints excluded: chain R residue 399 THR Chi-restraints excluded: chain R residue 440 VAL Chi-restraints excluded: chain R residue 514 THR Chi-restraints excluded: chain R residue 537 THR Chi-restraints excluded: chain R residue 578 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 0.0970 chunk 130 optimal weight: 0.0970 chunk 60 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 86 optimal weight: 0.2980 chunk 131 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 129 optimal weight: 0.2980 overall best weight: 0.2776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 333 GLN R 405 HIS R 494 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.219325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.174755 restraints weight = 13674.615| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 2.38 r_work: 0.3806 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12465 Z= 0.107 Angle : 0.510 7.686 17018 Z= 0.274 Chirality : 0.039 0.145 1884 Planarity : 0.004 0.042 2055 Dihedral : 16.427 177.705 1974 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.82 % Allowed : 20.97 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.53 % 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: -0.37 (0.22), residues: 1380 helix: 1.58 (0.24), residues: 479 sheet: -1.02 (0.39), residues: 168 loop : -1.35 (0.21), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 418 HIS 0.003 0.001 HIS K 512 PHE 0.016 0.001 PHE L 133 TYR 0.017 0.001 TYR K 83 ARG 0.006 0.000 ARG K 543 Details of bonding type rmsd hydrogen bonds : bond 0.03057 ( 479) hydrogen bonds : angle 4.54915 ( 1300) covalent geometry : bond 0.00234 (12465) covalent geometry : angle 0.50962 (17018) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 123 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 197 PHE cc_start: 0.7833 (t80) cc_final: 0.7495 (m-80) REVERT: K 213 LYS cc_start: 0.7678 (tttm) cc_final: 0.7131 (tmtt) REVERT: L 17 MET cc_start: 0.6581 (mmt) cc_final: 0.6295 (mmm) REVERT: L 142 ILE cc_start: 0.3716 (OUTLIER) cc_final: 0.3434 (mt) REVERT: L 324 VAL cc_start: 0.7183 (OUTLIER) cc_final: 0.6932 (m) REVERT: R 412 SER cc_start: 0.7929 (p) cc_final: 0.7613 (p) outliers start: 36 outliers final: 27 residues processed: 154 average time/residue: 0.2352 time to fit residues: 52.8409 Evaluate side-chains 142 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain K residue 255 SER Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 281 ILE Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 371 SER Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 236 ASP Chi-restraints excluded: chain L residue 245 GLU Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 313 VAL Chi-restraints excluded: chain L residue 324 VAL Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 331 VAL Chi-restraints excluded: chain L residue 362 SER Chi-restraints excluded: chain L residue 403 ASP Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain R residue 373 ASP Chi-restraints excluded: chain R residue 383 THR Chi-restraints excluded: chain R residue 399 THR Chi-restraints excluded: chain R residue 440 VAL Chi-restraints excluded: chain R residue 514 THR Chi-restraints excluded: chain R residue 537 THR Chi-restraints excluded: chain R residue 578 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 25 optimal weight: 7.9990 chunk 61 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 29 HIS L 333 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.216502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.171428 restraints weight = 13791.479| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 2.58 r_work: 0.3721 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12465 Z= 0.150 Angle : 0.542 7.272 17018 Z= 0.289 Chirality : 0.040 0.156 1884 Planarity : 0.004 0.043 2055 Dihedral : 16.561 177.184 1974 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.76 % Allowed : 19.95 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.53 % 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: -0.42 (0.22), residues: 1380 helix: 1.50 (0.24), residues: 480 sheet: -1.06 (0.38), residues: 169 loop : -1.34 (0.21), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 418 HIS 0.004 0.001 HIS K 512 PHE 0.014 0.001 PHE K 98 TYR 0.015 0.001 TYR K 83 ARG 0.004 0.000 ARG K 543 Details of bonding type rmsd hydrogen bonds : bond 0.03336 ( 479) hydrogen bonds : angle 4.62383 ( 1300) covalent geometry : bond 0.00347 (12465) covalent geometry : angle 0.54168 (17018) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 125 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 197 PHE cc_start: 0.7878 (t80) cc_final: 0.7537 (m-80) REVERT: K 300 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8332 (mtpt) REVERT: L 17 MET cc_start: 0.6706 (mmt) cc_final: 0.6469 (mmm) REVERT: L 142 ILE cc_start: 0.3787 (OUTLIER) cc_final: 0.3498 (mt) REVERT: L 181 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.7948 (pt0) REVERT: R 412 SER cc_start: 0.7963 (p) cc_final: 0.7645 (p) outliers start: 48 outliers final: 34 residues processed: 165 average time/residue: 0.2657 time to fit residues: 64.1214 Evaluate side-chains 155 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 148 PHE Chi-restraints excluded: chain K residue 255 SER Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 281 ILE Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain K residue 300 LYS Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 461 LEU Chi-restraints excluded: chain K residue 535 MET Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 15 SER Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 181 GLU Chi-restraints excluded: chain L residue 236 ASP Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 278 SER Chi-restraints excluded: chain L residue 313 VAL Chi-restraints excluded: chain L residue 324 VAL Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 331 VAL Chi-restraints excluded: chain L residue 334 THR Chi-restraints excluded: chain L residue 362 SER Chi-restraints excluded: chain L residue 403 ASP Chi-restraints excluded: chain L residue 405 GLU Chi-restraints excluded: chain L residue 498 ILE Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 505 THR Chi-restraints excluded: chain R residue 373 ASP Chi-restraints excluded: chain R residue 383 THR Chi-restraints excluded: chain R residue 399 THR Chi-restraints excluded: chain R residue 440 VAL Chi-restraints excluded: chain R residue 514 THR Chi-restraints excluded: chain R residue 537 THR Chi-restraints excluded: chain R residue 578 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 83 optimal weight: 0.9990 chunk 140 optimal weight: 0.0050 chunk 110 optimal weight: 0.9990 chunk 136 optimal weight: 0.6980 chunk 47 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 120 optimal weight: 0.8980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 29 HIS L 333 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.217510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.172893 restraints weight = 13672.490| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 2.45 r_work: 0.3754 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12465 Z= 0.124 Angle : 0.521 7.487 17018 Z= 0.278 Chirality : 0.040 0.155 1884 Planarity : 0.004 0.042 2055 Dihedral : 16.534 178.478 1974 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.68 % Allowed : 20.03 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.53 % 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: -0.37 (0.22), residues: 1380 helix: 1.54 (0.24), residues: 480 sheet: -1.02 (0.39), residues: 170 loop : -1.32 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 418 HIS 0.004 0.001 HIS K 512 PHE 0.011 0.001 PHE K 98 TYR 0.015 0.001 TYR K 83 ARG 0.003 0.000 ARG L 272 Details of bonding type rmsd hydrogen bonds : bond 0.03146 ( 479) hydrogen bonds : angle 4.52601 ( 1300) covalent geometry : bond 0.00282 (12465) covalent geometry : angle 0.52136 (17018) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 124 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 197 PHE cc_start: 0.7867 (t80) cc_final: 0.7536 (m-80) REVERT: K 216 ASP cc_start: 0.7180 (m-30) cc_final: 0.6867 (t0) REVERT: K 300 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8281 (mtpt) REVERT: L 17 MET cc_start: 0.6664 (mmt) cc_final: 0.6422 (mmm) REVERT: L 142 ILE cc_start: 0.3852 (OUTLIER) cc_final: 0.3537 (mt) REVERT: L 181 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.7922 (pt0) REVERT: R 412 SER cc_start: 0.7939 (p) cc_final: 0.7630 (p) REVERT: R 413 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7983 (ptpt) outliers start: 47 outliers final: 31 residues processed: 162 average time/residue: 0.2386 time to fit residues: 56.8217 Evaluate side-chains 156 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 121 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 148 PHE Chi-restraints excluded: chain K residue 255 SER Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 281 ILE Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain K residue 300 LYS Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 371 SER Chi-restraints excluded: chain K residue 535 MET Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 181 GLU Chi-restraints excluded: chain L residue 236 ASP Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 278 SER Chi-restraints excluded: chain L residue 313 VAL Chi-restraints excluded: chain L residue 314 THR Chi-restraints excluded: chain L residue 324 VAL Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 334 THR Chi-restraints excluded: chain L residue 362 SER Chi-restraints excluded: chain L residue 403 ASP Chi-restraints excluded: chain L residue 498 ILE Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain R residue 373 ASP Chi-restraints excluded: chain R residue 383 THR Chi-restraints excluded: chain R residue 399 THR Chi-restraints excluded: chain R residue 413 LYS Chi-restraints excluded: chain R residue 440 VAL Chi-restraints excluded: chain R residue 514 THR Chi-restraints excluded: chain R residue 537 THR Chi-restraints excluded: chain R residue 578 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 52 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 127 optimal weight: 0.9990 chunk 110 optimal weight: 0.0970 chunk 20 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 333 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.215981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.170970 restraints weight = 13814.251| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 2.59 r_work: 0.3713 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12465 Z= 0.146 Angle : 0.546 8.199 17018 Z= 0.290 Chirality : 0.041 0.160 1884 Planarity : 0.004 0.041 2055 Dihedral : 16.621 178.419 1974 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.68 % Allowed : 20.19 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.53 % 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: -0.42 (0.22), residues: 1380 helix: 1.46 (0.24), residues: 482 sheet: -1.11 (0.38), residues: 170 loop : -1.30 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 418 HIS 0.004 0.001 HIS K 512 PHE 0.014 0.001 PHE K 98 TYR 0.018 0.001 TYR K 394 ARG 0.004 0.000 ARG L 272 Details of bonding type rmsd hydrogen bonds : bond 0.03338 ( 479) hydrogen bonds : angle 4.57872 ( 1300) covalent geometry : bond 0.00341 (12465) covalent geometry : angle 0.54644 (17018) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 125 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 197 PHE cc_start: 0.7907 (t80) cc_final: 0.7477 (m-80) REVERT: K 216 ASP cc_start: 0.7212 (m-30) cc_final: 0.6880 (t0) REVERT: K 300 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8252 (mtpt) REVERT: L 142 ILE cc_start: 0.3962 (OUTLIER) cc_final: 0.3666 (mt) REVERT: L 181 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.7940 (pt0) REVERT: R 412 SER cc_start: 0.7973 (p) cc_final: 0.7658 (p) REVERT: R 413 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7990 (ptpt) outliers start: 47 outliers final: 36 residues processed: 166 average time/residue: 0.3089 time to fit residues: 76.4639 Evaluate side-chains 159 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 119 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 148 PHE Chi-restraints excluded: chain K residue 176 LYS Chi-restraints excluded: chain K residue 255 SER Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 281 ILE Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain K residue 300 LYS Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 371 SER Chi-restraints excluded: chain K residue 461 LEU Chi-restraints excluded: chain K residue 535 MET Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 15 SER Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 181 GLU Chi-restraints excluded: chain L residue 236 ASP Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 278 SER Chi-restraints excluded: chain L residue 313 VAL Chi-restraints excluded: chain L residue 314 THR Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 334 THR Chi-restraints excluded: chain L residue 362 SER Chi-restraints excluded: chain L residue 403 ASP Chi-restraints excluded: chain L residue 498 ILE Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 505 THR Chi-restraints excluded: chain R residue 373 ASP Chi-restraints excluded: chain R residue 383 THR Chi-restraints excluded: chain R residue 399 THR Chi-restraints excluded: chain R residue 413 LYS Chi-restraints excluded: chain R residue 440 VAL Chi-restraints excluded: chain R residue 514 THR Chi-restraints excluded: chain R residue 537 THR Chi-restraints excluded: chain R residue 578 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 138 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 73 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 87 optimal weight: 0.2980 chunk 108 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 333 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.216546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.171608 restraints weight = 13641.073| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 2.58 r_work: 0.3725 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12465 Z= 0.138 Angle : 0.542 9.571 17018 Z= 0.286 Chirality : 0.040 0.159 1884 Planarity : 0.004 0.041 2055 Dihedral : 16.619 179.119 1974 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.21 % Allowed : 21.05 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.53 % 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: -0.39 (0.22), residues: 1380 helix: 1.47 (0.24), residues: 481 sheet: -1.04 (0.38), residues: 168 loop : -1.29 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 418 HIS 0.004 0.001 HIS K 512 PHE 0.013 0.001 PHE K 98 TYR 0.018 0.001 TYR L 569 ARG 0.004 0.000 ARG L 272 Details of bonding type rmsd hydrogen bonds : bond 0.03241 ( 479) hydrogen bonds : angle 4.51643 ( 1300) covalent geometry : bond 0.00319 (12465) covalent geometry : angle 0.54180 (17018) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 122 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 197 PHE cc_start: 0.7895 (t80) cc_final: 0.7446 (m-80) REVERT: K 216 ASP cc_start: 0.7222 (m-30) cc_final: 0.6959 (t0) REVERT: K 218 GLU cc_start: 0.7491 (pm20) cc_final: 0.7070 (pm20) REVERT: K 300 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8176 (mtpt) REVERT: L 142 ILE cc_start: 0.3968 (OUTLIER) cc_final: 0.3639 (mt) REVERT: L 181 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.7936 (pt0) REVERT: R 412 SER cc_start: 0.7937 (p) cc_final: 0.7614 (p) REVERT: R 413 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7950 (ptpt) outliers start: 41 outliers final: 34 residues processed: 157 average time/residue: 0.2379 time to fit residues: 54.6759 Evaluate side-chains 154 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 116 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 148 PHE Chi-restraints excluded: chain K residue 176 LYS Chi-restraints excluded: chain K residue 255 SER Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 281 ILE Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain K residue 300 LYS Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 371 SER Chi-restraints excluded: chain K residue 535 MET Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 15 SER Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 181 GLU Chi-restraints excluded: chain L residue 236 ASP Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 278 SER Chi-restraints excluded: chain L residue 313 VAL Chi-restraints excluded: chain L residue 314 THR Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 334 THR Chi-restraints excluded: chain L residue 362 SER Chi-restraints excluded: chain L residue 403 ASP Chi-restraints excluded: chain L residue 498 ILE Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 505 THR Chi-restraints excluded: chain R residue 373 ASP Chi-restraints excluded: chain R residue 383 THR Chi-restraints excluded: chain R residue 399 THR Chi-restraints excluded: chain R residue 413 LYS Chi-restraints excluded: chain R residue 440 VAL Chi-restraints excluded: chain R residue 514 THR Chi-restraints excluded: chain R residue 537 THR Chi-restraints excluded: chain R residue 578 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 9 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 124 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 333 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.214755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.169779 restraints weight = 13626.177| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 2.53 r_work: 0.3713 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12465 Z= 0.161 Angle : 0.564 8.635 17018 Z= 0.298 Chirality : 0.041 0.163 1884 Planarity : 0.004 0.041 2055 Dihedral : 16.714 178.912 1974 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.29 % Allowed : 21.13 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.53 % 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: -0.47 (0.22), residues: 1380 helix: 1.35 (0.24), residues: 487 sheet: -1.06 (0.39), residues: 168 loop : -1.31 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 418 HIS 0.004 0.001 HIS K 512 PHE 0.015 0.001 PHE K 98 TYR 0.016 0.001 TYR K 394 ARG 0.004 0.000 ARG L 272 Details of bonding type rmsd hydrogen bonds : bond 0.03412 ( 479) hydrogen bonds : angle 4.60532 ( 1300) covalent geometry : bond 0.00379 (12465) covalent geometry : angle 0.56445 (17018) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 121 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 197 PHE cc_start: 0.7931 (t80) cc_final: 0.7510 (m-80) REVERT: K 245 THR cc_start: 0.8127 (p) cc_final: 0.7896 (p) REVERT: K 300 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8233 (mtpt) REVERT: K 537 ARG cc_start: 0.7664 (ttp-170) cc_final: 0.7325 (mtm110) REVERT: L 142 ILE cc_start: 0.4048 (OUTLIER) cc_final: 0.3719 (mt) REVERT: L 181 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.7982 (pt0) REVERT: L 506 THR cc_start: 0.7988 (m) cc_final: 0.7760 (t) REVERT: R 413 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.8024 (ptpt) outliers start: 42 outliers final: 36 residues processed: 157 average time/residue: 0.2391 time to fit residues: 54.8362 Evaluate side-chains 157 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 117 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 148 PHE Chi-restraints excluded: chain K residue 176 LYS Chi-restraints excluded: chain K residue 255 SER Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain K residue 266 ILE Chi-restraints excluded: chain K residue 281 ILE Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain K residue 300 LYS Chi-restraints excluded: chain K residue 302 VAL Chi-restraints excluded: chain K residue 371 SER Chi-restraints excluded: chain K residue 461 LEU Chi-restraints excluded: chain K residue 535 MET Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 15 SER Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 181 GLU Chi-restraints excluded: chain L residue 236 ASP Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 278 SER Chi-restraints excluded: chain L residue 313 VAL Chi-restraints excluded: chain L residue 314 THR Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 334 THR Chi-restraints excluded: chain L residue 362 SER Chi-restraints excluded: chain L residue 403 ASP Chi-restraints excluded: chain L residue 498 ILE Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 505 THR Chi-restraints excluded: chain R residue 373 ASP Chi-restraints excluded: chain R residue 383 THR Chi-restraints excluded: chain R residue 399 THR Chi-restraints excluded: chain R residue 413 LYS Chi-restraints excluded: chain R residue 440 VAL Chi-restraints excluded: chain R residue 514 THR Chi-restraints excluded: chain R residue 537 THR Chi-restraints excluded: chain R residue 578 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 38 optimal weight: 0.0370 chunk 45 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 29 optimal weight: 0.0370 chunk 19 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 88 optimal weight: 0.0970 chunk 4 optimal weight: 1.9990 overall best weight: 0.3334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 333 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.218079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.173461 restraints weight = 13614.408| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 2.51 r_work: 0.3750 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12465 Z= 0.113 Angle : 0.523 8.551 17018 Z= 0.278 Chirality : 0.039 0.154 1884 Planarity : 0.004 0.041 2055 Dihedral : 16.572 179.305 1974 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.82 % Allowed : 21.91 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.53 % 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: -0.29 (0.22), residues: 1380 helix: 1.61 (0.24), residues: 478 sheet: -0.96 (0.39), residues: 167 loop : -1.27 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 418 HIS 0.003 0.001 HIS K 512 PHE 0.009 0.001 PHE K 98 TYR 0.015 0.001 TYR K 83 ARG 0.004 0.000 ARG L 272 Details of bonding type rmsd hydrogen bonds : bond 0.03046 ( 479) hydrogen bonds : angle 4.44264 ( 1300) covalent geometry : bond 0.00251 (12465) covalent geometry : angle 0.52329 (17018) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6943.36 seconds wall clock time: 123 minutes 26.95 seconds (7406.95 seconds total)