Starting phenix.real_space_refine on Thu Aug 6 22:47:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bxg_16318/08_2026/8bxg_16318_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bxg_16318/08_2026/8bxg_16318.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8bxg_16318/08_2026/8bxg_16318_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bxg_16318/08_2026/8bxg_16318_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bxg_16318/08_2026/8bxg_16318.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bxg_16318/08_2026/8bxg_16318.map" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 7 Type Number sf(0) Gaussians K 2 8.98 5 P 4 5.49 5 S 54 5.16 5 C 5547 2.51 5 N 1426 2.21 5 O 1472 1.98 5 H 8796 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17301 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 8584 Classifications: {'peptide': 547} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 18, 'TRANS': 528} Chain breaks: 1 Chain: "B" Number of atoms: 8567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 8567 Classifications: {'peptide': 546} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 18, 'TRANS': 527} Chain breaks: 1 Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {' K': 1, 'AMP%rna2p': 1, 'PGW': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 2} Chain: "B" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {' K': 1, 'AMP%rna2p': 1, 'PGW': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 2} Time building chain proxies: 2.38, per 1000 atoms: 0.14 Number of scatterers: 17301 At special positions: 0 Unit cell: (92.6978, 73.7595, 111.636, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 2 19.00 S 54 16.00 P 4 15.00 O 1472 8.00 N 1426 7.00 C 5547 6.00 H 8796 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 339.5 milliseconds 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1990 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 2 sheets defined 78.8% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 2 through 26 removed outlier: 5.714A pdb=" N VAL A 20 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Proline residue: A 21 - end of helix Processing helix chain 'A' and resid 29 through 42 Processing helix chain 'A' and resid 52 through 72 Processing helix chain 'A' and resid 75 through 82 Processing helix chain 'A' and resid 82 through 97 removed outlier: 4.647A pdb=" N ALA A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU A 92 " --> pdb=" O GLY A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 109 Processing helix chain 'A' and resid 112 through 123 removed outlier: 3.843A pdb=" N GLU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU A 117 " --> pdb=" O GLN A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 136 removed outlier: 3.534A pdb=" N GLU A 136 " --> pdb=" O GLN A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 171 Proline residue: A 161 - end of helix removed outlier: 3.765A pdb=" N ILE A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) Proline residue: A 167 - end of helix removed outlier: 3.824A pdb=" N ALA A 170 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR A 171 " --> pdb=" O PRO A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 183 Processing helix chain 'A' and resid 185 through 200 removed outlier: 4.043A pdb=" N LEU A 198 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY A 199 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 212 Processing helix chain 'A' and resid 217 through 238 Processing helix chain 'A' and resid 240 through 255 removed outlier: 4.046A pdb=" N GLY A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A 245 " --> pdb=" O MET A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 284 Proline residue: A 267 - end of helix removed outlier: 4.637A pdb=" N GLY A 270 " --> pdb=" O GLU A 266 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N LEU A 271 " --> pdb=" O PRO A 267 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE A 276 " --> pdb=" O LEU A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 292 removed outlier: 3.767A pdb=" N LEU A 290 " --> pdb=" O PHE A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 316 removed outlier: 3.741A pdb=" N LEU A 299 " --> pdb=" O ARG A 295 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLY A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ILE A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ARG A 316 " --> pdb=" O TRP A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 333 Processing helix chain 'A' and resid 337 through 350 removed outlier: 3.861A pdb=" N VAL A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 370 removed outlier: 3.781A pdb=" N LYS A 358 " --> pdb=" O PRO A 354 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 385 removed outlier: 3.642A pdb=" N LEU A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN A 383 " --> pdb=" O ASN A 379 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER A 384 " --> pdb=" O ARG A 380 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 421 removed outlier: 3.630A pdb=" N SER A 421 " --> pdb=" O LEU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 440 removed outlier: 3.672A pdb=" N ARG A 439 " --> pdb=" O GLU A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 460 Processing helix chain 'A' and resid 473 through 488 Processing helix chain 'A' and resid 499 through 510 Processing helix chain 'A' and resid 519 through 534 Processing helix chain 'A' and resid 536 through 560 removed outlier: 3.775A pdb=" N GLU A 542 " --> pdb=" O TYR A 538 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N MET A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 27 removed outlier: 3.789A pdb=" N VAL B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Proline residue: B 21 - end of helix Processing helix chain 'B' and resid 31 through 42 removed outlier: 3.845A pdb=" N LEU B 35 " --> pdb=" O VAL B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 74 removed outlier: 3.574A pdb=" N LEU B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 82 removed outlier: 4.297A pdb=" N LYS B 81 " --> pdb=" O GLN B 77 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 82 " --> pdb=" O ARG B 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 77 through 82' Processing helix chain 'B' and resid 89 through 108 removed outlier: 3.846A pdb=" N GLN B 93 " --> pdb=" O GLY B 89 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY B 99 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU B 100 " --> pdb=" O ILE B 96 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU B 103 " --> pdb=" O GLY B 99 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU B 108 " --> pdb=" O PHE B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 123 removed outlier: 3.977A pdb=" N LEU B 117 " --> pdb=" O GLN B 113 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY B 119 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET B 120 " --> pdb=" O GLU B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 138 Processing helix chain 'B' and resid 142 through 158 Processing helix chain 'B' and resid 159 through 165 Processing helix chain 'B' and resid 165 through 172 Processing helix chain 'B' and resid 176 through 202 Processing helix chain 'B' and resid 203 through 213 removed outlier: 3.807A pdb=" N SER B 213 " --> pdb=" O PHE B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 237 removed outlier: 3.643A pdb=" N VAL B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 255 removed outlier: 3.835A pdb=" N LEU B 247 " --> pdb=" O MET B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 266 Processing helix chain 'B' and resid 268 through 284 removed outlier: 3.984A pdb=" N PHE B 276 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE B 277 " --> pdb=" O LEU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 292 Processing helix chain 'B' and resid 293 through 314 removed outlier: 3.876A pdb=" N VAL B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU B 299 " --> pdb=" O ARG B 295 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 319 Processing helix chain 'B' and resid 321 through 331 removed outlier: 4.411A pdb=" N ARG B 326 " --> pdb=" O ASN B 322 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N TRP B 327 " --> pdb=" O LYS B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 349 removed outlier: 3.925A pdb=" N VAL B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 370 Processing helix chain 'B' and resid 370 through 384 removed outlier: 3.930A pdb=" N LEU B 374 " --> pdb=" O ALA B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 422 removed outlier: 3.592A pdb=" N ILE B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU B 417 " --> pdb=" O ILE B 413 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU B 418 " --> pdb=" O THR B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 440 removed outlier: 3.552A pdb=" N ARG B 439 " --> pdb=" O GLU B 436 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LYS B 440 " --> pdb=" O THR B 437 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 436 through 440' Processing helix chain 'B' and resid 452 through 456 removed outlier: 3.611A pdb=" N LEU B 456 " --> pdb=" O MET B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 464 Processing helix chain 'B' and resid 473 through 488 removed outlier: 3.742A pdb=" N MET B 483 " --> pdb=" O GLN B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 510 removed outlier: 3.911A pdb=" N ARG B 505 " --> pdb=" O ASP B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 534 Processing helix chain 'B' and resid 536 through 560 removed outlier: 3.519A pdb=" N ALA B 544 " --> pdb=" O ALA B 540 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP B 545 " --> pdb=" O ARG B 541 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL B 546 " --> pdb=" O GLU B 542 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE B 547 " --> pdb=" O ARG B 543 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N MET B 560 " --> pdb=" O GLU B 556 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 445 through 447 removed outlier: 6.659A pdb=" N ILE A 403 " --> pdb=" O ILE A 468 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU A 467 " --> pdb=" O ILE A 494 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ARG A 496 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ASN A 469 " --> pdb=" O ARG A 496 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA A 495 " --> pdb=" O GLU A 515 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 424 through 428 removed outlier: 6.518A pdb=" N VAL B 402 " --> pdb=" O VAL B 426 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N LEU B 428 " --> pdb=" O VAL B 402 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE B 404 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL B 466 " --> pdb=" O ARG B 401 " (cutoff:3.500A) 558 hydrogen bonds defined for protein. 1644 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.91 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8790 1.03 - 1.23: 31 1.23 - 1.42: 3393 1.42 - 1.62: 5127 1.62 - 1.81: 106 Bond restraints: 17447 Sorted by residual: bond pdb=" CG PRO B 205 " pdb=" CD PRO B 205 " ideal model delta sigma weight residual 1.503 1.444 0.059 3.40e-02 8.65e+02 2.97e+00 bond pdb=" CB PRO B 317 " pdb=" CG PRO B 317 " ideal model delta sigma weight residual 1.492 1.557 -0.065 5.00e-02 4.00e+02 1.70e+00 bond pdb=" CB PRO B 205 " pdb=" CG PRO B 205 " ideal model delta sigma weight residual 1.492 1.556 -0.064 5.00e-02 4.00e+02 1.64e+00 bond pdb=" C4 AMP A 602 " pdb=" C5 AMP A 602 " ideal model delta sigma weight residual 1.490 1.465 0.025 2.00e-02 2.50e+03 1.60e+00 bond pdb=" C4 AMP B 602 " pdb=" C5 AMP B 602 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.49e+00 ... (remaining 17442 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 30933 1.41 - 2.82: 632 2.82 - 4.23: 48 4.23 - 5.65: 18 5.65 - 7.06: 3 Bond angle restraints: 31634 Sorted by residual: angle pdb=" CA PRO B 205 " pdb=" N PRO B 205 " pdb=" CD PRO B 205 " ideal model delta sigma weight residual 112.00 105.41 6.59 1.40e+00 5.10e-01 2.22e+01 angle pdb=" CA PRO B 317 " pdb=" N PRO B 317 " pdb=" CD PRO B 317 " ideal model delta sigma weight residual 112.00 106.38 5.62 1.40e+00 5.10e-01 1.61e+01 angle pdb=" N PRO B 205 " pdb=" CD PRO B 205 " pdb=" CG PRO B 205 " ideal model delta sigma weight residual 103.20 97.94 5.26 1.50e+00 4.44e-01 1.23e+01 angle pdb=" N GLY A 98 " pdb=" CA GLY A 98 " pdb=" C GLY A 98 " ideal model delta sigma weight residual 113.18 107.58 5.60 2.37e+00 1.78e-01 5.59e+00 angle pdb=" CB MET B 106 " pdb=" CG MET B 106 " pdb=" SD MET B 106 " ideal model delta sigma weight residual 112.70 119.76 -7.06 3.00e+00 1.11e-01 5.53e+00 ... (remaining 31629 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.50: 7647 34.50 - 69.01: 410 69.01 - 103.51: 24 103.51 - 138.01: 1 138.01 - 172.52: 6 Dihedral angle restraints: 8088 sinusoidal: 4519 harmonic: 3569 Sorted by residual: dihedral pdb=" C5' AMP B 602 " pdb=" O5' AMP B 602 " pdb=" P AMP B 602 " pdb=" O3P AMP B 602 " ideal model delta sinusoidal sigma weight residual -60.00 65.59 -125.59 1 2.00e+01 2.50e-03 3.80e+01 dihedral pdb=" C03 PGW B 603 " pdb=" C01 PGW B 603 " pdb=" C02 PGW B 603 " pdb=" O03 PGW B 603 " ideal model delta sinusoidal sigma weight residual 295.35 122.83 172.52 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" O01 PGW B 603 " pdb=" C01 PGW B 603 " pdb=" C02 PGW B 603 " pdb=" O03 PGW B 603 " ideal model delta sinusoidal sigma weight residual 59.30 -112.75 172.05 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 8085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 991 0.028 - 0.056: 253 0.056 - 0.084: 95 0.084 - 0.113: 46 0.113 - 0.141: 6 Chirality restraints: 1391 Sorted by residual: chirality pdb=" CA ILE A 494 " pdb=" N ILE A 494 " pdb=" C ILE A 494 " pdb=" CB ILE A 494 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.95e-01 chirality pdb=" CA VAL A 426 " pdb=" N VAL A 426 " pdb=" C VAL A 426 " pdb=" CB VAL A 426 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.11e-01 chirality pdb=" CA ILE B 494 " pdb=" N ILE B 494 " pdb=" C ILE B 494 " pdb=" CB ILE B 494 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.69e-01 ... (remaining 1388 not shown) Planarity restraints: 2501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 316 " 0.068 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO B 317 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO B 317 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 317 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 204 " 0.057 5.00e-02 4.00e+02 8.25e-02 1.09e+01 pdb=" N PRO B 205 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO B 205 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 205 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 160 " 0.046 5.00e-02 4.00e+02 6.87e-02 7.56e+00 pdb=" N PRO A 161 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 161 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 161 " 0.038 5.00e-02 4.00e+02 ... (remaining 2498 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.31: 3705 2.31 - 3.01: 47171 3.01 - 3.72: 60982 3.72 - 4.43: 91969 4.43 - 5.14: 144625 Nonbonded interactions: 348452 Sorted by model distance: nonbonded pdb=" HB2 GLN A 492 " pdb="HE21 GLN A 492 " model vdw 1.598 2.270 nonbonded pdb="HH22 ARG B 295 " pdb=" OE2 GLU B 355 " model vdw 1.679 2.450 nonbonded pdb=" OD1 ASP A 285 " pdb=" H GLY A 287 " model vdw 1.695 2.450 nonbonded pdb=" O VAL A 202 " pdb=" HG1 THR A 203 " model vdw 1.703 2.450 nonbonded pdb=" OE1 GLU A 436 " pdb=" H GLU A 436 " model vdw 1.745 2.450 ... (remaining 348447 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 385 or resid 400 through 603)) selection = chain 'B' } 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: 0.860 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: 0.100 Extract box with map and model: 0.240 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 13.460 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 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 0.065 8651 Z= 0.137 Angle : 0.537 7.057 11691 Z= 0.276 Chirality : 0.034 0.141 1391 Planarity : 0.005 0.100 1447 Dihedral : 19.913 172.517 3200 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.12 % Allowed : 26.93 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.28), residues: 1085 helix: 2.00 (0.19), residues: 811 sheet: -1.24 (0.69), residues: 60 loop : -2.71 (0.42), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 541 TYR 0.007 0.001 TYR B 503 PHE 0.009 0.001 PHE A 154 TRP 0.006 0.001 TRP A 80 HIS 0.003 0.001 HIS B 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 ( 8651) covalent geometry : angle 0.53710 / 0.28 (11691) hydrogen bonds : bond 0.06499 / 4.93 ( 558) hydrogen bonds : angle 3.75213 / 2.74 ( 1644) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 127 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Evaluate side-chains 131 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.339 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 130 average time/residue: 0.1197 time to fit residues: 24.5027 Evaluate side-chains 128 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.126781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.108853 restraints weight = 37299.208| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.01 r_work: 0.3224 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.0293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8651 Z= 0.148 Angle : 0.526 7.509 11691 Z= 0.264 Chirality : 0.034 0.153 1391 Planarity : 0.004 0.071 1447 Dihedral : 14.536 171.886 1281 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 1.15 % Allowed : 26.81 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.28), residues: 1085 helix: 2.00 (0.19), residues: 804 sheet: -1.36 (0.68), residues: 60 loop : -2.55 (0.42), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 25 TYR 0.008 0.001 TYR A 503 PHE 0.008 0.001 PHE A 154 TRP 0.007 0.001 TRP A 44 HIS 0.002 0.000 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 ( 8651) covalent geometry : angle 0.52628 / 0.26 (11691) hydrogen bonds : bond 0.04305 / 3.05 ( 558) hydrogen bonds : angle 3.78545 / 2.75 ( 1644) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 127 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Evaluate side-chains 140 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 HIS cc_start: 0.5848 (OUTLIER) cc_final: 0.5329 (m-70) outliers start: 10 outliers final: 5 residues processed: 135 average time/residue: 0.1221 time to fit residues: 25.8521 Evaluate side-chains 135 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 129 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain B residue 86 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 76 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 98 optimal weight: 0.0020 chunk 23 optimal weight: 3.9990 chunk 32 optimal weight: 0.0370 chunk 24 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 overall best weight: 1.0068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.127644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.109727 restraints weight = 37455.645| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.02 r_work: 0.3242 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.0334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8651 Z= 0.109 Angle : 0.503 6.378 11691 Z= 0.249 Chirality : 0.034 0.150 1391 Planarity : 0.004 0.062 1447 Dihedral : 14.001 173.092 1281 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 1.50 % Allowed : 26.24 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.28), residues: 1085 helix: 2.04 (0.19), residues: 810 sheet: -1.40 (0.69), residues: 60 loop : -2.51 (0.42), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 25 TYR 0.007 0.001 TYR A 538 PHE 0.009 0.001 PHE A 154 TRP 0.005 0.001 TRP A 44 HIS 0.004 0.001 HIS A 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 ( 8651) covalent geometry : angle 0.50318 / 0.25 (11691) hydrogen bonds : bond 0.03901 / 2.77 ( 558) hydrogen bonds : angle 3.70882 / 2.70 ( 1644) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 127 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Evaluate side-chains 146 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 HIS cc_start: 0.5675 (OUTLIER) cc_final: 0.5236 (m-70) outliers start: 13 outliers final: 8 residues processed: 139 average time/residue: 0.1216 time to fit residues: 26.1621 Evaluate side-chains 139 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 455 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.124835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.106871 restraints weight = 37566.486| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.00 r_work: 0.3189 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.0620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8651 Z= 0.213 Angle : 0.556 8.302 11691 Z= 0.284 Chirality : 0.035 0.145 1391 Planarity : 0.004 0.060 1447 Dihedral : 13.990 174.776 1281 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 1.84 % Allowed : 25.78 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.27), residues: 1085 helix: 1.69 (0.19), residues: 809 sheet: -1.55 (0.68), residues: 60 loop : -2.69 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 25 TYR 0.008 0.001 TYR A 201 PHE 0.011 0.001 PHE B 303 TRP 0.009 0.001 TRP A 44 HIS 0.004 0.001 HIS A 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.21 ( 8651) covalent geometry : angle 0.55644 / 0.28 (11691) hydrogen bonds : bond 0.04959 / 3.48 ( 558) hydrogen bonds : angle 3.99107 / 2.90 ( 1644) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 127 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 HIS cc_start: 0.5836 (OUTLIER) cc_final: 0.5399 (m-70) outliers start: 16 outliers final: 12 residues processed: 137 average time/residue: 0.1116 time to fit residues: 24.1316 Evaluate side-chains 138 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 455 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 38 optimal weight: 0.1980 chunk 39 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.127041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.109154 restraints weight = 37138.105| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.00 r_work: 0.3225 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.0561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8651 Z= 0.117 Angle : 0.512 7.000 11691 Z= 0.255 Chirality : 0.034 0.148 1391 Planarity : 0.004 0.055 1447 Dihedral : 13.604 174.601 1281 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.07 % Allowed : 25.43 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.28), residues: 1085 helix: 1.90 (0.19), residues: 808 sheet: -1.59 (0.67), residues: 60 loop : -2.65 (0.41), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 25 TYR 0.007 0.001 TYR B 503 PHE 0.009 0.001 PHE A 154 TRP 0.006 0.001 TRP A 44 HIS 0.003 0.001 HIS A 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 ( 8651) covalent geometry : angle 0.51201 / 0.25 (11691) hydrogen bonds : bond 0.04131 / 2.92 ( 558) hydrogen bonds : angle 3.79970 / 2.76 ( 1644) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 127 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8858 (tt) REVERT: A 334 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8140 (pm20) REVERT: A 434 HIS cc_start: 0.5812 (OUTLIER) cc_final: 0.5379 (m-70) REVERT: B 412 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8639 (mt0) outliers start: 18 outliers final: 13 residues processed: 146 average time/residue: 0.1166 time to fit residues: 26.7216 Evaluate side-chains 146 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 412 GLN Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 560 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 16 optimal weight: 0.0980 chunk 49 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.128793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.111012 restraints weight = 36941.021| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.00 r_work: 0.3252 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.0618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8651 Z= 0.094 Angle : 0.493 6.327 11691 Z= 0.242 Chirality : 0.034 0.147 1391 Planarity : 0.004 0.050 1447 Dihedral : 13.043 174.608 1281 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 1.84 % Allowed : 25.78 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.28), residues: 1085 helix: 2.15 (0.19), residues: 802 sheet: -1.56 (0.68), residues: 60 loop : -2.50 (0.41), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 25 TYR 0.007 0.001 TYR B 503 PHE 0.009 0.001 PHE A 154 TRP 0.005 0.000 TRP A 44 HIS 0.004 0.001 HIS A 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.09 ( 8651) covalent geometry : angle 0.49348 / 0.24 (11691) hydrogen bonds : bond 0.03556 / 2.53 ( 558) hydrogen bonds : angle 3.67113 / 2.67 ( 1644) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 127 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 HIS cc_start: 0.5843 (OUTLIER) cc_final: 0.5488 (m-70) REVERT: B 412 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8616 (mt0) outliers start: 16 outliers final: 9 residues processed: 148 average time/residue: 0.1250 time to fit residues: 28.6628 Evaluate side-chains 143 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 412 GLN Chi-restraints excluded: chain B residue 433 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 48 optimal weight: 5.9990 chunk 105 optimal weight: 0.1980 chunk 4 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.127645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.109768 restraints weight = 37237.182| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.00 r_work: 0.3242 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.0644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8651 Z= 0.118 Angle : 0.503 6.777 11691 Z= 0.249 Chirality : 0.034 0.146 1391 Planarity : 0.004 0.049 1447 Dihedral : 12.928 174.790 1281 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 1.38 % Allowed : 26.01 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.28), residues: 1085 helix: 2.08 (0.19), residues: 809 sheet: -1.57 (0.67), residues: 60 loop : -2.54 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 216 TYR 0.007 0.001 TYR B 503 PHE 0.008 0.001 PHE A 154 TRP 0.006 0.001 TRP A 44 HIS 0.003 0.001 HIS A 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 8651) covalent geometry : angle 0.50311 / 0.25 (11691) hydrogen bonds : bond 0.03813 / 2.70 ( 558) hydrogen bonds : angle 3.71401 / 2.70 ( 1644) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 127 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 HIS cc_start: 0.5659 (OUTLIER) cc_final: 0.5315 (m-70) REVERT: B 216 ARG cc_start: 0.6511 (ptm160) cc_final: 0.6295 (ptm160) REVERT: B 412 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8623 (mt0) outliers start: 12 outliers final: 9 residues processed: 138 average time/residue: 0.1194 time to fit residues: 25.9978 Evaluate side-chains 140 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 412 GLN Chi-restraints excluded: chain B residue 433 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 106 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.124812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.106787 restraints weight = 37475.075| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.01 r_work: 0.3198 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.0727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8651 Z= 0.207 Angle : 0.555 8.220 11691 Z= 0.282 Chirality : 0.035 0.140 1391 Planarity : 0.004 0.050 1447 Dihedral : 13.102 175.317 1281 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 1.96 % Allowed : 25.55 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.27), residues: 1085 helix: 1.75 (0.19), residues: 808 sheet: -1.60 (0.67), residues: 60 loop : -2.69 (0.41), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 25 TYR 0.013 0.002 TYR A 447 PHE 0.013 0.001 PHE B 303 TRP 0.008 0.001 TRP A 44 HIS 0.004 0.001 HIS A 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.21 ( 8651) covalent geometry : angle 0.55491 / 0.28 (11691) hydrogen bonds : bond 0.04864 / 3.41 ( 558) hydrogen bonds : angle 3.96707 / 2.88 ( 1644) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 127 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 HIS cc_start: 0.5797 (OUTLIER) cc_final: 0.5404 (m-70) REVERT: B 412 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8655 (mt0) outliers start: 17 outliers final: 13 residues processed: 136 average time/residue: 0.1237 time to fit residues: 26.2949 Evaluate side-chains 140 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 412 GLN Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 455 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 15 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.123657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.105732 restraints weight = 37475.321| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.00 r_work: 0.3180 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.0859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8651 Z= 0.241 Angle : 0.580 8.763 11691 Z= 0.297 Chirality : 0.036 0.145 1391 Planarity : 0.004 0.052 1447 Dihedral : 13.025 174.832 1281 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 2.19 % Allowed : 25.43 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.27), residues: 1085 helix: 1.47 (0.19), residues: 809 sheet: -1.74 (0.66), residues: 60 loop : -2.76 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 25 TYR 0.010 0.001 TYR A 447 PHE 0.013 0.001 PHE B 303 TRP 0.010 0.002 TRP A 44 HIS 0.005 0.001 HIS A 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.24 ( 8651) covalent geometry : angle 0.58048 / 0.30 (11691) hydrogen bonds : bond 0.05266 / 3.69 ( 558) hydrogen bonds : angle 4.11912 / 2.99 ( 1644) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 127 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 350 ASN cc_start: 0.8302 (t0) cc_final: 0.8058 (t0) REVERT: B 412 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8675 (mt0) outliers start: 19 outliers final: 17 residues processed: 140 average time/residue: 0.1177 time to fit residues: 26.1299 Evaluate side-chains 145 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 412 GLN Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 455 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 18 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.124990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.106953 restraints weight = 37257.474| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.00 r_work: 0.3200 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.0829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8651 Z= 0.167 Angle : 0.549 7.937 11691 Z= 0.275 Chirality : 0.035 0.140 1391 Planarity : 0.004 0.051 1447 Dihedral : 12.919 174.119 1281 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 1.73 % Allowed : 26.12 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.27), residues: 1085 helix: 1.62 (0.19), residues: 809 sheet: -1.71 (0.67), residues: 60 loop : -2.67 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 25 TYR 0.011 0.001 TYR A 447 PHE 0.008 0.001 PHE A 154 TRP 0.008 0.001 TRP A 44 HIS 0.004 0.001 HIS A 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 ( 8651) covalent geometry : angle 0.54872 / 0.28 (11691) hydrogen bonds : bond 0.04712 / 3.32 ( 558) hydrogen bonds : angle 3.98697 / 2.89 ( 1644) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 127 is missing expected H atoms. Skipping. Residue THR 127 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 412 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8671 (mt0) outliers start: 15 outliers final: 14 residues processed: 139 average time/residue: 0.1123 time to fit residues: 24.6441 Evaluate side-chains 143 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 412 GLN Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 455 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 98 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.125410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.107698 restraints weight = 37546.506| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.95 r_work: 0.3210 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.0809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8651 Z= 0.153 Angle : 0.539 7.600 11691 Z= 0.271 Chirality : 0.034 0.146 1391 Planarity : 0.004 0.051 1447 Dihedral : 12.857 173.936 1281 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 1.96 % Allowed : 25.89 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.27), residues: 1085 helix: 1.69 (0.19), residues: 809 sheet: -1.70 (0.67), residues: 60 loop : -2.65 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 25 TYR 0.011 0.001 TYR A 447 PHE 0.008 0.001 PHE A 154 TRP 0.008 0.001 TRP A 44 HIS 0.005 0.001 HIS A 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 8651) covalent geometry : angle 0.53887 / 0.27 (11691) hydrogen bonds : bond 0.04506 / 3.17 ( 558) hydrogen bonds : angle 3.94506 / 2.87 ( 1644) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3369.13 seconds wall clock time: 57 minutes 29.62 seconds (3449.62 seconds total)