Starting phenix.real_space_refine on Sun Jun 15 21:51:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bxg_16318/06_2025/8bxg_16318_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bxg_16318/06_2025/8bxg_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8bxg_16318/06_2025/8bxg_16318.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bxg_16318/06_2025/8bxg_16318.map" model { file = "/net/cci-nas-00/data/ceres_data/8bxg_16318/06_2025/8bxg_16318_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bxg_16318/06_2025/8bxg_16318_trim.cif" } resolution = 3.16 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= 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.95, per 1000 atoms: 0.52 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: 7.17 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.68 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: 8.67 Time building geometry restraints manager: 7.33 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=" C4' AMP A 602 " pdb=" O4' AMP A 602 " ideal model delta sigma weight residual 1.426 1.452 -0.026 2.00e-02 2.50e+03 1.66e+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 B 602 " pdb=" O4' AMP B 602 " ideal model delta sigma weight residual 1.426 1.451 -0.025 2.00e-02 2.50e+03 1.61e+00 ... (remaining 17442 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 31394 1.88 - 3.76: 199 3.76 - 5.64: 34 5.64 - 7.52: 5 7.52 - 9.39: 2 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=" C1' AMP A 602 " pdb=" C2' AMP A 602 " pdb=" C3' AMP A 602 " ideal model delta sigma weight residual 111.00 101.61 9.39 3.00e+00 1.11e-01 9.81e+00 angle pdb=" C1' AMP B 602 " pdb=" C2' AMP B 602 " pdb=" C3' AMP B 602 " ideal model delta sigma weight residual 111.00 101.79 9.21 3.00e+00 1.11e-01 9.43e+00 ... (remaining 31629 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.50: 7648 34.50 - 69.01: 409 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 - 0.040: 1125 0.040 - 0.080: 197 0.080 - 0.119: 63 0.119 - 0.159: 4 0.159 - 0.199: 2 Chirality restraints: 1391 Sorted by residual: chirality pdb=" C3' AMP A 602 " pdb=" C2' AMP A 602 " pdb=" C4' AMP A 602 " pdb=" O3' AMP A 602 " both_signs ideal model delta sigma weight residual False -2.51 -2.71 0.20 2.00e-01 2.50e+01 9.92e-01 chirality pdb=" C3' AMP B 602 " pdb=" C2' AMP B 602 " pdb=" C4' AMP B 602 " pdb=" O3' AMP B 602 " both_signs ideal model delta sigma weight residual False -2.51 -2.70 0.19 2.00e-01 2.50e+01 9.29e-01 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 ... (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 560 or resid 601 throug \ h 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: 1.730 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: 0.280 Extract box with map and model: 0.590 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 43.440 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 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= 0.142 Angle : 0.575 9.395 11691 Z= 0.283 Chirality : 0.035 0.199 1391 Planarity : 0.005 0.100 1447 Dihedral : 19.908 172.517 3200 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.29 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 (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: 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 TRP 0.006 0.001 TRP A 80 HIS 0.003 0.001 HIS B 434 PHE 0.009 0.001 PHE A 154 TYR 0.007 0.001 TYR B 503 ARG 0.002 0.000 ARG A 541 Details of bonding type rmsd hydrogen bonds : bond 0.06499 ( 558) hydrogen bonds : angle 3.75213 ( 1644) covalent geometry : bond 0.00312 ( 8651) covalent geometry : angle 0.57468 (11691) *********************** 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 : 1.726 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 130 average time/residue: 0.6267 time to fit residues: 126.7220 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 : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.3980 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.126329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.108515 restraints weight = 37291.409| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.99 r_work: 0.3219 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.0299 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= 0.161 Angle : 0.551 7.820 11691 Z= 0.271 Chirality : 0.035 0.152 1391 Planarity : 0.004 0.070 1447 Dihedral : 14.355 171.600 1281 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 1.15 % Allowed : 26.70 % 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 (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: 1.36 (0.28), residues: 1085 helix: 1.96 (0.19), residues: 804 sheet: -1.36 (0.68), residues: 60 loop : -2.56 (0.42), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 44 HIS 0.002 0.000 HIS A 502 PHE 0.008 0.001 PHE A 154 TYR 0.008 0.001 TYR A 503 ARG 0.003 0.000 ARG B 25 Details of bonding type rmsd hydrogen bonds : bond 0.04403 ( 558) hydrogen bonds : angle 3.80875 ( 1644) covalent geometry : bond 0.00348 ( 8651) covalent geometry : angle 0.55096 (11691) *********************** 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 138 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 HIS cc_start: 0.5805 (OUTLIER) cc_final: 0.5297 (m-70) outliers start: 10 outliers final: 5 residues processed: 133 average time/residue: 0.3553 time to fit residues: 72.6203 Evaluate side-chains 133 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 127 time to evaluate : 1.455 ------------------------------------------------------------------------------- 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 90 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.125267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.107341 restraints weight = 37263.460| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.00 r_work: 0.3209 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.0443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8651 Z= 0.180 Angle : 0.557 7.465 11691 Z= 0.276 Chirality : 0.035 0.149 1391 Planarity : 0.004 0.064 1447 Dihedral : 13.910 173.898 1281 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 1.73 % Allowed : 26.24 % 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 (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: 1.13 (0.27), residues: 1085 helix: 1.78 (0.19), residues: 809 sheet: -1.47 (0.68), residues: 60 loop : -2.63 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 44 HIS 0.005 0.001 HIS A 430 PHE 0.009 0.001 PHE B 303 TYR 0.007 0.001 TYR A 503 ARG 0.003 0.000 ARG B 25 Details of bonding type rmsd hydrogen bonds : bond 0.04684 ( 558) hydrogen bonds : angle 3.89697 ( 1644) covalent geometry : bond 0.00390 ( 8651) covalent geometry : angle 0.55707 (11691) *********************** 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 145 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 HIS cc_start: 0.5827 (OUTLIER) cc_final: 0.5336 (m-70) REVERT: A 507 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8447 (mmm160) outliers start: 15 outliers final: 11 residues processed: 139 average time/residue: 0.3500 time to fit residues: 75.1077 Evaluate side-chains 141 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 1.222 ------------------------------------------------------------------------------- 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 136 GLU 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 A residue 507 ARG Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 297 VAL 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 62 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 4 optimal weight: 0.2980 chunk 68 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.125576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.107717 restraints weight = 37331.451| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.99 r_work: 0.3208 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.0543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 8651 Z= 0.172 Angle : 0.557 7.858 11691 Z= 0.275 Chirality : 0.035 0.147 1391 Planarity : 0.004 0.059 1447 Dihedral : 13.665 174.377 1281 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 2.30 % Allowed : 25.89 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.27), residues: 1085 helix: 1.75 (0.19), residues: 809 sheet: -1.50 (0.68), residues: 60 loop : -2.67 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 44 HIS 0.004 0.001 HIS A 430 PHE 0.008 0.001 PHE B 303 TYR 0.007 0.001 TYR A 201 ARG 0.003 0.000 ARG B 25 Details of bonding type rmsd hydrogen bonds : bond 0.04636 ( 558) hydrogen bonds : angle 3.91269 ( 1644) covalent geometry : bond 0.00373 ( 8651) covalent geometry : angle 0.55709 (11691) *********************** 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 151 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 HIS cc_start: 0.5783 (OUTLIER) cc_final: 0.5355 (m-70) REVERT: A 507 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8441 (mmm160) REVERT: B 412 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8645 (mt0) outliers start: 20 outliers final: 15 residues processed: 145 average time/residue: 0.3360 time to fit residues: 73.7722 Evaluate side-chains 147 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 1.320 ------------------------------------------------------------------------------- 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 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 A residue 507 ARG 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 250 VAL 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 84 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 89 optimal weight: 0.1980 chunk 6 optimal weight: 0.0370 chunk 88 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.5060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.128133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.110410 restraints weight = 37354.813| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.01 r_work: 0.3251 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.0516 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= 0.091 Angle : 0.517 6.115 11691 Z= 0.249 Chirality : 0.034 0.151 1391 Planarity : 0.004 0.053 1447 Dihedral : 13.132 174.326 1281 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 1.96 % Allowed : 26.12 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.28), residues: 1085 helix: 2.06 (0.19), residues: 809 sheet: -1.52 (0.68), residues: 60 loop : -2.56 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP A 44 HIS 0.004 0.001 HIS A 430 PHE 0.009 0.001 PHE A 154 TYR 0.007 0.001 TYR B 503 ARG 0.002 0.000 ARG B 25 Details of bonding type rmsd hydrogen bonds : bond 0.03666 ( 558) hydrogen bonds : angle 3.70322 ( 1644) covalent geometry : bond 0.00188 ( 8651) covalent geometry : angle 0.51701 (11691) *********************** 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 157 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 334 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8157 (pm20) REVERT: A 434 HIS cc_start: 0.5655 (OUTLIER) cc_final: 0.5291 (m-70) REVERT: B 135 ASN cc_start: 0.8948 (m-40) cc_final: 0.8661 (m-40) REVERT: B 412 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8622 (mt0) outliers start: 17 outliers final: 10 residues processed: 150 average time/residue: 0.3461 time to fit residues: 78.9593 Evaluate side-chains 148 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 1.368 ------------------------------------------------------------------------------- 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 334 GLN Chi-restraints excluded: chain A residue 434 HIS 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 103 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 96 optimal weight: 7.9990 chunk 70 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.126428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.108533 restraints weight = 37252.615| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.00 r_work: 0.3228 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.0609 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= 0.143 Angle : 0.535 7.222 11691 Z= 0.261 Chirality : 0.035 0.145 1391 Planarity : 0.004 0.052 1447 Dihedral : 12.779 175.072 1281 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 1.96 % Allowed : 25.43 % 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 (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: 1.37 (0.28), residues: 1085 helix: 1.97 (0.19), residues: 809 sheet: -1.58 (0.67), residues: 60 loop : -2.61 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 44 HIS 0.003 0.001 HIS A 430 PHE 0.008 0.001 PHE A 154 TYR 0.008 0.001 TYR B 503 ARG 0.002 0.000 ARG B 25 Details of bonding type rmsd hydrogen bonds : bond 0.04180 ( 558) hydrogen bonds : angle 3.79522 ( 1644) covalent geometry : bond 0.00307 ( 8651) covalent geometry : angle 0.53516 (11691) *********************** 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 150 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 HIS cc_start: 0.5785 (OUTLIER) cc_final: 0.5392 (m-70) REVERT: B 412 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8645 (mt0) outliers start: 17 outliers final: 13 residues processed: 144 average time/residue: 0.3194 time to fit residues: 70.8470 Evaluate side-chains 145 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 1.244 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 95 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 103 optimal weight: 0.2980 chunk 3 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.126619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.108809 restraints weight = 37334.972| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.00 r_work: 0.3224 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.0612 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= 0.141 Angle : 0.540 7.165 11691 Z= 0.263 Chirality : 0.035 0.145 1391 Planarity : 0.004 0.051 1447 Dihedral : 12.664 175.014 1281 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 2.30 % Allowed : 25.09 % 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 (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: 1.31 (0.28), residues: 1085 helix: 1.91 (0.19), residues: 810 sheet: -1.58 (0.67), residues: 60 loop : -2.58 (0.42), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 44 HIS 0.005 0.001 HIS A 430 PHE 0.008 0.001 PHE A 410 TYR 0.007 0.001 TYR B 503 ARG 0.002 0.000 ARG B 25 Details of bonding type rmsd hydrogen bonds : bond 0.04231 ( 558) hydrogen bonds : angle 3.81418 ( 1644) covalent geometry : bond 0.00305 ( 8651) covalent geometry : angle 0.53950 (11691) *********************** 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 151 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 HIS cc_start: 0.5696 (OUTLIER) cc_final: 0.5309 (m-70) REVERT: B 412 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8648 (mt0) outliers start: 20 outliers final: 17 residues processed: 146 average time/residue: 0.3253 time to fit residues: 73.7384 Evaluate side-chains 148 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 1.212 ------------------------------------------------------------------------------- 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 334 GLN Chi-restraints excluded: chain A residue 430 HIS 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 250 VAL Chi-restraints excluded: chain B residue 285 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 45 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.125421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.107726 restraints weight = 37356.198| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.95 r_work: 0.3213 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.0716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8651 Z= 0.173 Angle : 0.560 7.743 11691 Z= 0.275 Chirality : 0.035 0.142 1391 Planarity : 0.004 0.051 1447 Dihedral : 12.685 174.930 1281 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 2.30 % Allowed : 25.09 % 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 (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: 1.15 (0.27), residues: 1085 helix: 1.81 (0.19), residues: 809 sheet: -1.60 (0.67), residues: 60 loop : -2.65 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 44 HIS 0.004 0.001 HIS A 430 PHE 0.009 0.001 PHE B 303 TYR 0.007 0.001 TYR A 201 ARG 0.002 0.000 ARG B 25 Details of bonding type rmsd hydrogen bonds : bond 0.04542 ( 558) hydrogen bonds : angle 3.89829 ( 1644) covalent geometry : bond 0.00379 ( 8651) covalent geometry : angle 0.56043 (11691) *********************** 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 148 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 HIS cc_start: 0.5795 (OUTLIER) cc_final: 0.5397 (m-70) REVERT: B 412 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8660 (mt0) outliers start: 20 outliers final: 18 residues processed: 143 average time/residue: 0.3267 time to fit residues: 71.6166 Evaluate side-chains 147 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 1.211 ------------------------------------------------------------------------------- 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 334 GLN Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 430 HIS 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 250 VAL Chi-restraints excluded: chain B residue 285 ASP 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 7 optimal weight: 2.9990 chunk 16 optimal weight: 0.2980 chunk 20 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 38 optimal weight: 0.0470 chunk 93 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 overall best weight: 1.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.126723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.108844 restraints weight = 37282.992| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.01 r_work: 0.3227 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.0675 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 : 0.537 6.918 11691 Z= 0.260 Chirality : 0.034 0.147 1391 Planarity : 0.004 0.050 1447 Dihedral : 12.580 174.298 1281 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 2.07 % Allowed : 25.55 % 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 (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: 1.31 (0.28), residues: 1085 helix: 1.93 (0.19), residues: 808 sheet: -1.61 (0.67), residues: 60 loop : -2.60 (0.42), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 44 HIS 0.005 0.001 HIS A 430 PHE 0.009 0.001 PHE A 154 TYR 0.008 0.001 TYR B 503 ARG 0.002 0.000 ARG B 25 Details of bonding type rmsd hydrogen bonds : bond 0.04069 ( 558) hydrogen bonds : angle 3.79324 ( 1644) covalent geometry : bond 0.00250 ( 8651) covalent geometry : angle 0.53667 (11691) *********************** 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: 18 poor density : 129 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 HIS cc_start: 0.5772 (OUTLIER) cc_final: 0.5372 (m-70) REVERT: B 412 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8647 (mt0) outliers start: 18 outliers final: 16 residues processed: 142 average time/residue: 0.3421 time to fit residues: 75.1101 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 : 1.310 ------------------------------------------------------------------------------- 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 334 GLN Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 430 HIS 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 250 VAL Chi-restraints excluded: chain B residue 285 ASP 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 14 optimal weight: 2.9990 chunk 58 optimal weight: 0.0770 chunk 94 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.128471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.110798 restraints weight = 37019.015| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.00 r_work: 0.3254 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.0734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8651 Z= 0.094 Angle : 0.521 8.416 11691 Z= 0.249 Chirality : 0.034 0.145 1391 Planarity : 0.004 0.049 1447 Dihedral : 12.169 174.367 1281 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 1.84 % Allowed : 25.66 % 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 (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: 1.52 (0.28), residues: 1085 helix: 2.12 (0.19), residues: 809 sheet: -1.53 (0.69), residues: 58 loop : -2.71 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 44 HIS 0.004 0.001 HIS A 430 PHE 0.010 0.001 PHE A 154 TYR 0.007 0.001 TYR A 447 ARG 0.001 0.000 ARG B 25 Details of bonding type rmsd hydrogen bonds : bond 0.03533 ( 558) hydrogen bonds : angle 3.67798 ( 1644) covalent geometry : bond 0.00198 ( 8651) covalent geometry : angle 0.52137 (11691) ********************** 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 153 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 HIS cc_start: 0.5688 (OUTLIER) cc_final: 0.5400 (m-70) outliers start: 16 outliers final: 12 residues processed: 148 average time/residue: 0.3245 time to fit residues: 73.8198 Evaluate side-chains 144 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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 196 VAL Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 367 SER 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 7 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.128016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.110280 restraints weight = 37187.138| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.01 r_work: 0.3246 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.0731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8651 Z= 0.107 Angle : 0.528 9.191 11691 Z= 0.253 Chirality : 0.034 0.147 1391 Planarity : 0.004 0.049 1447 Dihedral : 12.043 174.134 1281 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 1.61 % Allowed : 26.01 % 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 (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: 1.48 (0.28), residues: 1085 helix: 2.09 (0.19), residues: 809 sheet: -1.51 (0.69), residues: 58 loop : -2.70 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 44 HIS 0.006 0.001 HIS A 430 PHE 0.009 0.001 PHE A 154 TYR 0.007 0.001 TYR B 503 ARG 0.002 0.000 ARG B 25 Details of bonding type rmsd hydrogen bonds : bond 0.03652 ( 558) hydrogen bonds : angle 3.68632 ( 1644) covalent geometry : bond 0.00229 ( 8651) covalent geometry : angle 0.52781 (11691) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8939.37 seconds wall clock time: 153 minutes 60.00 seconds (9240.00 seconds total)