Starting phenix.real_space_refine on Sun May 25 22:11:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rn4_19386/05_2025/8rn4_19386.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rn4_19386/05_2025/8rn4_19386.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rn4_19386/05_2025/8rn4_19386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rn4_19386/05_2025/8rn4_19386.map" model { file = "/net/cci-nas-00/data/ceres_data/8rn4_19386/05_2025/8rn4_19386.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rn4_19386/05_2025/8rn4_19386.cif" } resolution = 2.87 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= -0.001 sd= 0.102 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: 6 Type Number sf(0) Gaussians Mg 2 5.21 5 S 110 5.16 5 C 8702 2.51 5 N 2344 2.21 5 O 2560 1.98 5 H 13780 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 27498 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 11257 Classifications: {'peptide': 701} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 26, 'TRANS': 674} Chain breaks: 2 Chain: "B" Number of atoms: 11346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 722, 11346 Classifications: {'peptide': 722} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 33, 'TRANS': 688} Chain breaks: 4 Chain: "C" Number of atoms: 4114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 4114 Classifications: {'peptide': 249} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 235} Chain: "E" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 271 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 1, 'TRANS': 14} Chain: "D" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 508 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 14.11, per 1000 atoms: 0.51 Number of scatterers: 27498 At special positions: 0 Unit cell: (120.96, 134.4, 110.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 110 16.00 Mg 2 11.99 O 2560 8.00 N 2344 7.00 C 8702 6.00 H 13780 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: 8.06 Conformation dependent library (CDL) restraints added in 2.4 seconds 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3218 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 17 sheets defined 52.1% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.36 Creating SS restraints... Processing helix chain 'A' and resid 1 through 9 Processing helix chain 'A' and resid 10 through 24 Processing helix chain 'A' and resid 31 through 50 Processing helix chain 'A' and resid 84 through 100 Processing helix chain 'A' and resid 127 through 140 removed outlier: 3.532A pdb=" N TYR A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 184 Processing helix chain 'A' and resid 206 through 214 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 237 through 246 Processing helix chain 'A' and resid 266 through 271 Processing helix chain 'A' and resid 301 through 313 Processing helix chain 'A' and resid 313 through 319 Processing helix chain 'A' and resid 332 through 349 Processing helix chain 'A' and resid 360 through 366 removed outlier: 3.943A pdb=" N TRP A 364 " --> pdb=" O ASN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 383 removed outlier: 3.651A pdb=" N ALA A 380 " --> pdb=" O MET A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 411 removed outlier: 4.151A pdb=" N GLN A 404 " --> pdb=" O ALA A 400 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER A 411 " --> pdb=" O MET A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 448 removed outlier: 4.645A pdb=" N TYR A 448 " --> pdb=" O ASN A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 472 removed outlier: 3.638A pdb=" N THR A 453 " --> pdb=" O CYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 563 through 572 Processing helix chain 'A' and resid 574 through 595 removed outlier: 3.925A pdb=" N LEU A 578 " --> pdb=" O ARG A 574 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN A 583 " --> pdb=" O GLN A 579 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N MET A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 605 Processing helix chain 'A' and resid 629 through 646 Processing helix chain 'A' and resid 648 through 670 removed outlier: 4.129A pdb=" N ARG A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU A 661 " --> pdb=" O GLU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 688 removed outlier: 4.116A pdb=" N MET A 682 " --> pdb=" O ASP A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 716 Processing helix chain 'B' and resid 7 through 12 removed outlier: 4.055A pdb=" N ASP B 11 " --> pdb=" O PHE B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 22 removed outlier: 3.881A pdb=" N THR B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE B 22 " --> pdb=" O ILE B 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 17 through 22' Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 118 through 124 Processing helix chain 'B' and resid 138 through 153 Processing helix chain 'B' and resid 157 through 161 removed outlier: 4.087A pdb=" N GLY B 161 " --> pdb=" O ALA B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.913A pdb=" N PHE B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 174 " --> pdb=" O ILE B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 245 through 264 removed outlier: 3.595A pdb=" N ARG B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY B 250 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 293 removed outlier: 4.173A pdb=" N ALA B 280 " --> pdb=" O ASN B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.629A pdb=" N LEU B 313 " --> pdb=" O TRP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 338 Processing helix chain 'B' and resid 338 through 346 removed outlier: 3.624A pdb=" N VAL B 342 " --> pdb=" O SER B 338 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN B 346 " --> pdb=" O VAL B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'B' and resid 377 through 381 Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 394 through 396 No H-bonds generated for 'chain 'B' and resid 394 through 396' Processing helix chain 'B' and resid 413 through 426 removed outlier: 3.632A pdb=" N SER B 417 " --> pdb=" O PHE B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 472 Processing helix chain 'B' and resid 517 through 537 removed outlier: 3.776A pdb=" N GLY B 537 " --> pdb=" O MET B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 559 Processing helix chain 'B' and resid 569 through 582 removed outlier: 4.056A pdb=" N ILE B 574 " --> pdb=" O LYS B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 588 removed outlier: 3.576A pdb=" N GLY B 587 " --> pdb=" O GLY B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 593 Processing helix chain 'B' and resid 606 through 611 Processing helix chain 'B' and resid 616 through 624 Processing helix chain 'B' and resid 679 through 699 Processing helix chain 'B' and resid 700 through 703 removed outlier: 4.087A pdb=" N SER B 703 " --> pdb=" O ASN B 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 700 through 703' Processing helix chain 'B' and resid 712 through 731 Processing helix chain 'B' and resid 735 through 750 Processing helix chain 'C' and resid 2 through 14 Processing helix chain 'C' and resid 15 through 25 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 44 through 54 removed outlier: 3.658A pdb=" N CYS C 54 " --> pdb=" O LYS C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 70 removed outlier: 3.596A pdb=" N ARG C 69 " --> pdb=" O ASP C 65 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE C 70 " --> pdb=" O MET C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 104 removed outlier: 3.506A pdb=" N VAL C 98 " --> pdb=" O SER C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 117 Processing helix chain 'C' and resid 117 through 129 Processing helix chain 'C' and resid 157 through 170 Processing helix chain 'C' and resid 171 through 174 Processing helix chain 'C' and resid 184 through 195 Processing helix chain 'C' and resid 201 through 214 Processing helix chain 'C' and resid 227 through 232 Processing helix chain 'C' and resid 233 through 237 Processing helix chain 'D' and resid 360 through 366 removed outlier: 3.827A pdb=" N TRP D 364 " --> pdb=" O ASN D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 383 removed outlier: 3.504A pdb=" N ALA D 380 " --> pdb=" O MET D 376 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 61 removed outlier: 4.082A pdb=" N ARG A 74 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 79 removed outlier: 6.674A pdb=" N PHE A 118 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N MET A 146 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N GLU A 120 " --> pdb=" O MET A 146 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N PHE A 148 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLY A 122 " --> pdb=" O PHE A 148 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASP A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 255 through 256 Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 295 removed outlier: 4.322A pdb=" N SER A 492 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N TYR A 497 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR A 515 " --> pdb=" O GLY A 503 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LYS A 551 " --> pdb=" O SER A 543 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N SER A 543 " --> pdb=" O LYS A 551 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL A 553 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL A 538 " --> pdb=" O ILE A 325 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 291 through 295 removed outlier: 4.322A pdb=" N SER A 492 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ILE A 481 " --> pdb=" O TYR A 497 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LEU A 499 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE A 479 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL A 501 " --> pdb=" O LYS A 477 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LYS A 477 " --> pdb=" O VAL A 501 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 373 through 374 removed outlier: 5.918A pdb=" N GLN A 373 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N GLN B 367 " --> pdb=" O GLN A 373 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 623 through 628 removed outlier: 6.418A pdb=" N GLY A 627 " --> pdb=" O SER A 616 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER A 616 " --> pdb=" O GLY A 627 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AB1, first strand: chain 'B' and resid 178 through 188 Processing sheet with id=AB2, first strand: chain 'B' and resid 240 through 244 removed outlier: 6.639A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 488 through 491 Processing sheet with id=AB4, first strand: chain 'B' and resid 641 through 642 removed outlier: 3.999A pdb=" N MET B 654 " --> pdb=" O ALA B 642 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 59 through 60 removed outlier: 4.454A pdb=" N MET C 92 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR C 81 " --> pdb=" O MET C 92 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 131 through 136 removed outlier: 5.818A pdb=" N TRP C 132 " --> pdb=" O HIS C 247 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N HIS C 247 " --> pdb=" O TRP C 132 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ARG C 134 " --> pdb=" O ILE C 245 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 143 through 148 Processing sheet with id=AB8, first strand: chain 'E' and resid 355 through 359 removed outlier: 3.556A pdb=" N LYS E 365 " --> pdb=" O GLN D 373 " (cutoff:3.500A) 704 hydrogen bonds defined for protein. 1977 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: 11.42 Time building geometry restraints manager: 9.56 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: 13747 1.03 - 1.23: 172 1.23 - 1.43: 5571 1.43 - 1.62: 8088 1.62 - 1.82: 187 Bond restraints: 27765 Sorted by residual: bond pdb=" CB PRO B 295 " pdb=" CG PRO B 295 " ideal model delta sigma weight residual 1.492 1.568 -0.076 5.00e-02 4.00e+02 2.29e+00 bond pdb=" CA THR A 253 " pdb=" C THR A 253 " ideal model delta sigma weight residual 1.524 1.535 -0.012 1.26e-02 6.30e+03 8.33e-01 bond pdb=" CB ASP C 109 " pdb=" CG ASP C 109 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.58e-01 bond pdb=" CB CYS A 343 " pdb=" SG CYS A 343 " ideal model delta sigma weight residual 1.808 1.780 0.028 3.30e-02 9.18e+02 7.26e-01 bond pdb=" CG1 ILE B 528 " pdb=" CD1 ILE B 528 " ideal model delta sigma weight residual 1.513 1.484 0.029 3.90e-02 6.57e+02 5.50e-01 ... (remaining 27760 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 49886 1.76 - 3.52: 336 3.52 - 5.28: 30 5.28 - 7.04: 1 7.04 - 8.81: 1 Bond angle restraints: 50254 Sorted by residual: angle pdb=" CB MET B 506 " pdb=" CG MET B 506 " pdb=" SD MET B 506 " ideal model delta sigma weight residual 112.70 121.51 -8.81 3.00e+00 1.11e-01 8.62e+00 angle pdb=" N THR A 359 " pdb=" CA THR A 359 " pdb=" CB THR A 359 " ideal model delta sigma weight residual 113.65 109.89 3.76 1.47e+00 4.63e-01 6.55e+00 angle pdb=" C GLN A 504 " pdb=" N SER A 505 " pdb=" CA SER A 505 " ideal model delta sigma weight residual 121.54 125.53 -3.99 1.91e+00 2.74e-01 4.36e+00 angle pdb=" CG MET B 506 " pdb=" SD MET B 506 " pdb=" CE MET B 506 " ideal model delta sigma weight residual 100.90 105.10 -4.20 2.20e+00 2.07e-01 3.65e+00 angle pdb=" CA ASP C 109 " pdb=" CB ASP C 109 " pdb=" CG ASP C 109 " ideal model delta sigma weight residual 112.60 114.50 -1.90 1.00e+00 1.00e+00 3.62e+00 ... (remaining 50249 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 11374 18.01 - 36.02: 1113 36.02 - 54.04: 402 54.04 - 72.05: 90 72.05 - 90.06: 22 Dihedral angle restraints: 13001 sinusoidal: 7192 harmonic: 5809 Sorted by residual: dihedral pdb=" CA PHE B 504 " pdb=" C PHE B 504 " pdb=" N ALA B 505 " pdb=" CA ALA B 505 " ideal model delta harmonic sigma weight residual 180.00 160.27 19.73 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA LYS A 327 " pdb=" C LYS A 327 " pdb=" N SER A 328 " pdb=" CA SER A 328 " ideal model delta harmonic sigma weight residual 180.00 -161.49 -18.51 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA PHE A 677 " pdb=" C PHE A 677 " pdb=" N ASP A 678 " pdb=" CA ASP A 678 " ideal model delta harmonic sigma weight residual 180.00 163.46 16.54 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 12998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1336 0.029 - 0.058: 525 0.058 - 0.087: 116 0.087 - 0.116: 70 0.116 - 0.144: 19 Chirality restraints: 2066 Sorted by residual: chirality pdb=" CA ILE E 368 " pdb=" N ILE E 368 " pdb=" C ILE E 368 " pdb=" CB ILE E 368 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" CA ILE B 368 " pdb=" N ILE B 368 " pdb=" C ILE B 368 " pdb=" CB ILE B 368 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.18e-01 chirality pdb=" CA ILE B 348 " pdb=" N ILE B 348 " pdb=" C ILE B 348 " pdb=" CB ILE B 348 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 2063 not shown) Planarity restraints: 4050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 294 " 0.041 5.00e-02 4.00e+02 6.22e-02 6.19e+00 pdb=" N PRO B 295 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 295 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 295 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 429 " -0.040 5.00e-02 4.00e+02 6.10e-02 5.94e+00 pdb=" N PRO A 430 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 430 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 430 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 99 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.13e+00 pdb=" N PRO B 100 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 100 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 100 " 0.025 5.00e-02 4.00e+02 ... (remaining 4047 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 1401 2.18 - 2.78: 55151 2.78 - 3.39: 77923 3.39 - 3.99: 101506 3.99 - 4.60: 159292 Nonbonded interactions: 395273 Sorted by model distance: nonbonded pdb=" OD2 ASP B 521 " pdb=" HH TYR B 558 " model vdw 1.575 2.450 nonbonded pdb="HD21 ASN B 306 " pdb=" O ASP B 444 " model vdw 1.592 2.450 nonbonded pdb=" O THR B 113 " pdb=" HG1 THR B 117 " model vdw 1.615 2.450 nonbonded pdb=" H GLY B 515 " pdb=" OD1 ASP B 521 " model vdw 1.634 2.450 nonbonded pdb="HH11 ARG A 438 " pdb=" OE2 GLU A 585 " model vdw 1.635 2.450 ... (remaining 395268 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 5.290 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: 0.470 Extract box with map and model: 1.080 Check model and map are aligned: 0.200 Set scattering table: 0.270 Process input model: 62.070 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.090 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:12.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 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 : 0.002 0.076 13985 Z= 0.101 Angle : 0.478 8.806 18846 Z= 0.247 Chirality : 0.036 0.144 2066 Planarity : 0.004 0.062 2414 Dihedral : 17.823 90.061 5324 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.94 % Favored : 97.00 % Rotamer: Outliers : 1.73 % Allowed : 25.20 % Favored : 73.07 % 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: 1.17 (0.20), residues: 1699 helix: 2.07 (0.18), residues: 812 sheet: -0.28 (0.38), residues: 179 loop : -0.44 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 101 HIS 0.002 0.000 HIS C 184 PHE 0.011 0.001 PHE B 449 TYR 0.021 0.001 TYR A 644 ARG 0.008 0.000 ARG B 726 Details of bonding type rmsd hydrogen bonds : bond 0.12574 ( 699) hydrogen bonds : angle 5.20981 ( 1977) covalent geometry : bond 0.00236 (13985) covalent geometry : angle 0.47802 (18846) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 188 time to evaluate : 2.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 167 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6820 (mp0) outliers start: 26 outliers final: 22 residues processed: 210 average time/residue: 2.2573 time to fit residues: 530.2235 Evaluate side-chains 209 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 398 ARG Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 714 SER Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 167 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 GLN B 168 GLN C 68 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.180620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.146806 restraints weight = 48427.998| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 1.95 r_work: 0.3604 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.0541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13985 Z= 0.127 Angle : 0.491 4.964 18846 Z= 0.257 Chirality : 0.037 0.148 2066 Planarity : 0.004 0.059 2414 Dihedral : 5.335 49.399 1893 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.06 % Favored : 96.88 % Rotamer: Outliers : 2.59 % Allowed : 23.20 % Favored : 74.20 % 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: 1.18 (0.21), residues: 1699 helix: 2.09 (0.18), residues: 809 sheet: -0.28 (0.39), residues: 176 loop : -0.45 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 437 HIS 0.003 0.001 HIS B 47 PHE 0.011 0.001 PHE B 449 TYR 0.012 0.001 TYR B 466 ARG 0.004 0.000 ARG B 726 Details of bonding type rmsd hydrogen bonds : bond 0.04079 ( 699) hydrogen bonds : angle 4.39615 ( 1977) covalent geometry : bond 0.00291 (13985) covalent geometry : angle 0.49079 (18846) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 199 time to evaluate : 1.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6310 (mp0) REVERT: B 486 THR cc_start: 0.8656 (m) cc_final: 0.8423 (m) REVERT: C 136 THR cc_start: 0.6671 (OUTLIER) cc_final: 0.6468 (m) REVERT: C 163 ASN cc_start: 0.8298 (m110) cc_final: 0.7496 (m110) REVERT: C 167 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6774 (mp0) REVERT: C 192 ARG cc_start: 0.7260 (mtt180) cc_final: 0.6999 (mtp180) outliers start: 39 outliers final: 18 residues processed: 226 average time/residue: 2.3676 time to fit residues: 598.0580 Evaluate side-chains 209 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 595 GLN Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 211 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 127 optimal weight: 0.1980 chunk 105 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 34 optimal weight: 0.0470 overall best weight: 0.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 GLN B 536 ASN C 68 ASN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.180635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.147431 restraints weight = 48499.774| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 1.94 r_work: 0.3614 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.0728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13985 Z= 0.118 Angle : 0.482 6.136 18846 Z= 0.250 Chirality : 0.037 0.152 2066 Planarity : 0.004 0.058 2414 Dihedral : 4.865 48.128 1879 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.06 % Favored : 96.88 % Rotamer: Outliers : 2.59 % Allowed : 23.07 % Favored : 74.34 % 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: 1.21 (0.21), residues: 1699 helix: 2.15 (0.18), residues: 810 sheet: -0.28 (0.39), residues: 176 loop : -0.48 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 437 HIS 0.003 0.001 HIS B 47 PHE 0.010 0.001 PHE B 449 TYR 0.012 0.001 TYR A 644 ARG 0.004 0.000 ARG B 726 Details of bonding type rmsd hydrogen bonds : bond 0.03901 ( 699) hydrogen bonds : angle 4.24338 ( 1977) covalent geometry : bond 0.00271 (13985) covalent geometry : angle 0.48179 (18846) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 192 time to evaluate : 2.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6448 (mp0) REVERT: B 486 THR cc_start: 0.8698 (m) cc_final: 0.8465 (m) REVERT: C 1 MET cc_start: 0.6420 (tpp) cc_final: 0.6188 (tpt) REVERT: C 163 ASN cc_start: 0.8491 (m110) cc_final: 0.7908 (m110) REVERT: C 178 ARG cc_start: 0.5418 (OUTLIER) cc_final: 0.5213 (mtt90) outliers start: 39 outliers final: 16 residues processed: 218 average time/residue: 2.4180 time to fit residues: 584.6975 Evaluate side-chains 202 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 2.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 211 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 97 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN B 604 HIS B 680 ASN C 68 ASN C 163 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.175922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.141424 restraints weight = 48664.245| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.22 r_work: 0.3539 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13985 Z= 0.226 Angle : 0.557 5.036 18846 Z= 0.296 Chirality : 0.040 0.149 2066 Planarity : 0.005 0.063 2414 Dihedral : 4.784 47.329 1870 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.88 % Favored : 96.06 % Rotamer: Outliers : 3.39 % Allowed : 22.54 % Favored : 74.07 % 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: 0.60 (0.20), residues: 1699 helix: 1.64 (0.18), residues: 811 sheet: -0.69 (0.37), residues: 179 loop : -0.75 (0.22), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 437 HIS 0.004 0.001 HIS A 268 PHE 0.016 0.002 PHE B 449 TYR 0.018 0.002 TYR B 466 ARG 0.015 0.001 ARG A 439 Details of bonding type rmsd hydrogen bonds : bond 0.04695 ( 699) hydrogen bonds : angle 4.41841 ( 1977) covalent geometry : bond 0.00537 (13985) covalent geometry : angle 0.55742 (18846) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 196 time to evaluate : 2.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 SER cc_start: 0.8216 (m) cc_final: 0.7987 (p) REVERT: A 468 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6973 (mp0) REVERT: C 1 MET cc_start: 0.6585 (tpp) cc_final: 0.6356 (tpt) REVERT: C 163 ASN cc_start: 0.8627 (m-40) cc_final: 0.8266 (m-40) outliers start: 51 outliers final: 20 residues processed: 230 average time/residue: 2.4357 time to fit residues: 620.8199 Evaluate side-chains 202 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 181 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 211 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 28 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 367 GLN B 536 ASN C 68 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.176701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.142554 restraints weight = 48604.648| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.96 r_work: 0.3551 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13985 Z= 0.163 Angle : 0.514 5.128 18846 Z= 0.270 Chirality : 0.038 0.162 2066 Planarity : 0.004 0.063 2414 Dihedral : 4.575 45.937 1869 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.24 % Favored : 96.70 % Rotamer: Outliers : 2.93 % Allowed : 23.47 % Favored : 73.60 % 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: 0.62 (0.20), residues: 1699 helix: 1.66 (0.18), residues: 817 sheet: -0.72 (0.37), residues: 179 loop : -0.73 (0.22), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 101 HIS 0.003 0.001 HIS B 663 PHE 0.014 0.001 PHE B 449 TYR 0.019 0.001 TYR A 644 ARG 0.012 0.000 ARG A 439 Details of bonding type rmsd hydrogen bonds : bond 0.04159 ( 699) hydrogen bonds : angle 4.30991 ( 1977) covalent geometry : bond 0.00384 (13985) covalent geometry : angle 0.51350 (18846) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 185 time to evaluate : 1.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.5616 (OUTLIER) cc_final: 0.5135 (mtt) REVERT: A 392 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7535 (tptp) REVERT: A 464 SER cc_start: 0.8170 (m) cc_final: 0.7892 (p) REVERT: B 356 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.8179 (tpt) REVERT: C 1 MET cc_start: 0.6586 (tpp) cc_final: 0.6362 (tpt) REVERT: C 8 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8157 (tt) REVERT: C 163 ASN cc_start: 0.8397 (m-40) cc_final: 0.8172 (m-40) REVERT: C 211 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.6314 (tpp-160) outliers start: 44 outliers final: 26 residues processed: 217 average time/residue: 2.4337 time to fit residues: 584.5001 Evaluate side-chains 213 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 182 time to evaluate : 2.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 715 GLU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 211 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 30 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 145 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN B 536 ASN C 68 ASN ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.175027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.140964 restraints weight = 48690.012| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.95 r_work: 0.3503 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13985 Z= 0.203 Angle : 0.540 4.985 18846 Z= 0.286 Chirality : 0.039 0.151 2066 Planarity : 0.004 0.064 2414 Dihedral : 4.668 45.100 1869 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.18 % Favored : 95.76 % Rotamer: Outliers : 3.52 % Allowed : 23.34 % Favored : 73.14 % 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: 0.42 (0.20), residues: 1699 helix: 1.51 (0.18), residues: 817 sheet: -0.85 (0.37), residues: 179 loop : -0.85 (0.22), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 101 HIS 0.003 0.001 HIS A 268 PHE 0.017 0.001 PHE A 442 TYR 0.023 0.002 TYR A 644 ARG 0.006 0.000 ARG C 185 Details of bonding type rmsd hydrogen bonds : bond 0.04426 ( 699) hydrogen bonds : angle 4.37348 ( 1977) covalent geometry : bond 0.00482 (13985) covalent geometry : angle 0.54043 (18846) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 186 time to evaluate : 2.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.5686 (OUTLIER) cc_final: 0.5194 (mtt) REVERT: A 392 LYS cc_start: 0.7797 (OUTLIER) cc_final: 0.7509 (tptp) REVERT: A 464 SER cc_start: 0.8212 (m) cc_final: 0.7883 (p) REVERT: A 468 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6858 (mp0) REVERT: B 1 MET cc_start: 0.8238 (tmt) cc_final: 0.7750 (tmt) REVERT: B 232 GLU cc_start: 0.6221 (tm-30) cc_final: 0.5696 (mm-30) REVERT: C 1 MET cc_start: 0.6620 (tpp) cc_final: 0.6373 (tpt) REVERT: C 8 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8169 (tt) REVERT: C 211 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.6327 (tpp-160) outliers start: 53 outliers final: 31 residues processed: 223 average time/residue: 2.4180 time to fit residues: 599.6888 Evaluate side-chains 220 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 184 time to evaluate : 2.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 654 MET Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 715 GLU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 211 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 54 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 164 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 168 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 367 GLN C 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.175701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.141903 restraints weight = 48593.030| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.99 r_work: 0.3548 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13985 Z= 0.158 Angle : 0.517 6.213 18846 Z= 0.271 Chirality : 0.038 0.144 2066 Planarity : 0.004 0.069 2414 Dihedral : 4.594 44.258 1869 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.30 % Favored : 96.65 % Rotamer: Outliers : 3.26 % Allowed : 23.87 % Favored : 72.87 % 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: 0.54 (0.20), residues: 1699 helix: 1.63 (0.18), residues: 817 sheet: -0.89 (0.37), residues: 179 loop : -0.80 (0.22), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 101 HIS 0.003 0.001 HIS B 663 PHE 0.019 0.001 PHE A 442 TYR 0.023 0.001 TYR A 644 ARG 0.013 0.000 ARG A 439 Details of bonding type rmsd hydrogen bonds : bond 0.04099 ( 699) hydrogen bonds : angle 4.28428 ( 1977) covalent geometry : bond 0.00372 (13985) covalent geometry : angle 0.51696 (18846) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 186 time to evaluate : 2.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7504 (tptp) REVERT: A 464 SER cc_start: 0.8182 (m) cc_final: 0.7891 (p) REVERT: A 468 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6865 (mp0) REVERT: B 232 GLU cc_start: 0.6185 (tm-30) cc_final: 0.5681 (mm-30) REVERT: C 1 MET cc_start: 0.6617 (tpp) cc_final: 0.6365 (tpt) REVERT: C 8 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8099 (tt) REVERT: C 163 ASN cc_start: 0.8369 (m-40) cc_final: 0.8119 (m-40) REVERT: C 211 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.6355 (tpp-160) outliers start: 49 outliers final: 30 residues processed: 220 average time/residue: 2.3533 time to fit residues: 576.9353 Evaluate side-chains 215 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 181 time to evaluate : 2.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 715 GLU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 211 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 33 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 19 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 127 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 ASN C 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.177227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.144129 restraints weight = 48538.160| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.91 r_work: 0.3562 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13985 Z= 0.121 Angle : 0.498 7.315 18846 Z= 0.259 Chirality : 0.037 0.150 2066 Planarity : 0.004 0.063 2414 Dihedral : 4.440 43.143 1869 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.12 % Favored : 96.82 % Rotamer: Outliers : 2.73 % Allowed : 24.27 % Favored : 73.01 % 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: 0.77 (0.20), residues: 1699 helix: 1.84 (0.18), residues: 818 sheet: -0.83 (0.36), residues: 187 loop : -0.69 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 101 HIS 0.002 0.001 HIS B 47 PHE 0.019 0.001 PHE A 442 TYR 0.028 0.001 TYR A 644 ARG 0.006 0.000 ARG C 185 Details of bonding type rmsd hydrogen bonds : bond 0.03759 ( 699) hydrogen bonds : angle 4.16810 ( 1977) covalent geometry : bond 0.00284 (13985) covalent geometry : angle 0.49835 (18846) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 182 time to evaluate : 2.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7510 (tptp) REVERT: A 464 SER cc_start: 0.8150 (m) cc_final: 0.7822 (p) REVERT: A 468 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6784 (mp0) REVERT: A 639 LYS cc_start: 0.8515 (tttp) cc_final: 0.8193 (ttmt) REVERT: B 232 GLU cc_start: 0.6142 (tm-30) cc_final: 0.5636 (mm-30) REVERT: B 486 THR cc_start: 0.8832 (m) cc_final: 0.8515 (m) REVERT: C 1 MET cc_start: 0.6598 (tpp) cc_final: 0.6382 (tpt) REVERT: C 8 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8062 (tt) REVERT: C 163 ASN cc_start: 0.8326 (m-40) cc_final: 0.8084 (m-40) REVERT: C 211 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.6343 (tpp-160) outliers start: 41 outliers final: 26 residues processed: 212 average time/residue: 2.2887 time to fit residues: 540.6004 Evaluate side-chains 205 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 175 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 715 GLU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 749 ILE Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 211 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 27 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 144 optimal weight: 0.1980 chunk 150 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 23 optimal weight: 0.0870 chunk 115 optimal weight: 0.5980 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN A 595 GLN A 610 ASN B 306 ASN C 68 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.177813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.144816 restraints weight = 48497.702| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 1.90 r_work: 0.3575 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13985 Z= 0.117 Angle : 0.496 7.257 18846 Z= 0.257 Chirality : 0.037 0.153 2066 Planarity : 0.004 0.063 2414 Dihedral : 4.344 42.047 1868 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.00 % Favored : 96.94 % Rotamer: Outliers : 2.53 % Allowed : 24.47 % Favored : 73.01 % 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: 0.89 (0.20), residues: 1699 helix: 1.96 (0.18), residues: 813 sheet: -0.81 (0.36), residues: 187 loop : -0.62 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 101 HIS 0.002 0.001 HIS B 47 PHE 0.020 0.001 PHE A 442 TYR 0.025 0.001 TYR A 644 ARG 0.006 0.000 ARG A 439 Details of bonding type rmsd hydrogen bonds : bond 0.03669 ( 699) hydrogen bonds : angle 4.12369 ( 1977) covalent geometry : bond 0.00273 (13985) covalent geometry : angle 0.49611 (18846) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 180 time to evaluate : 2.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 LYS cc_start: 0.7778 (OUTLIER) cc_final: 0.7509 (tptp) REVERT: A 464 SER cc_start: 0.8157 (m) cc_final: 0.7900 (p) REVERT: A 639 LYS cc_start: 0.8524 (tttp) cc_final: 0.8216 (ttmt) REVERT: B 232 GLU cc_start: 0.6259 (tm-30) cc_final: 0.5654 (mm-30) REVERT: B 356 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8162 (mmt) REVERT: B 486 THR cc_start: 0.8804 (m) cc_final: 0.8492 (m) REVERT: C 1 MET cc_start: 0.6613 (tpp) cc_final: 0.6386 (tpt) REVERT: C 8 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8055 (tt) REVERT: C 163 ASN cc_start: 0.8347 (m-40) cc_final: 0.8109 (m-40) outliers start: 38 outliers final: 30 residues processed: 207 average time/residue: 2.2963 time to fit residues: 532.6739 Evaluate side-chains 207 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 2.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 595 GLN Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 715 GLU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 749 ILE Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 211 ARG Chi-restraints excluded: chain C residue 233 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 38 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 71 optimal weight: 0.4980 chunk 40 optimal weight: 0.9980 chunk 51 optimal weight: 0.4980 chunk 106 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.177750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.144812 restraints weight = 48339.028| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 1.93 r_work: 0.3574 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.296 13985 Z= 0.231 Angle : 0.836 59.200 18846 Z= 0.533 Chirality : 0.039 0.504 2066 Planarity : 0.005 0.108 2414 Dihedral : 4.336 42.045 1868 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.00 % Favored : 96.94 % Rotamer: Outliers : 2.26 % Allowed : 25.07 % Favored : 72.67 % 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: 0.90 (0.20), residues: 1699 helix: 1.97 (0.18), residues: 812 sheet: -0.81 (0.36), residues: 187 loop : -0.61 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 101 HIS 0.002 0.001 HIS B 47 PHE 0.018 0.001 PHE A 442 TYR 0.022 0.001 TYR A 644 ARG 0.004 0.000 ARG A 439 Details of bonding type rmsd hydrogen bonds : bond 0.03695 ( 699) hydrogen bonds : angle 4.12291 ( 1977) covalent geometry : bond 0.00480 (13985) covalent geometry : angle 0.83646 (18846) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 2.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7519 (tptp) REVERT: A 464 SER cc_start: 0.8130 (m) cc_final: 0.7917 (p) REVERT: A 639 LYS cc_start: 0.8525 (tttp) cc_final: 0.8218 (ttmt) REVERT: B 232 GLU cc_start: 0.6271 (tm-30) cc_final: 0.5663 (mm-30) REVERT: B 356 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.8175 (mmt) REVERT: B 486 THR cc_start: 0.8812 (m) cc_final: 0.8500 (m) REVERT: C 1 MET cc_start: 0.6618 (tpp) cc_final: 0.6392 (tpt) REVERT: C 8 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8057 (tt) REVERT: C 163 ASN cc_start: 0.8346 (m-40) cc_final: 0.8101 (m-40) REVERT: C 173 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7395 (mt-10) outliers start: 34 outliers final: 29 residues processed: 200 average time/residue: 2.3944 time to fit residues: 533.0913 Evaluate side-chains 206 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 173 time to evaluate : 2.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 595 GLN Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 715 GLU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 749 ILE Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 211 ARG Chi-restraints excluded: chain C residue 233 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 101 optimal weight: 0.9980 chunk 167 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.177688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.144729 restraints weight = 48508.942| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 1.92 r_work: 0.3574 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.296 13985 Z= 0.231 Angle : 0.836 59.200 18846 Z= 0.533 Chirality : 0.039 0.504 2066 Planarity : 0.005 0.108 2414 Dihedral : 4.336 42.045 1868 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.00 % Favored : 96.94 % Rotamer: Outliers : 2.19 % Allowed : 25.13 % Favored : 72.67 % 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: 0.90 (0.20), residues: 1699 helix: 1.97 (0.18), residues: 812 sheet: -0.81 (0.36), residues: 187 loop : -0.61 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 101 HIS 0.002 0.001 HIS B 47 PHE 0.018 0.001 PHE A 442 TYR 0.022 0.001 TYR A 644 ARG 0.004 0.000 ARG A 439 Details of bonding type rmsd hydrogen bonds : bond 0.03695 ( 699) hydrogen bonds : angle 4.12291 ( 1977) covalent geometry : bond 0.00480 (13985) covalent geometry : angle 0.83646 (18846) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18429.72 seconds wall clock time: 315 minutes 33.91 seconds (18933.91 seconds total)