Starting phenix.real_space_refine on Mon Aug 25 10:47:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rn4_19386/08_2025/8rn4_19386.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rn4_19386/08_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_19386/08_2025/8rn4_19386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rn4_19386/08_2025/8rn4_19386.map" model { file = "/net/cci-nas-00/data/ceres_data/8rn4_19386/08_2025/8rn4_19386.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rn4_19386/08_2025/8rn4_19386.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.94, per 1000 atoms: 0.14 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: 2.30 Conformation dependent library (CDL) restraints added in 641.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.62 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: 6.67 Time building geometry restraints manager: 3.21 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: 9.220 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: 0.110 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 23.590 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.260 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.000 ARG B 726 TYR 0.021 0.001 TYR A 644 PHE 0.011 0.001 PHE B 449 TRP 0.028 0.001 TRP C 101 HIS 0.002 0.000 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00236 (13985) covalent geometry : angle 0.47802 (18846) hydrogen bonds : bond 0.12574 ( 699) hydrogen bonds : angle 5.20981 ( 1977) *********************** 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 : 0.564 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: 0.9826 time to fit residues: 230.4725 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 : 0.472 ------------------------------------------------------------------------------- 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 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.1980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.4050 r_free = 0.4050 target = 0.179465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.145431 restraints weight = 48772.027| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 1.99 r_work: 0.3590 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.0589 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= 0.149 Angle : 0.503 5.020 18846 Z= 0.264 Chirality : 0.038 0.148 2066 Planarity : 0.004 0.060 2414 Dihedral : 5.397 49.391 1893 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.18 % Favored : 96.76 % Rotamer: Outliers : 2.93 % Allowed : 22.94 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.20), residues: 1699 helix: 2.03 (0.18), residues: 808 sheet: -0.33 (0.38), residues: 176 loop : -0.50 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 726 TYR 0.013 0.001 TYR B 466 PHE 0.012 0.001 PHE B 449 TRP 0.011 0.001 TRP B 437 HIS 0.003 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00347 (13985) covalent geometry : angle 0.50325 (18846) hydrogen bonds : bond 0.04272 ( 699) hydrogen bonds : angle 4.41981 ( 1977) *********************** 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: 44 poor density : 194 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 486 THR cc_start: 0.8694 (m) cc_final: 0.8445 (m) REVERT: B 533 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7910 (mtt) REVERT: C 163 ASN cc_start: 0.8312 (m110) cc_final: 0.7487 (m110) REVERT: C 167 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6756 (mp0) REVERT: C 192 ARG cc_start: 0.7227 (mtt180) cc_final: 0.6988 (mtp180) outliers start: 44 outliers final: 21 residues processed: 224 average time/residue: 1.0702 time to fit residues: 266.3506 Evaluate side-chains 210 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 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 664 SER 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 162 SER 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 1 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 108 optimal weight: 0.0980 chunk 138 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 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 = 0.4035 r_free = 0.4035 target = 0.178089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.144069 restraints weight = 48705.824| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.97 r_work: 0.3576 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13985 Z= 0.164 Angle : 0.513 6.192 18846 Z= 0.269 Chirality : 0.038 0.163 2066 Planarity : 0.004 0.061 2414 Dihedral : 5.058 48.093 1879 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.18 % Favored : 96.76 % Rotamer: Outliers : 2.99 % Allowed : 22.87 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.20), residues: 1699 helix: 1.91 (0.18), residues: 808 sheet: -0.42 (0.38), residues: 173 loop : -0.61 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 178 TYR 0.014 0.001 TYR B 466 PHE 0.014 0.001 PHE B 449 TRP 0.011 0.001 TRP B 437 HIS 0.003 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00386 (13985) covalent geometry : angle 0.51330 (18846) hydrogen bonds : bond 0.04319 ( 699) hydrogen bonds : angle 4.35212 ( 1977) *********************** 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 239 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 194 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 486 THR cc_start: 0.8750 (m) cc_final: 0.8474 (m) REVERT: C 1 MET cc_start: 0.6419 (tpp) cc_final: 0.6199 (tpt) REVERT: C 33 ILE cc_start: 0.7644 (mt) cc_final: 0.7429 (mt) REVERT: C 163 ASN cc_start: 0.8431 (m110) cc_final: 0.7827 (m110) REVERT: C 192 ARG cc_start: 0.7278 (mtt180) cc_final: 0.7000 (mtp180) outliers start: 45 outliers final: 19 residues processed: 224 average time/residue: 1.0943 time to fit residues: 271.2988 Evaluate side-chains 205 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 472 SER 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 86 ASP Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 502 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 211 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 161 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 154 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 GLN B 367 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 = 0.4040 r_free = 0.4040 target = 0.178558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.144663 restraints weight = 48473.663| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 1.95 r_work: 0.3599 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1035 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= 0.134 Angle : 0.494 4.963 18846 Z= 0.258 Chirality : 0.038 0.155 2066 Planarity : 0.004 0.068 2414 Dihedral : 4.472 46.768 1870 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.41 % Favored : 96.53 % Rotamer: Outliers : 2.73 % Allowed : 23.27 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.20), residues: 1699 helix: 1.91 (0.18), residues: 810 sheet: -0.57 (0.38), residues: 179 loop : -0.59 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 439 TYR 0.017 0.001 TYR A 644 PHE 0.012 0.001 PHE B 449 TRP 0.012 0.001 TRP C 101 HIS 0.002 0.001 HIS A 433 Details of bonding type rmsd covalent geometry : bond 0.00314 (13985) covalent geometry : angle 0.49417 (18846) hydrogen bonds : bond 0.03900 ( 699) hydrogen bonds : angle 4.23894 ( 1977) *********************** 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 228 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 187 time to evaluate : 0.659 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: symmetry clash REVERT: A 246 MET cc_start: 0.8950 (ttm) cc_final: 0.8711 (ttm) REVERT: A 468 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6896 (mp0) REVERT: B 486 THR cc_start: 0.8783 (m) cc_final: 0.8535 (m) REVERT: C 1 MET cc_start: 0.6538 (tpp) cc_final: 0.6287 (tpt) REVERT: C 8 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8173 (tt) REVERT: C 33 ILE cc_start: 0.7751 (mt) cc_final: 0.7527 (mt) REVERT: C 163 ASN cc_start: 0.8550 (m110) cc_final: 0.8197 (m-40) REVERT: C 192 ARG cc_start: 0.7392 (mtt180) cc_final: 0.7192 (mtp180) outliers start: 41 outliers final: 25 residues processed: 213 average time/residue: 1.1105 time to fit residues: 261.6774 Evaluate side-chains 209 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 347 ILE Chi-restraints excluded: chain A residue 446 ILE 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 41 ASP Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 472 LEU 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 211 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 42 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 157 optimal weight: 0.4980 chunk 78 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 28 optimal weight: 0.0970 chunk 140 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 536 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 = 0.4043 r_free = 0.4043 target = 0.178775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.145344 restraints weight = 48467.015| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 1.92 r_work: 0.3586 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13985 Z= 0.124 Angle : 0.486 4.962 18846 Z= 0.253 Chirality : 0.037 0.151 2066 Planarity : 0.004 0.061 2414 Dihedral : 4.362 45.526 1869 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.30 % Favored : 96.65 % Rotamer: Outliers : 2.59 % Allowed : 23.94 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.20), residues: 1699 helix: 1.99 (0.18), residues: 812 sheet: -0.54 (0.38), residues: 179 loop : -0.58 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 439 TYR 0.019 0.001 TYR A 644 PHE 0.012 0.001 PHE B 449 TRP 0.013 0.001 TRP C 101 HIS 0.002 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00289 (13985) covalent geometry : angle 0.48602 (18846) hydrogen bonds : bond 0.03767 ( 699) hydrogen bonds : angle 4.17120 ( 1977) *********************** 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 232 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 193 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 232 GLU cc_start: 0.6368 (tm-30) cc_final: 0.5736 (mm-30) REVERT: B 486 THR cc_start: 0.8805 (m) cc_final: 0.8550 (m) REVERT: C 1 MET cc_start: 0.6585 (tpp) cc_final: 0.6356 (tpt) REVERT: C 8 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8107 (tt) REVERT: C 33 ILE cc_start: 0.7703 (mt) cc_final: 0.7481 (mt) REVERT: C 163 ASN cc_start: 0.8566 (m110) cc_final: 0.7834 (m-40) REVERT: C 167 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.6987 (mp0) REVERT: C 192 ARG cc_start: 0.7404 (mtt180) cc_final: 0.7172 (mtp180) outliers start: 39 outliers final: 24 residues processed: 220 average time/residue: 1.0703 time to fit residues: 261.7951 Evaluate side-chains 210 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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 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 86 ASP Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 472 LEU 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 211 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 103 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 126 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 536 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 = 0.4045 r_free = 0.4045 target = 0.179041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.145502 restraints weight = 48255.618| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.08 r_work: 0.3603 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1247 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= 0.119 Angle : 0.487 5.274 18846 Z= 0.253 Chirality : 0.037 0.150 2066 Planarity : 0.004 0.068 2414 Dihedral : 4.309 44.433 1869 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.24 % Favored : 96.70 % Rotamer: Outliers : 2.86 % Allowed : 23.40 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.20), residues: 1699 helix: 2.03 (0.18), residues: 812 sheet: -0.55 (0.38), residues: 179 loop : -0.55 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 439 TYR 0.012 0.001 TYR B 466 PHE 0.011 0.001 PHE B 449 TRP 0.013 0.001 TRP C 101 HIS 0.002 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00279 (13985) covalent geometry : angle 0.48747 (18846) hydrogen bonds : bond 0.03674 ( 699) hydrogen bonds : angle 4.12217 ( 1977) *********************** 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 227 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 184 time to evaluate : 0.456 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: B 1 MET cc_start: 0.8115 (tmt) cc_final: 0.7676 (tmt) REVERT: B 232 GLU cc_start: 0.6248 (tm-30) cc_final: 0.5654 (mm-30) REVERT: B 486 THR cc_start: 0.8783 (m) cc_final: 0.8510 (m) REVERT: C 1 MET cc_start: 0.6544 (tpp) cc_final: 0.6336 (tpt) REVERT: C 8 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8086 (tt) REVERT: C 33 ILE cc_start: 0.7658 (mt) cc_final: 0.7442 (mt) REVERT: C 163 ASN cc_start: 0.8425 (m-40) cc_final: 0.8051 (m-40) REVERT: C 192 ARG cc_start: 0.7353 (mtt180) cc_final: 0.7077 (mtp180) outliers start: 43 outliers final: 27 residues processed: 214 average time/residue: 1.0116 time to fit residues: 240.6054 Evaluate side-chains 206 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 178 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 427 ASP 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 41 ASP Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 664 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 8 LEU Chi-restraints excluded: chain C residue 136 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 147 optimal weight: 4.9990 chunk 157 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 0.0870 chunk 116 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.177777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.143984 restraints weight = 48422.245| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.95 r_work: 0.3568 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1378 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= 0.147 Angle : 0.504 6.139 18846 Z= 0.262 Chirality : 0.038 0.151 2066 Planarity : 0.004 0.060 2414 Dihedral : 4.352 43.558 1869 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 3.82 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.20), residues: 1699 helix: 1.96 (0.18), residues: 812 sheet: -0.60 (0.38), residues: 179 loop : -0.58 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 439 TYR 0.020 0.001 TYR A 644 PHE 0.013 0.001 PHE B 449 TRP 0.015 0.001 TRP C 101 HIS 0.002 0.001 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00347 (13985) covalent geometry : angle 0.50352 (18846) hydrogen bonds : bond 0.03870 ( 699) hydrogen bonds : angle 4.14408 ( 1977) *********************** 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 227 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 183 time to evaluate : 0.542 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: symmetry clash REVERT: B 1 MET cc_start: 0.8155 (tmt) cc_final: 0.7729 (tmt) REVERT: B 168 GLN cc_start: 0.8637 (tp40) cc_final: 0.8427 (tp40) REVERT: B 232 GLU cc_start: 0.6213 (tm-30) cc_final: 0.5622 (mm-30) REVERT: C 1 MET cc_start: 0.6528 (tpp) cc_final: 0.6315 (tpt) REVERT: C 8 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8041 (tt) REVERT: C 163 ASN cc_start: 0.8336 (m-40) cc_final: 0.7932 (m-40) REVERT: C 192 ARG cc_start: 0.7300 (mtt180) cc_final: 0.6972 (mtp180) outliers start: 44 outliers final: 28 residues processed: 215 average time/residue: 1.0540 time to fit residues: 252.0705 Evaluate side-chains 208 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 179 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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 427 ASP 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 472 LEU Chi-restraints excluded: chain B residue 502 SER 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 735 SER Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 136 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 155 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 113 optimal weight: 0.4980 chunk 7 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 108 optimal weight: 0.3980 chunk 83 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 GLN A 610 ASN B 484 ASN B 536 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 = 0.4037 r_free = 0.4037 target = 0.178215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.144578 restraints weight = 48505.019| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.96 r_work: 0.3575 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1444 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= 0.130 Angle : 0.496 6.837 18846 Z= 0.258 Chirality : 0.037 0.153 2066 Planarity : 0.004 0.059 2414 Dihedral : 4.298 42.503 1868 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.18 % Favored : 96.76 % Rotamer: Outliers : 2.79 % Allowed : 24.00 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.20), residues: 1699 helix: 2.00 (0.18), residues: 811 sheet: -0.61 (0.38), residues: 179 loop : -0.53 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 439 TYR 0.024 0.001 TYR A 644 PHE 0.018 0.001 PHE A 442 TRP 0.018 0.001 TRP C 101 HIS 0.002 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00305 (13985) covalent geometry : angle 0.49610 (18846) hydrogen bonds : bond 0.03748 ( 699) hydrogen bonds : angle 4.11952 ( 1977) *********************** 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 226 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 184 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 232 GLU cc_start: 0.6199 (tm-30) cc_final: 0.5615 (mm-30) REVERT: C 1 MET cc_start: 0.6563 (tpp) cc_final: 0.6320 (tpt) REVERT: C 8 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8032 (tt) REVERT: C 163 ASN cc_start: 0.8341 (m-40) cc_final: 0.7532 (m-40) REVERT: C 167 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6800 (mp0) REVERT: C 192 ARG cc_start: 0.7291 (mtt180) cc_final: 0.6953 (mtp180) outliers start: 42 outliers final: 29 residues processed: 217 average time/residue: 1.0365 time to fit residues: 250.4454 Evaluate side-chains 207 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 176 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 427 ASP 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 472 LEU 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 735 SER Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 136 THR 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 69 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 33 optimal weight: 0.0030 chunk 6 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 143 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 ASN B 484 ASN B 536 ASN C 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.178087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.144404 restraints weight = 48520.789| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.96 r_work: 0.3577 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13985 Z= 0.135 Angle : 0.505 7.681 18846 Z= 0.262 Chirality : 0.037 0.149 2066 Planarity : 0.004 0.059 2414 Dihedral : 4.312 41.695 1868 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.18 % Favored : 96.76 % Rotamer: Outliers : 2.33 % Allowed : 24.40 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.20), residues: 1699 helix: 1.99 (0.18), residues: 811 sheet: -0.63 (0.38), residues: 179 loop : -0.54 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 185 TYR 0.027 0.001 TYR A 644 PHE 0.015 0.001 PHE A 442 TRP 0.021 0.001 TRP C 101 HIS 0.002 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00319 (13985) covalent geometry : angle 0.50457 (18846) hydrogen bonds : bond 0.03797 ( 699) hydrogen bonds : angle 4.13102 ( 1977) *********************** 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 215 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 180 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 639 LYS cc_start: 0.8510 (tttp) cc_final: 0.8216 (ttmt) REVERT: B 232 GLU cc_start: 0.6178 (tm-30) cc_final: 0.5594 (mm-30) REVERT: C 1 MET cc_start: 0.6596 (tpp) cc_final: 0.6356 (tpt) REVERT: C 8 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8026 (tt) REVERT: C 163 ASN cc_start: 0.8339 (m-40) cc_final: 0.7522 (m-40) REVERT: C 167 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6822 (mp0) REVERT: C 192 ARG cc_start: 0.7324 (mtt180) cc_final: 0.6978 (mtp180) outliers start: 35 outliers final: 29 residues processed: 207 average time/residue: 1.0299 time to fit residues: 237.5692 Evaluate side-chains 208 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 427 ASP 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 472 LEU 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 735 SER Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 136 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 81 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 134 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 ASN 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 = 0.4036 r_free = 0.4036 target = 0.178133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.144473 restraints weight = 48341.515| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.98 r_work: 0.3579 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13985 Z= 0.128 Angle : 0.501 8.546 18846 Z= 0.261 Chirality : 0.037 0.154 2066 Planarity : 0.004 0.059 2414 Dihedral : 4.290 40.750 1868 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.12 % Favored : 96.82 % Rotamer: Outliers : 2.13 % Allowed : 24.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.20), residues: 1699 helix: 2.02 (0.18), residues: 811 sheet: -0.62 (0.37), residues: 179 loop : -0.49 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 185 TYR 0.026 0.001 TYR A 644 PHE 0.019 0.001 PHE A 442 TRP 0.024 0.001 TRP C 101 HIS 0.002 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00302 (13985) covalent geometry : angle 0.50112 (18846) hydrogen bonds : bond 0.03728 ( 699) hydrogen bonds : angle 4.13166 ( 1977) ********************** 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 208 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 176 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 639 LYS cc_start: 0.8509 (tttp) cc_final: 0.8221 (ttmt) REVERT: B 232 GLU cc_start: 0.6142 (tm-30) cc_final: 0.5563 (mm-30) REVERT: C 1 MET cc_start: 0.6598 (tpp) cc_final: 0.6369 (tpt) REVERT: C 8 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8049 (tt) REVERT: C 163 ASN cc_start: 0.8352 (m-40) cc_final: 0.7570 (m-40) REVERT: C 167 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6879 (mp0) REVERT: C 192 ARG cc_start: 0.7315 (mtt180) cc_final: 0.6953 (mtp180) outliers start: 32 outliers final: 28 residues processed: 202 average time/residue: 1.0126 time to fit residues: 227.0625 Evaluate side-chains 201 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 427 ASP 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 472 LEU 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 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 211 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 76 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 166 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 ASN B 314 ASN B 536 ASN B 680 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 = 0.4021 r_free = 0.4021 target = 0.176623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.142871 restraints weight = 48475.359| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.96 r_work: 0.3555 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3452 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13985 Z= 0.165 Angle : 0.524 7.311 18846 Z= 0.274 Chirality : 0.038 0.150 2066 Planarity : 0.004 0.059 2414 Dihedral : 4.400 40.306 1868 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.77 % Favored : 96.17 % Rotamer: Outliers : 2.19 % Allowed : 24.87 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.20), residues: 1699 helix: 1.91 (0.18), residues: 809 sheet: -0.69 (0.37), residues: 187 loop : -0.57 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 185 TYR 0.030 0.001 TYR A 644 PHE 0.019 0.001 PHE A 442 TRP 0.028 0.002 TRP C 101 HIS 0.002 0.001 HIS A 433 Details of bonding type rmsd covalent geometry : bond 0.00394 (13985) covalent geometry : angle 0.52364 (18846) hydrogen bonds : bond 0.04025 ( 699) hydrogen bonds : angle 4.19384 ( 1977) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8400.76 seconds wall clock time: 142 minutes 42.15 seconds (8562.15 seconds total)