Starting phenix.real_space_refine on Thu Sep 18 00:41:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bkv_44646/09_2025/9bkv_44646.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bkv_44646/09_2025/9bkv_44646.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bkv_44646/09_2025/9bkv_44646.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bkv_44646/09_2025/9bkv_44646.map" model { file = "/net/cci-nas-00/data/ceres_data/9bkv_44646/09_2025/9bkv_44646.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bkv_44646/09_2025/9bkv_44646.cif" } resolution = 3.43 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= 0.084 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 2 7.16 5 S 66 5.16 5 C 7968 2.51 5 N 2186 2.21 5 O 2340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12562 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 6260 Classifications: {'peptide': 788} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 35, 'TRANS': 752} Chain: "B" Number of atoms: 6216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 6216 Classifications: {'peptide': 783} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 747} Chain breaks: 1 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.69, per 1000 atoms: 0.21 Number of scatterers: 12562 At special positions: 0 Unit cell: (102.554, 107.882, 198.449, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 2 26.01 S 66 16.00 O 2340 8.00 N 2186 7.00 C 7968 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 459.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2962 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 16 sheets defined 47.8% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 21 through 29 Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 64 through 69 Processing helix chain 'A' and resid 70 through 77 Proline residue: A 75 - end of helix Processing helix chain 'A' and resid 78 through 88 Processing helix chain 'A' and resid 133 through 152 Processing helix chain 'A' and resid 170 through 175 Processing helix chain 'A' and resid 188 through 193 Processing helix chain 'A' and resid 199 through 212 Processing helix chain 'A' and resid 257 through 276 removed outlier: 3.503A pdb=" N SER A 275 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 294 Processing helix chain 'A' and resid 352 through 382 removed outlier: 3.583A pdb=" N ILE A 356 " --> pdb=" O THR A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 408 Processing helix chain 'A' and resid 421 through 430 Processing helix chain 'A' and resid 430 through 447 removed outlier: 3.527A pdb=" N ALA A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLN A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 485 removed outlier: 3.627A pdb=" N GLN A 477 " --> pdb=" O SER A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 530 removed outlier: 3.841A pdb=" N ASN A 530 " --> pdb=" O TYR A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 563 removed outlier: 3.830A pdb=" N GLU A 544 " --> pdb=" O PRO A 540 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N MET A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL A 546 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL A 551 " --> pdb=" O LYS A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 610 Proline residue: A 604 - end of helix Processing helix chain 'A' and resid 611 through 631 Processing helix chain 'A' and resid 653 through 665 removed outlier: 3.595A pdb=" N TRP A 665 " --> pdb=" O ALA A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 698 Processing helix chain 'A' and resid 710 through 720 removed outlier: 3.773A pdb=" N LEU A 720 " --> pdb=" O ARG A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 733 removed outlier: 3.578A pdb=" N VAL A 732 " --> pdb=" O ASP A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 756 Processing helix chain 'A' and resid 766 through 776 removed outlier: 3.554A pdb=" N PHE A 770 " --> pdb=" O THR A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 800 removed outlier: 4.210A pdb=" N SER A 800 " --> pdb=" O PRO A 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 29 Processing helix chain 'B' and resid 46 through 54 Processing helix chain 'B' and resid 56 through 61 removed outlier: 4.119A pdb=" N ILE B 61 " --> pdb=" O ARG B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 88 removed outlier: 4.359A pdb=" N GLU B 79 " --> pdb=" O PRO B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 149 removed outlier: 4.250A pdb=" N ALA B 138 " --> pdb=" O SER B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 188 through 193 Processing helix chain 'B' and resid 200 through 212 removed outlier: 4.618A pdb=" N LEU B 206 " --> pdb=" O ASN B 202 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN B 207 " --> pdb=" O ARG B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 274 Processing helix chain 'B' and resid 278 through 294 Processing helix chain 'B' and resid 352 through 378 Processing helix chain 'B' and resid 394 through 407 Processing helix chain 'B' and resid 422 through 430 Processing helix chain 'B' and resid 430 through 448 removed outlier: 3.619A pdb=" N ALA B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLN B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS B 448 " --> pdb=" O ARG B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 486 removed outlier: 4.142A pdb=" N VAL B 486 " --> pdb=" O LEU B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 531 removed outlier: 3.581A pdb=" N LEU B 516 " --> pdb=" O ASN B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 562 removed outlier: 4.133A pdb=" N LYS B 547 " --> pdb=" O ASN B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 610 Proline residue: B 604 - end of helix Processing helix chain 'B' and resid 611 through 634 removed outlier: 3.856A pdb=" N ILE B 615 " --> pdb=" O GLU B 611 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLN B 633 " --> pdb=" O GLU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 665 removed outlier: 4.413A pdb=" N ALA B 661 " --> pdb=" O GLN B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 683 removed outlier: 3.802A pdb=" N MET B 682 " --> pdb=" O GLU B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 699 removed outlier: 3.955A pdb=" N LYS B 690 " --> pdb=" O THR B 686 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU B 695 " --> pdb=" O ARG B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 720 removed outlier: 3.692A pdb=" N GLY B 713 " --> pdb=" O THR B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 733 Processing helix chain 'B' and resid 738 through 755 Processing helix chain 'B' and resid 766 through 776 removed outlier: 3.942A pdb=" N PHE B 770 " --> pdb=" O THR B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 802 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 168 removed outlier: 3.908A pdb=" N GLN A 168 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 219 through 223 Processing sheet with id=AA4, first strand: chain 'A' and resid 308 through 314 removed outlier: 6.858A pdb=" N LEU A 301 " --> pdb=" O TRP A 312 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N SER A 314 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL A 299 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA A 339 " --> pdb=" O LEU A 304 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 308 through 314 removed outlier: 6.858A pdb=" N LEU A 301 " --> pdb=" O TRP A 312 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N SER A 314 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL A 299 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA A 339 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE A 331 " --> pdb=" O ALA A 339 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ILE A 341 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ALA A 329 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 454 through 459 removed outlier: 3.669A pdb=" N ILE A 458 " --> pdb=" O GLN A 462 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLN A 462 " --> pdb=" O ILE A 458 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 490 through 491 Processing sheet with id=AA8, first strand: chain 'A' and resid 595 through 597 removed outlier: 3.997A pdb=" N TRP A 589 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU A 580 " --> pdb=" O PHE A 574 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N PHE A 574 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 595 through 597 removed outlier: 3.997A pdb=" N TRP A 589 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASN A 643 " --> pdb=" O ALA A 585 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N ALA A 587 " --> pdb=" O ASN A 643 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU A 640 " --> pdb=" O THR A 673 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N GLU A 675 " --> pdb=" O LEU A 640 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL A 642 " --> pdb=" O GLU A 675 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEU A 672 " --> pdb=" O GLY A 701 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N SER A 703 " --> pdb=" O LEU A 672 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL A 674 " --> pdb=" O SER A 703 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU A 702 " --> pdb=" O GLU A 724 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N LYS A 726 " --> pdb=" O LEU A 702 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL A 704 " --> pdb=" O LYS A 726 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE A 725 " --> pdb=" O VAL A 760 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N GLU A 762 " --> pdb=" O ILE A 725 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE A 727 " --> pdb=" O GLU A 762 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL A 759 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N GLN A 782 " --> pdb=" O VAL A 759 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ALA A 761 " --> pdb=" O GLN A 782 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 42 through 45 removed outlier: 3.999A pdb=" N PHE B 44 " --> pdb=" O LEU B 35 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 166 through 169 removed outlier: 6.817A pdb=" N VAL B 159 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N CYS B 169 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N VAL B 157 " --> pdb=" O CYS B 169 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 308 through 314 removed outlier: 6.948A pdb=" N LEU B 301 " --> pdb=" O TRP B 312 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N SER B 314 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL B 299 " --> pdb=" O SER B 314 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ALA B 339 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY B 340 " --> pdb=" O ILE B 331 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 454 through 457 Processing sheet with id=AB5, first strand: chain 'B' and resid 490 through 491 removed outlier: 3.631A pdb=" N ILE B 490 " --> pdb=" O PHE B 497 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE B 497 " --> pdb=" O ILE B 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 595 through 597 removed outlier: 4.387A pdb=" N TRP B 589 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASN B 643 " --> pdb=" O ALA B 585 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ALA B 587 " --> pdb=" O ASN B 643 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 595 through 597 removed outlier: 4.387A pdb=" N TRP B 589 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU B 580 " --> pdb=" O PHE B 574 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N PHE B 574 " --> pdb=" O LEU B 580 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N GLY B 783 " --> pdb=" O PRO B 571 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL B 759 " --> pdb=" O VAL B 780 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N GLN B 782 " --> pdb=" O VAL B 759 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ALA B 761 " --> pdb=" O GLN B 782 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE B 725 " --> pdb=" O VAL B 760 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N GLU B 762 " --> pdb=" O ILE B 725 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ILE B 727 " --> pdb=" O GLU B 762 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N VAL B 764 " --> pdb=" O ILE B 727 " (cutoff:3.500A) 691 hydrogen bonds defined for protein. 1971 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.40 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.38: 4990 1.38 - 1.54: 7670 1.54 - 1.70: 46 1.70 - 1.87: 116 1.87 - 2.03: 8 Bond restraints: 12830 Sorted by residual: bond pdb=" N MET B 273 " pdb=" CA MET B 273 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.32e-02 5.74e+03 4.23e+00 bond pdb=" CG1 ILE B 285 " pdb=" CD1 ILE B 285 " ideal model delta sigma weight residual 1.513 1.435 0.078 3.90e-02 6.57e+02 3.97e+00 bond pdb=" CB VAL A 597 " pdb=" CG2 VAL A 597 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.35e+00 bond pdb=" C ASP A 387 " pdb=" N PRO A 388 " ideal model delta sigma weight residual 1.337 1.317 0.019 1.11e-02 8.12e+03 3.01e+00 bond pdb=" CA GLN A 385 " pdb=" CB GLN A 385 " ideal model delta sigma weight residual 1.530 1.556 -0.026 1.69e-02 3.50e+03 2.34e+00 ... (remaining 12825 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 17009 2.40 - 4.81: 329 4.81 - 7.21: 52 7.21 - 9.61: 15 9.61 - 12.01: 7 Bond angle restraints: 17412 Sorted by residual: angle pdb=" C ALA B 272 " pdb=" N MET B 273 " pdb=" CA MET B 273 " ideal model delta sigma weight residual 121.94 110.14 11.80 2.00e+00 2.50e-01 3.48e+01 angle pdb=" N ARG A 779 " pdb=" CA ARG A 779 " pdb=" CB ARG A 779 " ideal model delta sigma weight residual 114.17 108.08 6.09 1.14e+00 7.69e-01 2.86e+01 angle pdb=" C ASN B 64 " pdb=" CA ASN B 64 " pdb=" CB ASN B 64 " ideal model delta sigma weight residual 117.23 110.49 6.74 1.36e+00 5.41e-01 2.46e+01 angle pdb=" C GLN B 385 " pdb=" CA GLN B 385 " pdb=" CB GLN B 385 " ideal model delta sigma weight residual 109.16 115.48 -6.32 1.29e+00 6.01e-01 2.40e+01 angle pdb=" CA GLN B 385 " pdb=" CB GLN B 385 " pdb=" CG GLN B 385 " ideal model delta sigma weight residual 114.10 123.72 -9.62 2.00e+00 2.50e-01 2.31e+01 ... (remaining 17407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 6683 17.92 - 35.84: 819 35.84 - 53.76: 202 53.76 - 71.68: 32 71.68 - 89.60: 16 Dihedral angle restraints: 7752 sinusoidal: 3190 harmonic: 4562 Sorted by residual: dihedral pdb=" CA LEU A 294 " pdb=" C LEU A 294 " pdb=" N ASN A 295 " pdb=" CA ASN A 295 " ideal model delta harmonic sigma weight residual -180.00 -158.15 -21.85 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA HIS A 77 " pdb=" C HIS A 77 " pdb=" N PRO A 78 " pdb=" CA PRO A 78 " ideal model delta harmonic sigma weight residual -180.00 -159.07 -20.93 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA VAL B 150 " pdb=" C VAL B 150 " pdb=" N ASP B 151 " pdb=" CA ASP B 151 " ideal model delta harmonic sigma weight residual -180.00 -160.38 -19.62 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 7749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1790 0.092 - 0.183: 135 0.183 - 0.275: 1 0.275 - 0.366: 0 0.366 - 0.458: 1 Chirality restraints: 1927 Sorted by residual: chirality pdb=" CG LEU A 550 " pdb=" CB LEU A 550 " pdb=" CD1 LEU A 550 " pdb=" CD2 LEU A 550 " both_signs ideal model delta sigma weight residual False -2.59 -2.13 -0.46 2.00e-01 2.50e+01 5.23e+00 chirality pdb=" CB ILE B 285 " pdb=" CA ILE B 285 " pdb=" CG1 ILE B 285 " pdb=" CG2 ILE B 285 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA PHE B 707 " pdb=" N PHE B 707 " pdb=" C PHE B 707 " pdb=" CB PHE B 707 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.24e-01 ... (remaining 1924 not shown) Planarity restraints: 2265 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 452 " -0.016 2.00e-02 2.50e+03 3.10e-02 9.63e+00 pdb=" C ASP B 452 " 0.054 2.00e-02 2.50e+03 pdb=" O ASP B 452 " -0.020 2.00e-02 2.50e+03 pdb=" N GLN B 453 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 570 " -0.043 5.00e-02 4.00e+02 6.51e-02 6.79e+00 pdb=" N PRO B 571 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 571 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 571 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 779 " -0.011 2.00e-02 2.50e+03 2.12e-02 4.48e+00 pdb=" C ARG A 779 " 0.037 2.00e-02 2.50e+03 pdb=" O ARG A 779 " -0.014 2.00e-02 2.50e+03 pdb=" N VAL A 780 " -0.013 2.00e-02 2.50e+03 ... (remaining 2262 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 190 2.63 - 3.20: 11769 3.20 - 3.77: 19943 3.77 - 4.33: 26293 4.33 - 4.90: 42366 Nonbonded interactions: 100561 Sorted by model distance: nonbonded pdb=" OD1 ASN A 394 " pdb=" N ARG A 395 " model vdw 2.064 3.120 nonbonded pdb=" OG SER A 632 " pdb=" OE1 GLN A 633 " model vdw 2.195 3.040 nonbonded pdb=" O PRO A 78 " pdb=" NH1 ARG A 82 " model vdw 2.213 3.120 nonbonded pdb=" OD1 ASP B 66 " pdb=" NH1 ARG B 74 " model vdw 2.216 3.120 nonbonded pdb=" O GLY A 336 " pdb=" NH2 ARG B 205 " model vdw 2.231 3.120 ... (remaining 100556 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 20 through 378 or resid 384 through 901)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.110 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 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 : 0.006 0.215 12831 Z= 0.244 Angle : 0.839 12.013 17412 Z= 0.440 Chirality : 0.049 0.458 1927 Planarity : 0.005 0.065 2265 Dihedral : 16.685 89.602 4790 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.13 % Favored : 93.74 % Rotamer: Outliers : 0.44 % Allowed : 25.86 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: -0.45 (0.21), residues: 1565 helix: 0.57 (0.20), residues: 669 sheet: -0.12 (0.28), residues: 321 loop : -1.37 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 788 TYR 0.024 0.002 TYR B 581 PHE 0.033 0.003 PHE A 602 TRP 0.016 0.002 TRP B 231 HIS 0.009 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00568 (12830) covalent geometry : angle 0.83930 (17412) hydrogen bonds : bond 0.12721 ( 671) hydrogen bonds : angle 6.31800 ( 1971) Misc. bond : bond 0.21513 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 210 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 MET cc_start: 0.7526 (tpt) cc_final: 0.7304 (tpt) REVERT: A 491 MET cc_start: 0.8634 (tpp) cc_final: 0.8425 (tpp) outliers start: 6 outliers final: 2 residues processed: 216 average time/residue: 0.1365 time to fit residues: 40.6167 Evaluate side-chains 118 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 116 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain B residue 22 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 5.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN A 142 GLN A 311 HIS A 399 HIS ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 ASN B 84 ASN ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 GLN B 245 HIS ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.066957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.048348 restraints weight = 68347.303| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 5.89 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 12831 Z= 0.333 Angle : 0.824 8.549 17412 Z= 0.425 Chirality : 0.049 0.396 1927 Planarity : 0.006 0.058 2265 Dihedral : 6.526 77.636 1715 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.62 % Favored : 94.25 % Rotamer: Outliers : 4.56 % Allowed : 23.07 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: -0.54 (0.21), residues: 1565 helix: 0.41 (0.19), residues: 695 sheet: -0.44 (0.27), residues: 330 loop : -1.16 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 788 TYR 0.025 0.002 TYR B 581 PHE 0.033 0.003 PHE A 602 TRP 0.018 0.002 TRP B 312 HIS 0.009 0.002 HIS A 521 Details of bonding type rmsd covalent geometry : bond 0.00749 (12830) covalent geometry : angle 0.82436 (17412) hydrogen bonds : bond 0.04378 ( 671) hydrogen bonds : angle 5.55125 ( 1971) Misc. bond : bond 0.03708 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 111 time to evaluate : 0.524 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 161 ASP cc_start: 0.8569 (OUTLIER) cc_final: 0.8118 (p0) REVERT: A 167 VAL cc_start: 0.7248 (OUTLIER) cc_final: 0.7039 (p) REVERT: A 273 MET cc_start: 0.8209 (tpt) cc_final: 0.7976 (tpt) REVERT: A 299 VAL cc_start: 0.8922 (t) cc_final: 0.8722 (m) REVERT: A 366 MET cc_start: 0.8357 (mmm) cc_final: 0.7846 (mmm) REVERT: A 550 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.9006 (pp) REVERT: A 607 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8622 (mm-30) REVERT: B 251 MET cc_start: 0.8548 (mtp) cc_final: 0.8332 (mtp) REVERT: B 312 TRP cc_start: 0.8878 (t60) cc_final: 0.8663 (t60) REVERT: B 542 MET cc_start: 0.8731 (ppp) cc_final: 0.8299 (ppp) REVERT: B 545 MET cc_start: 0.8474 (tmm) cc_final: 0.8161 (tmm) REVERT: B 680 MET cc_start: 0.9197 (ttp) cc_final: 0.8462 (ptm) REVERT: B 806 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7905 (tppt) outliers start: 62 outliers final: 32 residues processed: 161 average time/residue: 0.1042 time to fit residues: 24.9403 Evaluate side-chains 128 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 92 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 HIS Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain B residue 22 PHE Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 415 TYR Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 766 THR Chi-restraints excluded: chain B residue 806 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 48 optimal weight: 0.8980 chunk 140 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 142 optimal weight: 0.0870 chunk 68 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 58 optimal weight: 0.2980 chunk 47 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 GLN ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 GLN B 142 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 ASN B 378 GLN ** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.072802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.053322 restraints weight = 65632.707| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 5.88 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12831 Z= 0.133 Angle : 0.687 10.885 17412 Z= 0.340 Chirality : 0.045 0.362 1927 Planarity : 0.005 0.058 2265 Dihedral : 6.236 75.104 1715 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.18 % Favored : 94.70 % Rotamer: Outliers : 2.72 % Allowed : 23.66 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: -0.02 (0.22), residues: 1565 helix: 0.92 (0.20), residues: 700 sheet: -0.18 (0.29), residues: 311 loop : -1.04 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 358 TYR 0.019 0.001 TYR B 581 PHE 0.024 0.002 PHE B 707 TRP 0.012 0.001 TRP B 665 HIS 0.013 0.001 HIS B 663 Details of bonding type rmsd covalent geometry : bond 0.00309 (12830) covalent geometry : angle 0.68739 (17412) hydrogen bonds : bond 0.03541 ( 671) hydrogen bonds : angle 4.94901 ( 1971) Misc. bond : bond 0.01288 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 106 time to evaluate : 0.538 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: symmetry clash REVERT: A 31 MET cc_start: 0.7144 (tpp) cc_final: 0.6791 (tpp) REVERT: A 137 MET cc_start: 0.8748 (ttm) cc_final: 0.8512 (ttm) REVERT: A 299 VAL cc_start: 0.8741 (t) cc_final: 0.8463 (m) REVERT: B 95 MET cc_start: 0.7161 (mpp) cc_final: 0.6794 (mpp) REVERT: B 542 MET cc_start: 0.8720 (ppp) cc_final: 0.8083 (ppp) REVERT: B 680 MET cc_start: 0.9078 (ttp) cc_final: 0.8345 (ptm) REVERT: B 772 MET cc_start: 0.8213 (ppp) cc_final: 0.8012 (ppp) REVERT: B 806 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7934 (tppt) outliers start: 37 outliers final: 19 residues processed: 134 average time/residue: 0.0984 time to fit residues: 20.3794 Evaluate side-chains 108 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 83 HIS Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain B residue 22 PHE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 456 CYS Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 806 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 39 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 117 optimal weight: 0.0980 chunk 88 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 18 optimal weight: 0.4980 chunk 46 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 43 optimal weight: 0.0060 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.068453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.049184 restraints weight = 67238.745| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 5.76 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12831 Z= 0.151 Angle : 0.668 10.935 17412 Z= 0.330 Chirality : 0.044 0.378 1927 Planarity : 0.005 0.059 2265 Dihedral : 6.145 76.529 1712 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.30 % Favored : 94.57 % Rotamer: Outliers : 2.94 % Allowed : 23.22 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 0.06 (0.22), residues: 1565 helix: 1.04 (0.20), residues: 702 sheet: -0.25 (0.28), residues: 316 loop : -1.00 (0.28), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 82 TYR 0.015 0.001 TYR B 581 PHE 0.025 0.002 PHE A 602 TRP 0.048 0.002 TRP B 312 HIS 0.006 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00355 (12830) covalent geometry : angle 0.66796 (17412) hydrogen bonds : bond 0.03335 ( 671) hydrogen bonds : angle 4.82966 ( 1971) Misc. bond : bond 0.01463 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 98 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.6996 (tpp) cc_final: 0.6652 (tpp) REVERT: A 137 MET cc_start: 0.8767 (ttm) cc_final: 0.8560 (ttm) REVERT: A 161 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.8008 (p0) REVERT: A 187 MET cc_start: 0.8694 (ppp) cc_final: 0.8000 (ppp) REVERT: A 366 MET cc_start: 0.8359 (mmm) cc_final: 0.8003 (mmm) REVERT: B 95 MET cc_start: 0.7244 (mpp) cc_final: 0.6577 (mpp) REVERT: B 151 ASP cc_start: 0.8213 (t70) cc_final: 0.7951 (t70) REVERT: B 273 MET cc_start: 0.8722 (pmm) cc_final: 0.8211 (pmm) REVERT: B 424 ASP cc_start: 0.9323 (m-30) cc_final: 0.8992 (t0) REVERT: B 542 MET cc_start: 0.8554 (ppp) cc_final: 0.8278 (ppp) REVERT: B 680 MET cc_start: 0.9123 (ttp) cc_final: 0.8348 (ptm) REVERT: B 772 MET cc_start: 0.8350 (ppp) cc_final: 0.8067 (ppp) REVERT: B 806 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7973 (tppt) outliers start: 40 outliers final: 28 residues processed: 128 average time/residue: 0.0901 time to fit residues: 18.3142 Evaluate side-chains 117 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 87 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 83 HIS Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain B residue 22 PHE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 456 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 641 SER Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 787 SER Chi-restraints excluded: chain B residue 806 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 132 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 43 optimal weight: 0.1980 chunk 67 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 chunk 129 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.072796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.053105 restraints weight = 65433.834| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 5.88 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12831 Z= 0.141 Angle : 0.652 12.628 17412 Z= 0.319 Chirality : 0.044 0.406 1927 Planarity : 0.004 0.061 2265 Dihedral : 6.126 75.965 1712 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.18 % Favored : 94.70 % Rotamer: Outliers : 3.38 % Allowed : 23.81 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 0.18 (0.22), residues: 1565 helix: 1.13 (0.20), residues: 708 sheet: -0.21 (0.29), residues: 313 loop : -0.93 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 82 TYR 0.013 0.001 TYR B 581 PHE 0.025 0.002 PHE A 602 TRP 0.059 0.002 TRP B 312 HIS 0.005 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00336 (12830) covalent geometry : angle 0.65195 (17412) hydrogen bonds : bond 0.03198 ( 671) hydrogen bonds : angle 4.71181 ( 1971) Misc. bond : bond 0.00612 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 90 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7064 (tpp) cc_final: 0.6710 (tpp) REVERT: A 99 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7788 (mm) REVERT: A 167 VAL cc_start: 0.7317 (OUTLIER) cc_final: 0.7084 (p) REVERT: A 187 MET cc_start: 0.8576 (ppp) cc_final: 0.8014 (ppp) REVERT: A 372 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8099 (mm-30) REVERT: A 480 ASP cc_start: 0.9027 (m-30) cc_final: 0.8803 (m-30) REVERT: A 698 MET cc_start: 0.9153 (mpp) cc_final: 0.8941 (mpp) REVERT: A 702 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8715 (mm) REVERT: B 95 MET cc_start: 0.7505 (mpp) cc_final: 0.7171 (mpp) REVERT: B 151 ASP cc_start: 0.8173 (t70) cc_final: 0.7919 (t70) REVERT: B 273 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8104 (pmm) REVERT: B 542 MET cc_start: 0.8562 (ppp) cc_final: 0.6841 (ppp) REVERT: B 545 MET cc_start: 0.8083 (tmm) cc_final: 0.7469 (ppp) REVERT: B 640 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8306 (tp) REVERT: B 662 MET cc_start: 0.8519 (ppp) cc_final: 0.7659 (ppp) REVERT: B 680 MET cc_start: 0.9103 (ttp) cc_final: 0.8415 (ptm) REVERT: B 772 MET cc_start: 0.8402 (ppp) cc_final: 0.8101 (ppp) REVERT: B 806 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7897 (tppt) outliers start: 46 outliers final: 27 residues processed: 126 average time/residue: 0.0841 time to fit residues: 16.8549 Evaluate side-chains 123 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 89 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 83 HIS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain B residue 22 PHE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 456 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 641 SER Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 704 VAL Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 787 SER Chi-restraints excluded: chain B residue 806 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 663 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.067836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.049527 restraints weight = 67457.276| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 5.43 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12831 Z= 0.139 Angle : 0.646 13.568 17412 Z= 0.316 Chirality : 0.044 0.418 1927 Planarity : 0.004 0.063 2265 Dihedral : 6.112 77.058 1712 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.30 % Favored : 94.57 % Rotamer: Outliers : 3.89 % Allowed : 23.22 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 0.26 (0.22), residues: 1565 helix: 1.23 (0.20), residues: 707 sheet: -0.16 (0.29), residues: 313 loop : -0.96 (0.28), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 288 TYR 0.013 0.001 TYR A 415 PHE 0.025 0.001 PHE A 602 TRP 0.071 0.002 TRP B 312 HIS 0.013 0.001 HIS B 663 Details of bonding type rmsd covalent geometry : bond 0.00333 (12830) covalent geometry : angle 0.64628 (17412) hydrogen bonds : bond 0.03077 ( 671) hydrogen bonds : angle 4.62351 ( 1971) Misc. bond : bond 0.01557 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 91 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7105 (tpp) cc_final: 0.6775 (tpp) REVERT: A 99 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8072 (mm) REVERT: A 161 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.8117 (p0) REVERT: A 167 VAL cc_start: 0.7302 (OUTLIER) cc_final: 0.7062 (p) REVERT: A 176 MET cc_start: 0.7808 (tpp) cc_final: 0.7535 (tpp) REVERT: A 185 SER cc_start: 0.8134 (OUTLIER) cc_final: 0.7861 (t) REVERT: A 187 MET cc_start: 0.8657 (ppp) cc_final: 0.8111 (ppp) REVERT: A 366 MET cc_start: 0.8759 (mmm) cc_final: 0.7943 (mmm) REVERT: A 372 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8053 (mm-30) REVERT: A 480 ASP cc_start: 0.9038 (m-30) cc_final: 0.8745 (m-30) REVERT: A 702 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8734 (mm) REVERT: B 151 ASP cc_start: 0.8177 (t70) cc_final: 0.7899 (t70) REVERT: B 273 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.7877 (pmm) REVERT: B 424 ASP cc_start: 0.9295 (m-30) cc_final: 0.8982 (t0) REVERT: B 494 ASP cc_start: 0.9160 (p0) cc_final: 0.8905 (p0) REVERT: B 542 MET cc_start: 0.8590 (ppp) cc_final: 0.6865 (ppp) REVERT: B 640 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8259 (tp) REVERT: B 680 MET cc_start: 0.9124 (ttp) cc_final: 0.8382 (ptm) REVERT: B 772 MET cc_start: 0.8465 (ppp) cc_final: 0.8149 (ppp) REVERT: B 806 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7982 (mmmt) outliers start: 53 outliers final: 34 residues processed: 133 average time/residue: 0.0877 time to fit residues: 18.3204 Evaluate side-chains 130 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 87 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 83 HIS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain B residue 22 PHE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 456 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 641 SER Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 704 VAL Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 787 SER Chi-restraints excluded: chain B residue 806 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 27 optimal weight: 5.9990 chunk 78 optimal weight: 0.0980 chunk 87 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 139 optimal weight: 0.0010 chunk 94 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 overall best weight: 1.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 663 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.071234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.052300 restraints weight = 65343.568| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 5.98 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.301 12831 Z= 0.153 Angle : 0.666 13.095 17412 Z= 0.324 Chirality : 0.044 0.415 1927 Planarity : 0.004 0.065 2265 Dihedral : 6.199 76.752 1712 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.62 % Favored : 94.25 % Rotamer: Outliers : 3.67 % Allowed : 24.32 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 0.31 (0.22), residues: 1565 helix: 1.26 (0.20), residues: 707 sheet: -0.16 (0.29), residues: 308 loop : -0.89 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 288 TYR 0.014 0.001 TYR A 415 PHE 0.026 0.001 PHE A 602 TRP 0.046 0.002 TRP B 312 HIS 0.007 0.001 HIS B 663 Details of bonding type rmsd covalent geometry : bond 0.00361 (12830) covalent geometry : angle 0.66632 (17412) hydrogen bonds : bond 0.03129 ( 671) hydrogen bonds : angle 4.61702 ( 1971) Misc. bond : bond 0.30095 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 92 time to evaluate : 0.507 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 31 MET cc_start: 0.7232 (tpp) cc_final: 0.6897 (tpp) REVERT: A 99 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8132 (mm) REVERT: A 137 MET cc_start: 0.8732 (ttm) cc_final: 0.8503 (ttm) REVERT: A 161 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.8145 (p0) REVERT: A 167 VAL cc_start: 0.7397 (OUTLIER) cc_final: 0.7189 (p) REVERT: A 176 MET cc_start: 0.7825 (tpp) cc_final: 0.7551 (tpp) REVERT: A 185 SER cc_start: 0.8243 (OUTLIER) cc_final: 0.8026 (t) REVERT: A 372 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8057 (mm-30) REVERT: A 480 ASP cc_start: 0.9017 (m-30) cc_final: 0.8728 (m-30) REVERT: A 702 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8679 (mm) REVERT: A 772 MET cc_start: 0.8896 (tmm) cc_final: 0.8622 (ppp) REVERT: B 95 MET cc_start: 0.6712 (mpp) cc_final: 0.5730 (mpp) REVERT: B 273 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.7841 (pmm) REVERT: B 424 ASP cc_start: 0.9270 (m-30) cc_final: 0.8943 (t0) REVERT: B 542 MET cc_start: 0.8315 (ppp) cc_final: 0.7769 (ppp) REVERT: B 680 MET cc_start: 0.9048 (ttp) cc_final: 0.8380 (ptm) REVERT: B 772 MET cc_start: 0.8408 (ppp) cc_final: 0.8098 (ppp) REVERT: B 806 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7981 (mmmt) outliers start: 50 outliers final: 35 residues processed: 131 average time/residue: 0.0927 time to fit residues: 19.0211 Evaluate side-chains 129 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 86 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 83 HIS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain B residue 22 PHE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 456 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 641 SER Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 704 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 787 SER Chi-restraints excluded: chain B residue 806 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 10 optimal weight: 9.9990 chunk 113 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.068167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.049900 restraints weight = 67780.849| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 5.36 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.157 12831 Z= 0.143 Angle : 0.686 14.251 17412 Z= 0.328 Chirality : 0.044 0.422 1927 Planarity : 0.004 0.066 2265 Dihedral : 6.182 76.815 1712 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.37 % Favored : 94.50 % Rotamer: Outliers : 3.67 % Allowed : 24.39 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 0.36 (0.22), residues: 1565 helix: 1.31 (0.20), residues: 706 sheet: -0.16 (0.29), residues: 308 loop : -0.86 (0.28), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 288 TYR 0.014 0.001 TYR A 415 PHE 0.024 0.001 PHE A 602 TRP 0.040 0.002 TRP B 312 HIS 0.012 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00340 (12830) covalent geometry : angle 0.68564 (17412) hydrogen bonds : bond 0.03090 ( 671) hydrogen bonds : angle 4.60250 ( 1971) Misc. bond : bond 0.15680 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 92 time to evaluate : 0.419 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 31 MET cc_start: 0.7184 (tpp) cc_final: 0.6831 (tpp) REVERT: A 99 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8035 (mm) REVERT: A 137 MET cc_start: 0.8662 (ttm) cc_final: 0.8397 (ttm) REVERT: A 161 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.8097 (p0) REVERT: A 176 MET cc_start: 0.7827 (tpp) cc_final: 0.7575 (tpp) REVERT: A 366 MET cc_start: 0.8743 (mmm) cc_final: 0.7949 (mmm) REVERT: A 372 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8067 (mm-30) REVERT: A 480 ASP cc_start: 0.9033 (m-30) cc_final: 0.8747 (m-30) REVERT: A 702 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8708 (mm) REVERT: B 95 MET cc_start: 0.6673 (mpp) cc_final: 0.5362 (mpp) REVERT: B 273 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.7775 (pmm) REVERT: B 424 ASP cc_start: 0.9279 (m-30) cc_final: 0.8942 (t0) REVERT: B 542 MET cc_start: 0.8204 (ppp) cc_final: 0.7687 (ppp) REVERT: B 680 MET cc_start: 0.9058 (ttp) cc_final: 0.8353 (ptm) REVERT: B 772 MET cc_start: 0.8442 (ppp) cc_final: 0.8121 (ppp) REVERT: B 806 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7965 (mmmt) outliers start: 50 outliers final: 37 residues processed: 133 average time/residue: 0.0931 time to fit residues: 19.5274 Evaluate side-chains 130 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 87 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 83 HIS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain B residue 22 PHE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 456 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 641 SER Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 704 VAL Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 787 SER Chi-restraints excluded: chain B residue 806 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 20 optimal weight: 0.4980 chunk 146 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 124 optimal weight: 0.1980 chunk 11 optimal weight: 1.9990 chunk 91 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.068508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.049780 restraints weight = 67816.235| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 5.55 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 12831 Z= 0.125 Angle : 0.693 14.576 17412 Z= 0.330 Chirality : 0.044 0.421 1927 Planarity : 0.004 0.067 2265 Dihedral : 6.156 77.112 1712 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.30 % Favored : 94.57 % Rotamer: Outliers : 3.01 % Allowed : 25.13 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 0.41 (0.22), residues: 1565 helix: 1.34 (0.20), residues: 707 sheet: -0.10 (0.29), residues: 308 loop : -0.85 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 288 TYR 0.012 0.001 TYR A 415 PHE 0.023 0.001 PHE A 602 TRP 0.037 0.002 TRP B 312 HIS 0.005 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00299 (12830) covalent geometry : angle 0.69340 (17412) hydrogen bonds : bond 0.03044 ( 671) hydrogen bonds : angle 4.54915 ( 1971) Misc. bond : bond 0.10961 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 90 time to evaluate : 0.513 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 31 MET cc_start: 0.7146 (tpp) cc_final: 0.6801 (tpp) REVERT: A 99 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8046 (mm) REVERT: A 137 MET cc_start: 0.8696 (ttm) cc_final: 0.8440 (ttm) REVERT: A 161 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.8137 (p0) REVERT: A 176 MET cc_start: 0.7759 (tpp) cc_final: 0.7512 (tpp) REVERT: A 366 MET cc_start: 0.8757 (mmm) cc_final: 0.7884 (mmm) REVERT: A 372 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8059 (mm-30) REVERT: A 480 ASP cc_start: 0.9049 (m-30) cc_final: 0.8771 (m-30) REVERT: B 43 MET cc_start: 0.8060 (mpp) cc_final: 0.7834 (mpp) REVERT: B 95 MET cc_start: 0.6934 (mpp) cc_final: 0.5352 (mpp) REVERT: B 273 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.7663 (pmm) REVERT: B 424 ASP cc_start: 0.9250 (m-30) cc_final: 0.8925 (t0) REVERT: B 542 MET cc_start: 0.8226 (ppp) cc_final: 0.7710 (ppp) REVERT: B 640 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8265 (tp) REVERT: B 680 MET cc_start: 0.9049 (ttp) cc_final: 0.8394 (ptm) REVERT: B 772 MET cc_start: 0.8436 (ppp) cc_final: 0.8109 (ppp) REVERT: B 806 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7949 (mmmt) outliers start: 41 outliers final: 32 residues processed: 123 average time/residue: 0.0917 time to fit residues: 17.4188 Evaluate side-chains 125 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 87 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 83 HIS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain B residue 22 PHE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 456 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 641 SER Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 704 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 787 SER Chi-restraints excluded: chain B residue 806 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 27 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 chunk 134 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 86 optimal weight: 0.0980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 HIS ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.068246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.049994 restraints weight = 67953.116| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 5.40 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.518 12831 Z= 0.138 Angle : 0.730 15.100 17412 Z= 0.340 Chirality : 0.045 0.432 1927 Planarity : 0.004 0.067 2265 Dihedral : 6.276 82.338 1712 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.43 % Favored : 94.44 % Rotamer: Outliers : 2.94 % Allowed : 25.13 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 0.36 (0.22), residues: 1565 helix: 1.29 (0.20), residues: 710 sheet: -0.08 (0.29), residues: 308 loop : -0.89 (0.28), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 288 TYR 0.012 0.001 TYR B 581 PHE 0.024 0.001 PHE A 602 TRP 0.037 0.002 TRP B 312 HIS 0.005 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00320 (12830) covalent geometry : angle 0.73020 (17412) hydrogen bonds : bond 0.03091 ( 671) hydrogen bonds : angle 4.54609 ( 1971) Misc. bond : bond 0.51755 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 90 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7202 (tpp) cc_final: 0.6852 (tpp) REVERT: A 99 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8109 (mm) REVERT: A 137 MET cc_start: 0.8707 (ttm) cc_final: 0.8443 (ttm) REVERT: A 161 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.8132 (p0) REVERT: A 176 MET cc_start: 0.7796 (tpp) cc_final: 0.7543 (tpp) REVERT: A 366 MET cc_start: 0.8773 (mmm) cc_final: 0.7877 (mmm) REVERT: A 372 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8060 (mm-30) REVERT: A 389 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.7483 (tmm) REVERT: A 480 ASP cc_start: 0.9047 (m-30) cc_final: 0.8772 (m-30) REVERT: B 43 MET cc_start: 0.7972 (mpp) cc_final: 0.7758 (mpp) REVERT: B 95 MET cc_start: 0.6495 (mpp) cc_final: 0.5443 (mpp) REVERT: B 273 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.7754 (pmm) REVERT: B 424 ASP cc_start: 0.9241 (m-30) cc_final: 0.8915 (t0) REVERT: B 542 MET cc_start: 0.8246 (ppp) cc_final: 0.7717 (ppp) REVERT: B 640 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8281 (tp) REVERT: B 680 MET cc_start: 0.9040 (ttp) cc_final: 0.8402 (ptm) REVERT: B 772 MET cc_start: 0.8418 (ppp) cc_final: 0.8058 (ppp) REVERT: B 806 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7969 (mmmt) outliers start: 40 outliers final: 32 residues processed: 124 average time/residue: 0.0964 time to fit residues: 18.6307 Evaluate side-chains 126 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 87 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 83 HIS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain B residue 22 PHE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 456 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 641 SER Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 787 SER Chi-restraints excluded: chain B residue 806 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 0.3980 chunk 96 optimal weight: 0.8980 chunk 114 optimal weight: 0.0570 chunk 101 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 108 optimal weight: 0.1980 chunk 98 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 126 optimal weight: 0.3980 chunk 59 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 overall best weight: 0.3298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.068223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.050124 restraints weight = 67488.302| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 5.42 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.475 12831 Z= 0.120 Angle : 0.728 15.284 17412 Z= 0.336 Chirality : 0.045 0.416 1927 Planarity : 0.004 0.065 2265 Dihedral : 6.134 78.735 1712 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.05 % Favored : 94.82 % Rotamer: Outliers : 2.57 % Allowed : 25.72 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 0.46 (0.22), residues: 1565 helix: 1.39 (0.20), residues: 703 sheet: 0.05 (0.30), residues: 308 loop : -0.89 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 288 TYR 0.010 0.001 TYR A 415 PHE 0.022 0.001 PHE B 602 TRP 0.033 0.001 TRP B 312 HIS 0.004 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00274 (12830) covalent geometry : angle 0.72829 (17412) hydrogen bonds : bond 0.02977 ( 671) hydrogen bonds : angle 4.45079 ( 1971) Misc. bond : bond 0.47500 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2663.12 seconds wall clock time: 46 minutes 32.83 seconds (2792.83 seconds total)