Starting phenix.real_space_refine on Sat Jan 18 18:31:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bkv_44646/01_2025/9bkv_44646.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bkv_44646/01_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_44646/01_2025/9bkv_44646.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bkv_44646/01_2025/9bkv_44646.map" model { file = "/net/cci-nas-00/data/ceres_data/9bkv_44646/01_2025/9bkv_44646.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bkv_44646/01_2025/9bkv_44646.cif" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.084 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 8.07, per 1000 atoms: 0.64 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: 3.32 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.73 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: 5.24 Time building geometry restraints manager: 3.79 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 807 or resid 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: 3.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 33.240 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.070 ------------------------------------------------------------------------------- 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 0.100 12830 Z= 0.371 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 : 17.52 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (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 TRP 0.016 0.002 TRP B 231 HIS 0.009 0.001 HIS A 165 PHE 0.033 0.003 PHE A 602 TYR 0.024 0.002 TYR B 581 ARG 0.015 0.001 ARG A 788 *********************** 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 : 1.440 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: 0.2977 time to fit residues: 88.8144 Evaluate side-chains 119 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 117 time to evaluate : 1.463 ------------------------------------------------------------------------------- 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 131 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 141 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 GLN ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 GLN ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 ASN ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS B 289 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.075242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.055735 restraints weight = 62774.303| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 5.90 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12830 Z= 0.249 Angle : 0.746 10.275 17412 Z= 0.375 Chirality : 0.046 0.364 1927 Planarity : 0.005 0.060 2265 Dihedral : 6.213 77.759 1715 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.24 % Favored : 94.63 % Rotamer: Outliers : 3.01 % Allowed : 23.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.21), residues: 1565 helix: 0.90 (0.20), residues: 687 sheet: -0.03 (0.28), residues: 314 loop : -1.16 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 312 HIS 0.006 0.001 HIS B 245 PHE 0.026 0.002 PHE A 602 TYR 0.017 0.001 TYR B 581 ARG 0.007 0.001 ARG A 788 *********************** 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 163 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 122 time to evaluate : 1.514 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: symmetry clash revert: symmetry clash REVERT: A 161 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.7988 (p0) REVERT: A 217 GLN cc_start: 0.9002 (pp30) cc_final: 0.8795 (pp30) REVERT: A 286 ILE cc_start: 0.8659 (mt) cc_final: 0.8396 (mt) REVERT: A 550 LEU cc_start: 0.9226 (mm) cc_final: 0.8972 (pp) REVERT: A 607 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8756 (mm-30) REVERT: A 698 MET cc_start: 0.8929 (mtm) cc_final: 0.8662 (mtm) REVERT: A 702 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8628 (mm) REVERT: B 151 ASP cc_start: 0.7916 (m-30) cc_final: 0.7516 (m-30) REVERT: B 251 MET cc_start: 0.8507 (mtp) cc_final: 0.8285 (mtp) REVERT: B 273 MET cc_start: 0.8559 (pmm) cc_final: 0.8281 (pmm) REVERT: B 424 ASP cc_start: 0.9235 (m-30) cc_final: 0.8919 (t0) REVERT: B 542 MET cc_start: 0.8748 (ppp) cc_final: 0.8379 (ppp) REVERT: B 545 MET cc_start: 0.8393 (tmm) cc_final: 0.8113 (tmm) REVERT: B 640 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8405 (tp) REVERT: B 680 MET cc_start: 0.9104 (ttp) cc_final: 0.8541 (ptm) REVERT: B 806 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7951 (tppt) outliers start: 41 outliers final: 18 residues processed: 154 average time/residue: 0.2299 time to fit residues: 53.3402 Evaluate side-chains 125 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 1.486 ------------------------------------------------------------------------------- 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 180 CYS Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 806 LYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 145 GLN 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 15 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 47 optimal weight: 0.0970 chunk 120 optimal weight: 0.0870 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** 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 = 0.3901 r_free = 0.3901 target = 0.071640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.053515 restraints weight = 70350.627| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 6.05 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12830 Z= 0.197 Angle : 0.676 10.108 17412 Z= 0.335 Chirality : 0.044 0.279 1927 Planarity : 0.005 0.056 2265 Dihedral : 5.989 77.228 1710 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.05 % Favored : 94.82 % Rotamer: Outliers : 2.79 % Allowed : 20.94 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.22), residues: 1565 helix: 1.00 (0.20), residues: 704 sheet: 0.05 (0.29), residues: 312 loop : -1.06 (0.28), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP B 312 HIS 0.008 0.001 HIS B 663 PHE 0.024 0.002 PHE A 602 TYR 0.016 0.001 TYR B 581 ARG 0.004 0.000 ARG A 740 *********************** 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 151 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 113 time to evaluate : 1.452 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: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.6995 (tpp) cc_final: 0.6369 (tpp) REVERT: A 95 MET cc_start: 0.8927 (mmm) cc_final: 0.8703 (mmm) REVERT: A 137 MET cc_start: 0.8719 (ttm) cc_final: 0.8504 (ttm) REVERT: A 167 VAL cc_start: 0.7200 (OUTLIER) cc_final: 0.6911 (p) REVERT: A 217 GLN cc_start: 0.8971 (pp30) cc_final: 0.8642 (pp30) REVERT: A 477 GLN cc_start: 0.8392 (pp30) cc_final: 0.8173 (pp30) REVERT: A 480 ASP cc_start: 0.8924 (m-30) cc_final: 0.8706 (m-30) REVERT: A 702 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8525 (mm) REVERT: B 95 MET cc_start: 0.6152 (mpp) cc_final: 0.4603 (mpp) REVERT: B 284 GLU cc_start: 0.9322 (OUTLIER) cc_final: 0.9057 (tt0) REVERT: B 424 ASP cc_start: 0.9315 (m-30) cc_final: 0.9000 (t0) REVERT: B 542 MET cc_start: 0.8680 (ppp) cc_final: 0.8075 (ppp) REVERT: B 640 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8391 (tp) REVERT: B 680 MET cc_start: 0.9179 (ttp) cc_final: 0.8519 (ptm) REVERT: B 806 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7980 (tppt) outliers start: 38 outliers final: 20 residues processed: 139 average time/residue: 0.2287 time to fit residues: 48.6055 Evaluate side-chains 123 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 1.407 ------------------------------------------------------------------------------- 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 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 232 ILE Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 390 THR 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 702 LEU Chi-restraints excluded: chain A residue 725 ILE 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 284 GLU Chi-restraints excluded: chain B residue 299 VAL 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 105 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 116 optimal weight: 4.9990 chunk 151 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 311 HIS ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.070739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.051884 restraints weight = 70023.641| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 5.74 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12830 Z= 0.222 Angle : 0.647 10.125 17412 Z= 0.324 Chirality : 0.043 0.171 1927 Planarity : 0.004 0.059 2265 Dihedral : 5.975 77.498 1710 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.11 % Favored : 94.76 % Rotamer: Outliers : 2.87 % Allowed : 22.34 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.22), residues: 1565 helix: 1.08 (0.20), residues: 706 sheet: 0.03 (0.29), residues: 312 loop : -0.98 (0.28), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 312 HIS 0.010 0.001 HIS B 663 PHE 0.025 0.002 PHE A 602 TYR 0.018 0.001 TYR B 581 ARG 0.003 0.000 ARG B 288 *********************** 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 143 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 104 time to evaluate : 1.530 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.6727 (tpp) cc_final: 0.6111 (tpp) REVERT: A 161 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.8094 (p0) REVERT: A 167 VAL cc_start: 0.7266 (OUTLIER) cc_final: 0.6960 (p) REVERT: A 176 MET cc_start: 0.7792 (tpp) cc_final: 0.7509 (tpp) REVERT: A 187 MET cc_start: 0.8543 (ppp) cc_final: 0.7703 (ppp) REVERT: A 480 ASP cc_start: 0.8946 (m-30) cc_final: 0.8715 (m-30) REVERT: A 702 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8636 (mm) REVERT: B 43 MET cc_start: 0.8333 (mpp) cc_final: 0.8016 (mpp) REVERT: B 273 MET cc_start: 0.8751 (pmm) cc_final: 0.8458 (pmm) REVERT: B 424 ASP cc_start: 0.9347 (m-30) cc_final: 0.9042 (t0) REVERT: B 542 MET cc_start: 0.8529 (ppp) cc_final: 0.8226 (ppp) REVERT: B 640 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8402 (tp) REVERT: B 680 MET cc_start: 0.9099 (ttp) cc_final: 0.8358 (ptm) REVERT: B 806 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7860 (tppt) outliers start: 39 outliers final: 27 residues processed: 132 average time/residue: 0.2424 time to fit residues: 48.5346 Evaluate side-chains 130 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 1.614 ------------------------------------------------------------------------------- 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 167 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 524 MET 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 725 ILE 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 299 VAL Chi-restraints excluded: chain B residue 597 VAL 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 717 LEU Chi-restraints excluded: chain B residue 759 VAL 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 79 optimal weight: 9.9990 chunk 16 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 HIS ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3867 r_free = 0.3867 target = 0.070010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.051167 restraints weight = 70908.642| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 5.72 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12830 Z= 0.246 Angle : 0.652 10.079 17412 Z= 0.324 Chirality : 0.043 0.167 1927 Planarity : 0.004 0.060 2265 Dihedral : 6.018 76.297 1710 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.37 % Favored : 94.50 % Rotamer: Outliers : 3.97 % Allowed : 22.56 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.22), residues: 1565 helix: 1.04 (0.20), residues: 706 sheet: -0.04 (0.29), residues: 310 loop : -0.88 (0.28), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 312 HIS 0.006 0.001 HIS B 663 PHE 0.025 0.002 PHE A 602 TYR 0.019 0.001 TYR B 581 ARG 0.003 0.000 ARG B 288 *********************** 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 156 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 102 time to evaluate : 1.507 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.6863 (tpp) cc_final: 0.6239 (tpp) REVERT: A 99 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7617 (mm) REVERT: A 137 MET cc_start: 0.8768 (ttm) cc_final: 0.8435 (ttm) REVERT: A 167 VAL cc_start: 0.7317 (OUTLIER) cc_final: 0.7049 (p) REVERT: A 176 MET cc_start: 0.7812 (tpp) cc_final: 0.7522 (tpp) REVERT: A 187 MET cc_start: 0.8624 (ppp) cc_final: 0.7977 (ppp) REVERT: A 480 ASP cc_start: 0.8996 (m-30) cc_final: 0.8751 (m-30) REVERT: B 95 MET cc_start: 0.6188 (mpp) cc_final: 0.4309 (mpp) REVERT: B 273 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8109 (pmm) REVERT: B 424 ASP cc_start: 0.9409 (m-30) cc_final: 0.9079 (t0) REVERT: B 640 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8310 (tp) REVERT: B 680 MET cc_start: 0.9118 (ttp) cc_final: 0.8351 (ptm) REVERT: B 806 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7876 (tppt) outliers start: 54 outliers final: 30 residues processed: 145 average time/residue: 0.2440 time to fit residues: 53.6448 Evaluate side-chains 128 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 93 time to evaluate : 1.607 ------------------------------------------------------------------------------- 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 180 CYS Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 725 ILE 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 717 LEU Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 766 THR 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 1 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 121 optimal weight: 0.4980 chunk 0 optimal weight: 9.9990 chunk 151 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 chunk 154 optimal weight: 0.7980 chunk 128 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 GLN ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 HIS B 245 HIS ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.068073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.049715 restraints weight = 67584.635| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 5.47 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12830 Z= 0.203 Angle : 0.651 10.151 17412 Z= 0.317 Chirality : 0.043 0.166 1927 Planarity : 0.004 0.062 2265 Dihedral : 6.003 77.576 1710 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.18 % Favored : 94.70 % Rotamer: Outliers : 3.82 % Allowed : 23.07 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.22), residues: 1565 helix: 1.13 (0.20), residues: 707 sheet: -0.04 (0.29), residues: 310 loop : -0.83 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 312 HIS 0.010 0.001 HIS B 245 PHE 0.025 0.001 PHE A 602 TYR 0.016 0.001 TYR B 581 ARG 0.003 0.000 ARG B 288 *********************** 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 149 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 97 time to evaluate : 1.650 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: 0.6850 (tpp) cc_final: 0.6239 (tpp) REVERT: A 99 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8018 (mm) REVERT: A 137 MET cc_start: 0.8728 (ttm) cc_final: 0.8369 (ttm) REVERT: A 159 VAL cc_start: 0.7770 (OUTLIER) cc_final: 0.7552 (t) REVERT: A 161 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.8040 (p0) REVERT: A 176 MET cc_start: 0.7837 (tpp) cc_final: 0.7569 (tpp) REVERT: A 480 ASP cc_start: 0.8991 (m-30) cc_final: 0.8742 (m-30) REVERT: A 702 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8626 (mm) REVERT: B 43 MET cc_start: 0.8208 (mpp) cc_final: 0.8002 (mpp) REVERT: B 95 MET cc_start: 0.6712 (mpp) cc_final: 0.5232 (mpp) REVERT: B 273 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8078 (pmm) REVERT: B 424 ASP cc_start: 0.9374 (m-30) cc_final: 0.9072 (t0) REVERT: B 494 ASP cc_start: 0.9267 (p0) cc_final: 0.9008 (p0) REVERT: B 542 MET cc_start: 0.8477 (ppp) cc_final: 0.7039 (ppp) REVERT: B 545 MET cc_start: 0.8068 (tmm) cc_final: 0.7494 (ppp) REVERT: B 640 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8231 (tp) REVERT: B 680 MET cc_start: 0.9122 (ttp) cc_final: 0.8371 (ptm) REVERT: B 806 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7944 (mmmt) outliers start: 52 outliers final: 29 residues processed: 138 average time/residue: 0.2338 time to fit residues: 49.2748 Evaluate side-chains 124 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 88 time to evaluate : 1.569 ------------------------------------------------------------------------------- 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 99 LEU Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 159 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 224 THR Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 725 ILE 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 640 LEU Chi-restraints excluded: chain B residue 641 SER Chi-restraints excluded: chain B residue 685 ASP 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 109 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 GLN ** A 562 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.067261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.048795 restraints weight = 67697.294| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 5.47 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12830 Z= 0.253 Angle : 0.667 11.686 17412 Z= 0.326 Chirality : 0.044 0.210 1927 Planarity : 0.004 0.063 2265 Dihedral : 6.118 77.086 1710 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.50 % Favored : 94.38 % Rotamer: Outliers : 3.97 % Allowed : 23.59 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.22), residues: 1565 helix: 1.12 (0.20), residues: 705 sheet: -0.08 (0.29), residues: 307 loop : -0.86 (0.28), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 312 HIS 0.008 0.001 HIS B 245 PHE 0.026 0.002 PHE A 602 TYR 0.018 0.001 TYR B 581 ARG 0.006 0.000 ARG A 164 *********************** 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 144 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 90 time to evaluate : 1.552 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: 0.7014 (tpp) cc_final: 0.6524 (tpp) REVERT: A 99 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8227 (mm) REVERT: A 159 VAL cc_start: 0.7770 (OUTLIER) cc_final: 0.7552 (t) REVERT: A 176 MET cc_start: 0.7898 (tpp) cc_final: 0.7631 (tpp) REVERT: A 480 ASP cc_start: 0.9026 (m-30) cc_final: 0.8787 (m-30) REVERT: A 702 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8613 (mm) REVERT: A 773 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8342 (mp) REVERT: B 95 MET cc_start: 0.6763 (mpp) cc_final: 0.5366 (mpp) REVERT: B 187 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7819 (pmm) REVERT: B 273 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8111 (pmm) REVERT: B 542 MET cc_start: 0.8483 (ppp) cc_final: 0.6955 (ppp) REVERT: B 640 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8260 (tp) REVERT: B 680 MET cc_start: 0.9136 (ttp) cc_final: 0.8444 (ptm) REVERT: B 806 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7981 (mmmt) outliers start: 54 outliers final: 36 residues processed: 130 average time/residue: 0.2306 time to fit residues: 46.2499 Evaluate side-chains 129 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 85 time to evaluate : 1.581 ------------------------------------------------------------------------------- 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 159 VAL 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 224 THR Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 286 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 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 678 GLU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 773 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 187 MET Chi-restraints excluded: chain B residue 245 HIS 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 759 VAL Chi-restraints excluded: chain B residue 766 THR 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 136 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 84 optimal weight: 0.0570 chunk 19 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 GLN ** A 562 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.067439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.049169 restraints weight = 67792.954| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 5.41 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12830 Z= 0.223 Angle : 0.689 13.607 17412 Z= 0.329 Chirality : 0.044 0.183 1927 Planarity : 0.004 0.065 2265 Dihedral : 6.101 76.651 1710 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.11 % Favored : 94.76 % Rotamer: Outliers : 4.04 % Allowed : 23.66 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.22), residues: 1565 helix: 1.18 (0.20), residues: 706 sheet: -0.05 (0.30), residues: 305 loop : -0.84 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 312 HIS 0.004 0.001 HIS A 245 PHE 0.024 0.002 PHE A 602 TYR 0.017 0.001 TYR B 581 ARG 0.003 0.000 ARG B 288 *********************** 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 144 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 89 time to evaluate : 1.370 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: symmetry clash REVERT: A 31 MET cc_start: 0.7133 (tpp) cc_final: 0.6492 (tpp) REVERT: A 99 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8048 (mm) REVERT: A 137 MET cc_start: 0.8612 (ttm) cc_final: 0.8362 (ttm) REVERT: A 159 VAL cc_start: 0.7818 (OUTLIER) cc_final: 0.7587 (t) REVERT: A 176 MET cc_start: 0.7781 (tpp) cc_final: 0.7539 (tpp) REVERT: A 372 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7930 (mm-30) REVERT: A 480 ASP cc_start: 0.8987 (m-30) cc_final: 0.8695 (m-30) REVERT: A 702 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8648 (mm) REVERT: B 31 MET cc_start: 0.6269 (tpt) cc_final: 0.4865 (tpt) REVERT: B 43 MET cc_start: 0.8066 (mpp) cc_final: 0.7851 (mpp) REVERT: B 95 MET cc_start: 0.7013 (mpp) cc_final: 0.5852 (mpp) REVERT: B 130 VAL cc_start: 0.9442 (t) cc_final: 0.8973 (m) REVERT: B 187 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7792 (pmm) REVERT: B 273 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8057 (pmm) REVERT: B 640 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8208 (tp) REVERT: B 680 MET cc_start: 0.9060 (ttp) cc_final: 0.8366 (ptm) REVERT: B 806 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7908 (mmmt) outliers start: 55 outliers final: 39 residues processed: 131 average time/residue: 0.2302 time to fit residues: 46.2009 Evaluate side-chains 133 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 86 time to evaluate : 1.533 ------------------------------------------------------------------------------- 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 159 VAL Chi-restraints excluded: chain A residue 163 GLU 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 224 THR Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 372 GLU 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 631 ARG Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 698 MET Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 725 ILE 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 187 MET 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 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 704 VAL Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 759 VAL 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 155 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 25 optimal weight: 0.0050 chunk 88 optimal weight: 0.8980 chunk 145 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 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 = 0.3846 r_free = 0.3846 target = 0.068094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.049796 restraints weight = 67123.148| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 5.40 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12830 Z= 0.193 Angle : 0.696 12.181 17412 Z= 0.332 Chirality : 0.044 0.183 1927 Planarity : 0.004 0.065 2265 Dihedral : 6.096 76.462 1710 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.56 % Favored : 94.31 % Rotamer: Outliers : 3.31 % Allowed : 24.25 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.22), residues: 1565 helix: 1.28 (0.20), residues: 706 sheet: 0.04 (0.30), residues: 305 loop : -0.86 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 312 HIS 0.004 0.001 HIS A 245 PHE 0.023 0.001 PHE A 602 TYR 0.012 0.001 TYR B 581 ARG 0.003 0.000 ARG B 288 *********************** 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 133 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 88 time to evaluate : 1.540 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: 0.7051 (tpp) cc_final: 0.6383 (tpp) REVERT: A 99 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8036 (mm) REVERT: A 137 MET cc_start: 0.8694 (ttm) cc_final: 0.8417 (ttm) REVERT: A 159 VAL cc_start: 0.7774 (OUTLIER) cc_final: 0.7541 (t) REVERT: A 176 MET cc_start: 0.7773 (tpp) cc_final: 0.7528 (tpp) REVERT: A 372 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7708 (mp0) REVERT: A 480 ASP cc_start: 0.9027 (m-30) cc_final: 0.8717 (m-30) REVERT: A 702 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8595 (mm) REVERT: A 772 MET cc_start: 0.8942 (ppp) cc_final: 0.8704 (ppp) REVERT: B 31 MET cc_start: 0.6384 (tpt) cc_final: 0.5015 (tpt) REVERT: B 43 MET cc_start: 0.8205 (mpp) cc_final: 0.8003 (mpp) REVERT: B 95 MET cc_start: 0.6868 (mpp) cc_final: 0.5800 (mpp) REVERT: B 130 VAL cc_start: 0.9398 (t) cc_final: 0.8916 (m) REVERT: B 187 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7754 (pmm) REVERT: B 273 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.7916 (pmm) REVERT: B 424 ASP cc_start: 0.9362 (m-30) cc_final: 0.9096 (t0) REVERT: B 542 MET cc_start: 0.8281 (ppp) cc_final: 0.7649 (ppp) REVERT: B 640 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8210 (tp) REVERT: B 680 MET cc_start: 0.9053 (ttp) cc_final: 0.8388 (ptm) REVERT: B 806 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7919 (mmmt) outliers start: 45 outliers final: 36 residues processed: 120 average time/residue: 0.2173 time to fit residues: 39.9779 Evaluate side-chains 130 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 86 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 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 159 VAL Chi-restraints excluded: chain A residue 163 GLU 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 224 THR Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 372 GLU 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 524 MET Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 698 MET Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 725 ILE 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 187 MET 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 151 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 36 optimal weight: 0.1980 chunk 61 optimal weight: 0.0060 chunk 117 optimal weight: 2.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- 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 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 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 = 0.3837 r_free = 0.3837 target = 0.067909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.049707 restraints weight = 66991.289| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 5.38 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12830 Z= 0.197 Angle : 0.706 12.359 17412 Z= 0.335 Chirality : 0.044 0.189 1927 Planarity : 0.004 0.065 2265 Dihedral : 6.073 76.873 1710 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.30 % Favored : 94.57 % Rotamer: Outliers : 3.16 % Allowed : 24.61 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.22), residues: 1565 helix: 1.32 (0.20), residues: 701 sheet: 0.10 (0.30), residues: 304 loop : -0.88 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 312 HIS 0.004 0.001 HIS A 245 PHE 0.023 0.001 PHE A 602 TYR 0.012 0.001 TYR B 581 ARG 0.003 0.000 ARG B 288 ********************** 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: 43 poor density : 87 time to evaluate : 1.629 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: 0.7040 (tpp) cc_final: 0.6366 (tpp) REVERT: A 99 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8039 (mm) REVERT: A 137 MET cc_start: 0.8716 (ttm) cc_final: 0.8426 (ttm) REVERT: A 159 VAL cc_start: 0.7732 (OUTLIER) cc_final: 0.7504 (t) REVERT: A 176 MET cc_start: 0.7768 (tpp) cc_final: 0.7519 (tpp) REVERT: A 372 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7753 (mm-30) REVERT: A 389 MET cc_start: 0.7704 (OUTLIER) cc_final: 0.7426 (tmm) REVERT: A 480 ASP cc_start: 0.9057 (m-30) cc_final: 0.8742 (m-30) REVERT: A 702 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8563 (mm) REVERT: B 31 MET cc_start: 0.6217 (tpt) cc_final: 0.4759 (tpt) REVERT: B 95 MET cc_start: 0.6836 (mpp) cc_final: 0.5881 (mpp) REVERT: B 130 VAL cc_start: 0.9422 (t) cc_final: 0.8898 (m) REVERT: B 273 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.7860 (pmm) REVERT: B 424 ASP cc_start: 0.9348 (m-30) cc_final: 0.9043 (t0) REVERT: B 542 MET cc_start: 0.8297 (ppp) cc_final: 0.7662 (ppp) REVERT: B 640 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8197 (tp) REVERT: B 680 MET cc_start: 0.9050 (ttp) cc_final: 0.8404 (ptm) REVERT: B 806 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7963 (mmmt) outliers start: 43 outliers final: 31 residues processed: 119 average time/residue: 0.2396 time to fit residues: 43.7771 Evaluate side-chains 124 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 85 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 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 159 VAL 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 286 ILE Chi-restraints excluded: chain A residue 372 GLU 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 524 MET Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 698 MET Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 725 ILE 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 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 704 VAL Chi-restraints excluded: chain B residue 759 VAL 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 104 optimal weight: 0.6980 chunk 30 optimal weight: 6.9990 chunk 36 optimal weight: 0.3980 chunk 33 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 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 636 HIS ** 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 = 0.3835 r_free = 0.3835 target = 0.067698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.049487 restraints weight = 67528.072| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 5.40 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12830 Z= 0.210 Angle : 0.711 12.063 17412 Z= 0.337 Chirality : 0.044 0.174 1927 Planarity : 0.004 0.063 2265 Dihedral : 6.119 77.443 1710 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.43 % Favored : 94.44 % Rotamer: Outliers : 2.87 % Allowed : 25.06 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.22), residues: 1565 helix: 1.29 (0.20), residues: 703 sheet: 0.13 (0.30), residues: 304 loop : -0.89 (0.28), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 312 HIS 0.006 0.001 HIS B 636 PHE 0.024 0.002 PHE A 602 TYR 0.013 0.001 TYR B 581 ARG 0.003 0.000 ARG B 288 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5454.79 seconds wall clock time: 98 minutes 50.64 seconds (5930.64 seconds total)