Starting phenix.real_space_refine on Thu May 15 03:41:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bkv_44646/05_2025/9bkv_44646.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bkv_44646/05_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_44646/05_2025/9bkv_44646.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bkv_44646/05_2025/9bkv_44646.map" model { file = "/net/cci-nas-00/data/ceres_data/9bkv_44646/05_2025/9bkv_44646.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bkv_44646/05_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-5687/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: 7.92, per 1000 atoms: 0.63 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: 3.35 Conformation dependent library (CDL) restraints added in 1.6 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: 1.61 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: 5.03 Time building geometry restraints manager: 3.81 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: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 31.590 Find NCS groups from input model: 0.560 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.215 12831 Z= 0.244 Angle : 0.839 12.013 17412 Z= 0.440 Chirality : 0.049 0.458 1927 Planarity : 0.005 0.065 2265 Dihedral : 16.685 89.602 4790 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 17.52 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 Details of bonding type rmsd hydrogen bonds : bond 0.12721 ( 671) hydrogen bonds : angle 6.31800 ( 1971) covalent geometry : bond 0.00568 (12830) covalent geometry : angle 0.83930 (17412) Misc. bond : bond 0.21513 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 210 time to evaluate : 1.473 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: 0.2893 time to fit residues: 86.0055 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 : 1.444 ------------------------------------------------------------------------------- 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 0.091 12831 Z= 0.169 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 Details of bonding type rmsd hydrogen bonds : bond 0.04023 ( 671) hydrogen bonds : angle 5.23030 ( 1971) covalent geometry : bond 0.00379 (12830) covalent geometry : angle 0.74582 (17412) Misc. bond : bond 0.09081 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 122 time to evaluate : 1.528 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: 0.2334 time to fit residues: 54.1552 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 : 1.447 ------------------------------------------------------------------------------- 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 0.063 12831 Z= 0.129 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 Details of bonding type rmsd hydrogen bonds : bond 0.03488 ( 671) hydrogen bonds : angle 4.88776 ( 1971) covalent geometry : bond 0.00300 (12830) covalent geometry : angle 0.67563 (17412) Misc. bond : bond 0.06267 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 113 time to evaluate : 1.517 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: 0.2167 time to fit residues: 46.0712 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 : 1.497 ------------------------------------------------------------------------------- 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 0.057 12831 Z= 0.144 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 Details of bonding type rmsd hydrogen bonds : bond 0.03251 ( 671) hydrogen bonds : angle 4.75907 ( 1971) covalent geometry : bond 0.00339 (12830) covalent geometry : angle 0.64742 (17412) Misc. bond : bond 0.05694 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 104 time to evaluate : 1.443 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: 0.2355 time to fit residues: 46.9749 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 : 1.422 ------------------------------------------------------------------------------- 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 0.051 12831 Z= 0.159 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 Details of bonding type rmsd hydrogen bonds : bond 0.03207 ( 671) hydrogen bonds : angle 4.75406 ( 1971) covalent geometry : bond 0.00376 (12830) covalent geometry : angle 0.65195 (17412) Misc. bond : bond 0.05067 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 102 time to evaluate : 1.397 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: 0.2180 time to fit residues: 47.5838 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 : 1.371 ------------------------------------------------------------------------------- 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: 9.9990 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 : 0.004 0.222 12831 Z= 0.131 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 Details of bonding type rmsd hydrogen bonds : bond 0.03073 ( 671) hydrogen bonds : angle 4.65118 ( 1971) covalent geometry : bond 0.00311 (12830) covalent geometry : angle 0.65123 (17412) Misc. bond : bond 0.22221 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 97 time to evaluate : 1.453 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: 0.2265 time to fit residues: 47.3483 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 : 1.400 ------------------------------------------------------------------------------- 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: 50.0000 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: 1.3988 ------------------------------------------------------------------------------- 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 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.066690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.048208 restraints weight = 68203.813| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 5.46 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.374 12831 Z= 0.193 Angle : 0.684 12.255 17412 Z= 0.338 Chirality : 0.044 0.212 1927 Planarity : 0.005 0.063 2265 Dihedral : 6.218 77.782 1710 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.75 % Favored : 94.12 % Rotamer: Outliers : 4.04 % Allowed : 23.37 % Favored : 72.59 % 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: 0.13 (0.22), residues: 1565 helix: 1.02 (0.20), residues: 705 sheet: -0.15 (0.29), residues: 307 loop : -0.89 (0.28), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 312 HIS 0.007 0.001 HIS B 245 PHE 0.028 0.002 PHE A 602 TYR 0.021 0.001 TYR B 581 ARG 0.007 0.000 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.03282 ( 671) hydrogen bonds : angle 4.77144 ( 1971) covalent geometry : bond 0.00444 (12830) covalent geometry : angle 0.68437 (17412) Misc. bond : bond 0.37432 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 89 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7111 (tpp) cc_final: 0.6617 (tpp) REVERT: A 99 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8183 (mm) REVERT: A 159 VAL cc_start: 0.7788 (OUTLIER) cc_final: 0.7570 (t) REVERT: A 176 MET cc_start: 0.7937 (tpp) cc_final: 0.7468 (tpp) REVERT: A 480 ASP cc_start: 0.9065 (m-30) cc_final: 0.8821 (m-30) REVERT: A 702 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8705 (mm) REVERT: B 95 MET cc_start: 0.6781 (mpp) cc_final: 0.5343 (mpp) REVERT: B 187 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.7716 (pmm) REVERT: B 273 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8145 (pmm) REVERT: B 542 MET cc_start: 0.8524 (ppp) cc_final: 0.6999 (ppp) REVERT: B 640 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8287 (tp) REVERT: B 680 MET cc_start: 0.9159 (ttp) cc_final: 0.8474 (ptm) REVERT: B 806 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7930 (tppt) outliers start: 55 outliers final: 34 residues processed: 131 average time/residue: 0.2302 time to fit residues: 45.5090 Evaluate side-chains 121 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 80 time to evaluate : 1.494 ------------------------------------------------------------------------------- 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 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 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 678 GLU 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 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 806 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 136 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 68 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.067554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.049086 restraints weight = 67824.509| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 5.41 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.297 12831 Z= 0.139 Angle : 0.688 11.518 17412 Z= 0.331 Chirality : 0.044 0.177 1927 Planarity : 0.004 0.065 2265 Dihedral : 6.163 76.780 1710 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.37 % Favored : 94.50 % Rotamer: Outliers : 3.53 % Allowed : 23.95 % Favored : 72.52 % 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: 0.27 (0.22), residues: 1565 helix: 1.16 (0.20), residues: 706 sheet: -0.09 (0.29), residues: 305 loop : -0.85 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 312 HIS 0.009 0.001 HIS B 245 PHE 0.025 0.002 PHE A 649 TYR 0.016 0.001 TYR B 581 ARG 0.003 0.000 ARG A 215 Details of bonding type rmsd hydrogen bonds : bond 0.03141 ( 671) hydrogen bonds : angle 4.68237 ( 1971) covalent geometry : bond 0.00325 (12830) covalent geometry : angle 0.68782 (17412) Misc. bond : bond 0.29677 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 88 time to evaluate : 1.432 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: 0.7173 (tpp) cc_final: 0.6521 (tpp) REVERT: A 99 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8060 (mm) REVERT: A 137 MET cc_start: 0.8695 (ttm) cc_final: 0.8442 (ttm) REVERT: A 159 VAL cc_start: 0.7782 (OUTLIER) cc_final: 0.7552 (t) REVERT: A 176 MET cc_start: 0.7826 (tpp) cc_final: 0.7369 (tpp) REVERT: A 480 ASP cc_start: 0.9072 (m-30) cc_final: 0.8761 (m-30) REVERT: A 702 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8674 (mm) REVERT: B 31 MET cc_start: 0.6356 (tpt) cc_final: 0.4943 (tpt) REVERT: B 43 MET cc_start: 0.8098 (mpp) cc_final: 0.7877 (mpp) REVERT: B 95 MET cc_start: 0.6942 (mpp) cc_final: 0.5791 (mpp) REVERT: B 130 VAL cc_start: 0.9463 (t) cc_final: 0.8982 (m) REVERT: B 187 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7768 (pmm) REVERT: B 273 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8010 (pmm) REVERT: B 640 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8260 (tp) REVERT: B 680 MET cc_start: 0.9070 (ttp) cc_final: 0.8365 (ptm) REVERT: B 806 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7941 (mmmt) outliers start: 48 outliers final: 37 residues processed: 124 average time/residue: 0.2145 time to fit residues: 41.1058 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 : 1.387 ------------------------------------------------------------------------------- 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 390 THR Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 631 ARG 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 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 299 VAL Chi-restraints excluded: chain B residue 456 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 641 SER Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 704 VAL Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 787 SER Chi-restraints excluded: chain B residue 806 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 155 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 86 optimal weight: 0.1980 chunk 73 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 91 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 107 optimal weight: 0.0770 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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 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 = 0.3850 r_free = 0.3850 target = 0.068352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.050061 restraints weight = 67057.248| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 5.40 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.253 12831 Z= 0.121 Angle : 0.702 12.183 17412 Z= 0.334 Chirality : 0.044 0.181 1927 Planarity : 0.004 0.065 2265 Dihedral : 6.117 76.463 1710 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.30 % Favored : 94.57 % Rotamer: Outliers : 3.09 % Allowed : 24.10 % Favored : 72.81 % 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: 0.42 (0.22), residues: 1565 helix: 1.32 (0.20), residues: 700 sheet: 0.05 (0.30), residues: 304 loop : -0.85 (0.28), residues: 561 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 0.023 0.001 PHE A 602 TYR 0.013 0.001 TYR B 581 ARG 0.003 0.000 ARG A 215 Details of bonding type rmsd hydrogen bonds : bond 0.03029 ( 671) hydrogen bonds : angle 4.63097 ( 1971) covalent geometry : bond 0.00284 (12830) covalent geometry : angle 0.70196 (17412) Misc. bond : bond 0.25306 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 89 time to evaluate : 1.600 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: 0.7028 (tpp) cc_final: 0.6352 (tpp) REVERT: A 99 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8028 (mm) REVERT: A 137 MET cc_start: 0.8690 (ttm) cc_final: 0.8413 (ttm) REVERT: A 159 VAL cc_start: 0.7758 (OUTLIER) cc_final: 0.7519 (t) REVERT: A 176 MET cc_start: 0.7744 (tpp) cc_final: 0.7290 (tpp) REVERT: A 480 ASP cc_start: 0.9029 (m-30) cc_final: 0.8723 (m-30) REVERT: A 702 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8585 (mm) REVERT: B 31 MET cc_start: 0.6345 (tpt) cc_final: 0.4991 (tpt) REVERT: B 43 MET cc_start: 0.8176 (mpp) cc_final: 0.7975 (mpp) REVERT: B 95 MET cc_start: 0.6831 (mpp) cc_final: 0.5859 (mpp) REVERT: B 130 VAL cc_start: 0.9436 (t) cc_final: 0.8940 (m) REVERT: B 273 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.7895 (pmm) REVERT: B 424 ASP cc_start: 0.9364 (m-30) cc_final: 0.9047 (t0) REVERT: B 542 MET cc_start: 0.8205 (ppp) cc_final: 0.7995 (ppp) REVERT: B 640 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8193 (tp) REVERT: B 680 MET cc_start: 0.9047 (ttp) cc_final: 0.8390 (ptm) REVERT: B 806 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7935 (mmmt) outliers start: 42 outliers final: 33 residues processed: 121 average time/residue: 0.2199 time to fit residues: 41.0422 Evaluate side-chains 126 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 87 time to evaluate : 1.500 ------------------------------------------------------------------------------- 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 293 VAL 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 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 A residue 780 VAL Chi-restraints excluded: chain B residue 22 PHE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 279 PHE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 456 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 641 SER Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 704 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 787 SER Chi-restraints excluded: chain B residue 806 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 151 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 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 168 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 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 = 0.3826 r_free = 0.3826 target = 0.067257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.048815 restraints weight = 67407.949| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 5.37 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.205 12831 Z= 0.162 Angle : 0.717 11.967 17412 Z= 0.343 Chirality : 0.044 0.164 1927 Planarity : 0.004 0.066 2265 Dihedral : 6.187 77.508 1710 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.88 % Favored : 93.99 % Rotamer: Outliers : 2.72 % Allowed : 24.83 % 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: 0.32 (0.22), residues: 1565 helix: 1.22 (0.20), residues: 706 sheet: -0.01 (0.30), residues: 305 loop : -0.90 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 312 HIS 0.004 0.001 HIS A 245 PHE 0.026 0.002 PHE A 602 TYR 0.016 0.001 TYR B 581 ARG 0.003 0.000 ARG B 288 Details of bonding type rmsd hydrogen bonds : bond 0.03154 ( 671) hydrogen bonds : angle 4.68151 ( 1971) covalent geometry : bond 0.00382 (12830) covalent geometry : angle 0.71721 (17412) Misc. bond : bond 0.20479 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 83 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7293 (tpp) cc_final: 0.6659 (tpp) REVERT: A 67 MET cc_start: 0.8666 (ptm) cc_final: 0.8454 (ptm) REVERT: A 99 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8072 (mm) REVERT: A 137 MET cc_start: 0.8643 (ttm) cc_final: 0.8358 (ttm) REVERT: A 176 MET cc_start: 0.7803 (tpp) cc_final: 0.7354 (tpp) REVERT: A 480 ASP cc_start: 0.9019 (m-30) cc_final: 0.8720 (m-30) REVERT: A 702 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8718 (mm) REVERT: B 31 MET cc_start: 0.6321 (tpt) cc_final: 0.4872 (tpt) REVERT: B 43 MET cc_start: 0.8163 (mpp) cc_final: 0.7962 (mpp) REVERT: B 95 MET cc_start: 0.7023 (mpp) cc_final: 0.5686 (mpp) REVERT: B 130 VAL cc_start: 0.9473 (t) cc_final: 0.8975 (m) REVERT: B 273 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8037 (pmm) REVERT: B 542 MET cc_start: 0.8196 (ppp) cc_final: 0.7962 (ppp) REVERT: B 680 MET cc_start: 0.9039 (ttp) cc_final: 0.8397 (ptm) REVERT: B 806 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7950 (mmmt) outliers start: 37 outliers final: 31 residues processed: 112 average time/residue: 0.2335 time to fit residues: 40.0095 Evaluate side-chains 118 residues out of total 1361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 83 time to evaluate : 1.478 ------------------------------------------------------------------------------- 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 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 293 VAL 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 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 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 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 806 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 104 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 chunk 36 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 121 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 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 = 0.3838 r_free = 0.3838 target = 0.067655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.049275 restraints weight = 67456.421| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 5.40 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.193 12831 Z= 0.135 Angle : 0.719 12.295 17412 Z= 0.340 Chirality : 0.044 0.163 1927 Planarity : 0.004 0.063 2265 Dihedral : 6.174 78.299 1710 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.86 % Favored : 95.02 % Rotamer: Outliers : 3.01 % Allowed : 24.76 % Favored : 72.23 % 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: 0.35 (0.22), residues: 1565 helix: 1.26 (0.20), residues: 703 sheet: 0.04 (0.30), residues: 305 loop : -0.90 (0.28), residues: 557 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 0.024 0.001 PHE A 602 TYR 0.013 0.001 TYR A 415 ARG 0.004 0.000 ARG A 215 Details of bonding type rmsd hydrogen bonds : bond 0.03062 ( 671) hydrogen bonds : angle 4.62800 ( 1971) covalent geometry : bond 0.00320 (12830) covalent geometry : angle 0.71925 (17412) Misc. bond : bond 0.19290 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5683.61 seconds wall clock time: 99 minutes 19.84 seconds (5959.84 seconds total)