Starting phenix.real_space_refine on Mon Jun 9 00:18:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dbq_46724/06_2025/9dbq_46724.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dbq_46724/06_2025/9dbq_46724.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dbq_46724/06_2025/9dbq_46724.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dbq_46724/06_2025/9dbq_46724.map" model { file = "/net/cci-nas-00/data/ceres_data/9dbq_46724/06_2025/9dbq_46724.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dbq_46724/06_2025/9dbq_46724.cif" } resolution = 2.9 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= 0.002 sd= 0.021 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: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 6636 2.51 5 N 1622 2.21 5 O 1770 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 10062 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4681 Classifications: {'peptide': 591} Link IDs: {'PTRANS': 13, 'TRANS': 577} Chain: "B" Number of atoms: 4681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4681 Classifications: {'peptide': 591} Link IDs: {'PTRANS': 13, 'TRANS': 577} Chain: "A" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 350 Unusual residues: {'Y01': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 350 Unusual residues: {'Y01': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Time building chain proxies: 6.54, per 1000 atoms: 0.65 Number of scatterers: 10062 At special positions: 0 Unit cell: (116.33, 83.7144, 136.987, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 1770 8.00 N 1622 7.00 C 6636 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.13 Conformation dependent library (CDL) restraints added in 1.1 seconds 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 8 sheets defined 71.8% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 237 through 254 Processing helix chain 'A' and resid 258 through 295 removed outlier: 3.974A pdb=" N GLN A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 263 " --> pdb=" O PRO A 259 " (cutoff:3.500A) Proline residue: A 283 - end of helix removed outlier: 3.589A pdb=" N GLU A 295 " --> pdb=" O ASN A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 317 removed outlier: 3.893A pdb=" N TRP A 304 " --> pdb=" O ASN A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 356 removed outlier: 3.691A pdb=" N ILE A 335 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ARG A 336 " --> pdb=" O PHE A 332 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 364 Processing helix chain 'A' and resid 365 through 390 removed outlier: 3.856A pdb=" N VAL A 369 " --> pdb=" O ARG A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 409 removed outlier: 3.761A pdb=" N THR A 394 " --> pdb=" O ASN A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 459 removed outlier: 4.056A pdb=" N GLY A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A 433 " --> pdb=" O ILE A 429 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TRP A 434 " --> pdb=" O VAL A 430 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ALA A 441 " --> pdb=" O LYS A 437 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N MET A 442 " --> pdb=" O PHE A 438 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASN A 443 " --> pdb=" O ARG A 439 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR A 444 " --> pdb=" O ARG A 440 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN A 459 " --> pdb=" O ASP A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 467 Processing helix chain 'A' and resid 468 through 522 Processing helix chain 'A' and resid 526 through 542 removed outlier: 3.884A pdb=" N TYR A 530 " --> pdb=" O GLN A 526 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE A 538 " --> pdb=" O GLY A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 545 No H-bonds generated for 'chain 'A' and resid 543 through 545' Processing helix chain 'A' and resid 546 through 570 removed outlier: 3.879A pdb=" N GLN A 555 " --> pdb=" O TYR A 551 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N THR A 556 " --> pdb=" O ARG A 552 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 637 removed outlier: 3.595A pdb=" N ILE A 632 " --> pdb=" O GLY A 628 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 633 " --> pdb=" O LYS A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 665 removed outlier: 3.577A pdb=" N LEU A 662 " --> pdb=" O THR A 658 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N HIS A 665 " --> pdb=" O SER A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 685 Processing helix chain 'A' and resid 686 through 688 No H-bonds generated for 'chain 'A' and resid 686 through 688' Processing helix chain 'A' and resid 692 through 704 Processing helix chain 'A' and resid 705 through 712 Processing helix chain 'A' and resid 728 through 744 removed outlier: 3.622A pdb=" N ALA A 744 " --> pdb=" O THR A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 773 Processing helix chain 'A' and resid 807 through 815 Processing helix chain 'A' and resid 816 through 827 removed outlier: 3.926A pdb=" N ASP A 820 " --> pdb=" O GLY A 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 254 Processing helix chain 'B' and resid 258 through 295 removed outlier: 3.946A pdb=" N GLN B 262 " --> pdb=" O SER B 258 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU B 263 " --> pdb=" O PRO B 259 " (cutoff:3.500A) Proline residue: B 283 - end of helix removed outlier: 3.604A pdb=" N GLU B 295 " --> pdb=" O ASN B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 317 removed outlier: 3.878A pdb=" N TRP B 304 " --> pdb=" O ASN B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 356 removed outlier: 3.689A pdb=" N ILE B 335 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ARG B 336 " --> pdb=" O PHE B 332 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL B 337 " --> pdb=" O LEU B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 364 Processing helix chain 'B' and resid 365 through 390 removed outlier: 3.866A pdb=" N VAL B 369 " --> pdb=" O ARG B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 409 removed outlier: 3.872A pdb=" N THR B 394 " --> pdb=" O ASN B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 459 removed outlier: 4.050A pdb=" N GLY B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU B 433 " --> pdb=" O ILE B 429 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N TRP B 434 " --> pdb=" O VAL B 430 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA B 441 " --> pdb=" O LYS B 437 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N MET B 442 " --> pdb=" O PHE B 438 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASN B 443 " --> pdb=" O ARG B 439 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR B 444 " --> pdb=" O ARG B 440 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG B 450 " --> pdb=" O GLU B 446 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN B 459 " --> pdb=" O ASP B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 467 Processing helix chain 'B' and resid 468 through 522 Processing helix chain 'B' and resid 526 through 542 removed outlier: 3.885A pdb=" N TYR B 530 " --> pdb=" O GLN B 526 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL B 531 " --> pdb=" O VAL B 527 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE B 538 " --> pdb=" O GLY B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 545 No H-bonds generated for 'chain 'B' and resid 543 through 545' Processing helix chain 'B' and resid 546 through 570 removed outlier: 3.872A pdb=" N GLN B 555 " --> pdb=" O TYR B 551 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N THR B 556 " --> pdb=" O ARG B 552 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU B 570 " --> pdb=" O ASP B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 637 removed outlier: 3.575A pdb=" N ILE B 632 " --> pdb=" O GLY B 628 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 633 " --> pdb=" O LYS B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 665 removed outlier: 3.585A pdb=" N LEU B 662 " --> pdb=" O THR B 658 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N HIS B 665 " --> pdb=" O SER B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 685 Processing helix chain 'B' and resid 686 through 688 No H-bonds generated for 'chain 'B' and resid 686 through 688' Processing helix chain 'B' and resid 692 through 704 Processing helix chain 'B' and resid 705 through 712 Processing helix chain 'B' and resid 728 through 744 removed outlier: 3.643A pdb=" N ALA B 744 " --> pdb=" O THR B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 773 Processing helix chain 'B' and resid 807 through 815 Processing helix chain 'B' and resid 816 through 827 removed outlier: 3.917A pdb=" N ASP B 820 " --> pdb=" O GLY B 816 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 611 through 613 removed outlier: 3.828A pdb=" N GLU A 593 " --> pdb=" O CYS A 646 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N CYS A 646 " --> pdb=" O GLU A 593 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 619 through 622 removed outlier: 3.510A pdb=" N VAL A 622 " --> pdb=" O LEU A 795 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 797 " --> pdb=" O VAL A 622 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A 804 " --> pdb=" O VAL A 796 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 666 through 669 removed outlier: 6.879A pdb=" N GLY A 667 " --> pdb=" O LEU A 749 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 678 through 679 removed outlier: 3.913A pdb=" N ASP A 678 " --> pdb=" O VAL A 720 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 611 through 613 removed outlier: 3.864A pdb=" N GLU B 593 " --> pdb=" O CYS B 646 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N CYS B 646 " --> pdb=" O GLU B 593 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 619 through 622 removed outlier: 6.192A pdb=" N ALA B 620 " --> pdb=" O LEU B 795 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ILE B 797 " --> pdb=" O ALA B 620 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N VAL B 622 " --> pdb=" O ILE B 797 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE B 794 " --> pdb=" O ARG B 805 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ARG B 805 " --> pdb=" O ILE B 794 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL B 796 " --> pdb=" O VAL B 803 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N CYS B 801 " --> pdb=" O LYS B 798 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 666 through 669 removed outlier: 6.781A pdb=" N GLY B 667 " --> pdb=" O LEU B 749 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 678 through 679 removed outlier: 3.861A pdb=" N ASP B 678 " --> pdb=" O VAL B 720 " (cutoff:3.500A) 631 hydrogen bonds defined for protein. 1875 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: 3.12 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1667 1.32 - 1.45: 2597 1.45 - 1.57: 5988 1.57 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 10308 Sorted by residual: bond pdb=" N SER B 237 " pdb=" CA SER B 237 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.71e+00 bond pdb=" N SER A 237 " pdb=" CA SER A 237 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.54e+00 bond pdb=" CAT Y01 B 906 " pdb=" CBH Y01 B 906 " ideal model delta sigma weight residual 1.545 1.528 0.017 2.00e-02 2.50e+03 7.00e-01 bond pdb=" CBE Y01 B 901 " pdb=" CBI Y01 B 901 " ideal model delta sigma weight residual 1.550 1.567 -0.017 2.00e-02 2.50e+03 6.84e-01 bond pdb=" CA VAL B 282 " pdb=" CB VAL B 282 " ideal model delta sigma weight residual 1.539 1.543 -0.004 5.40e-03 3.43e+04 6.26e-01 ... (remaining 10303 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 13536 1.26 - 2.52: 435 2.52 - 3.78: 102 3.78 - 5.05: 9 5.05 - 6.31: 6 Bond angle restraints: 14088 Sorted by residual: angle pdb=" N VAL A 803 " pdb=" CA VAL A 803 " pdb=" C VAL A 803 " ideal model delta sigma weight residual 111.81 109.81 2.00 8.60e-01 1.35e+00 5.39e+00 angle pdb=" CAO Y01 B 907 " pdb=" CBB Y01 B 907 " pdb=" CBE Y01 B 907 " ideal model delta sigma weight residual 109.88 116.19 -6.31 3.00e+00 1.11e-01 4.42e+00 angle pdb=" CAO Y01 A 905 " pdb=" CBB Y01 A 905 " pdb=" CBE Y01 A 905 " ideal model delta sigma weight residual 109.88 116.14 -6.26 3.00e+00 1.11e-01 4.36e+00 angle pdb=" CAO Y01 A 910 " pdb=" CBB Y01 A 910 " pdb=" CBE Y01 A 910 " ideal model delta sigma weight residual 109.88 115.91 -6.03 3.00e+00 1.11e-01 4.04e+00 angle pdb=" CAO Y01 B 902 " pdb=" CBB Y01 B 902 " pdb=" CBE Y01 B 902 " ideal model delta sigma weight residual 109.88 115.90 -6.02 3.00e+00 1.11e-01 4.03e+00 ... (remaining 14083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.11: 6294 15.11 - 30.23: 544 30.23 - 45.34: 138 45.34 - 60.46: 60 60.46 - 75.57: 6 Dihedral angle restraints: 7042 sinusoidal: 3646 harmonic: 3396 Sorted by residual: dihedral pdb=" CB MET B 407 " pdb=" CG MET B 407 " pdb=" SD MET B 407 " pdb=" CE MET B 407 " ideal model delta sinusoidal sigma weight residual 60.00 119.23 -59.23 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB MET A 407 " pdb=" CG MET A 407 " pdb=" SD MET A 407 " pdb=" CE MET A 407 " ideal model delta sinusoidal sigma weight residual 60.00 119.16 -59.16 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB MET A 614 " pdb=" CG MET A 614 " pdb=" SD MET A 614 " pdb=" CE MET A 614 " ideal model delta sinusoidal sigma weight residual 180.00 121.40 58.60 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 7039 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1172 0.031 - 0.062: 328 0.062 - 0.092: 105 0.092 - 0.123: 33 0.123 - 0.154: 12 Chirality restraints: 1650 Sorted by residual: chirality pdb=" CBE Y01 A 910 " pdb=" CAP Y01 A 910 " pdb=" CBB Y01 A 910 " pdb=" CBI Y01 A 910 " both_signs ideal model delta sigma weight residual False 2.57 2.41 0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CBE Y01 B 902 " pdb=" CAP Y01 B 902 " pdb=" CBB Y01 B 902 " pdb=" CBI Y01 B 902 " both_signs ideal model delta sigma weight residual False 2.57 2.42 0.15 2.00e-01 2.50e+01 5.74e-01 chirality pdb=" CA VAL A 669 " pdb=" N VAL A 669 " pdb=" C VAL A 669 " pdb=" CB VAL A 669 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.87e-01 ... (remaining 1647 not shown) Planarity restraints: 1676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 297 " 0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO B 298 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO B 298 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 298 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 297 " 0.019 5.00e-02 4.00e+02 2.82e-02 1.27e+00 pdb=" N PRO A 298 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 298 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 298 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 254 " 0.017 5.00e-02 4.00e+02 2.57e-02 1.06e+00 pdb=" N PRO B 255 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO B 255 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 255 " 0.014 5.00e-02 4.00e+02 ... (remaining 1673 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 79 2.63 - 3.19: 9224 3.19 - 3.76: 14894 3.76 - 4.33: 20025 4.33 - 4.90: 33424 Nonbonded interactions: 77646 Sorted by model distance: nonbonded pdb=" OG SER A 379 " pdb=" OD1 ASN A 557 " model vdw 2.057 3.040 nonbonded pdb=" OG SER B 456 " pdb=" OE1 GLU B 472 " model vdw 2.078 3.040 nonbonded pdb=" OG SER A 456 " pdb=" OE1 GLU A 472 " model vdw 2.095 3.040 nonbonded pdb=" O ALA A 627 " pdb=" OG1 THR A 631 " model vdw 2.215 3.040 nonbonded pdb=" OG SER B 379 " pdb=" OD1 ASN B 557 " model vdw 2.223 3.040 ... (remaining 77641 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' 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=0.50 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.760 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 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 : 0.003 0.039 10310 Z= 0.140 Angle : 0.559 6.307 14088 Z= 0.263 Chirality : 0.035 0.154 1650 Planarity : 0.003 0.030 1676 Dihedral : 12.628 75.574 4870 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.10 % Allowed : 0.80 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.25), residues: 1178 helix: 1.88 (0.19), residues: 792 sheet: -0.52 (0.80), residues: 48 loop : -1.83 (0.30), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 434 HIS 0.004 0.001 HIS A 596 PHE 0.010 0.001 PHE B 637 TYR 0.009 0.001 TYR B 286 ARG 0.002 0.000 ARG A 240 Details of bonding type rmsd hydrogen bonds : bond 0.16494 ( 631) hydrogen bonds : angle 5.44529 ( 1875) covalent geometry : bond 0.00310 (10308) covalent geometry : angle 0.55897 (14088) Misc. bond : bond 0.00212 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 213 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7751 (mt-10) REVERT: A 546 TRP cc_start: 0.8596 (m100) cc_final: 0.8233 (m100) REVERT: A 553 MET cc_start: 0.7514 (ttm) cc_final: 0.7119 (ttp) REVERT: A 569 LYS cc_start: 0.7495 (mttt) cc_final: 0.7087 (mttp) REVERT: A 621 LEU cc_start: 0.7179 (tp) cc_final: 0.6869 (mp) REVERT: A 635 LEU cc_start: 0.7050 (tp) cc_final: 0.6801 (mt) REVERT: A 710 MET cc_start: 0.6766 (tpt) cc_final: 0.6036 (mtm) REVERT: A 772 VAL cc_start: 0.7516 (p) cc_final: 0.7312 (m) REVERT: A 779 ILE cc_start: 0.7854 (mt) cc_final: 0.7625 (mm) REVERT: B 346 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7704 (mt-10) REVERT: B 546 TRP cc_start: 0.8604 (m100) cc_final: 0.8240 (m100) REVERT: B 553 MET cc_start: 0.7501 (ttm) cc_final: 0.7217 (ttm) REVERT: B 635 LEU cc_start: 0.7043 (tp) cc_final: 0.6696 (mt) REVERT: B 772 VAL cc_start: 0.7730 (p) cc_final: 0.7505 (m) REVERT: B 779 ILE cc_start: 0.7735 (mt) cc_final: 0.7524 (mm) REVERT: B 785 LEU cc_start: 0.7905 (mt) cc_final: 0.7541 (mm) outliers start: 1 outliers final: 0 residues processed: 214 average time/residue: 1.3927 time to fit residues: 316.7147 Evaluate side-chains 108 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.0070 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 47 optimal weight: 0.4980 chunk 92 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 107 optimal weight: 0.2980 overall best weight: 0.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN A 484 GLN A 539 GLN A 557 ASN A 563 ASN B 279 ASN B 484 GLN B 539 GLN B 701 GLN B 706 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.174857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.133056 restraints weight = 14656.320| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 2.67 r_work: 0.3768 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3782 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3782 r_free = 0.3782 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3778 r_free = 0.3778 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10310 Z= 0.142 Angle : 0.564 5.903 14088 Z= 0.293 Chirality : 0.037 0.145 1650 Planarity : 0.004 0.044 1676 Dihedral : 8.571 58.952 2728 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.20 % Allowed : 9.60 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.25), residues: 1178 helix: 2.32 (0.19), residues: 800 sheet: -1.51 (0.64), residues: 66 loop : -1.71 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 434 HIS 0.003 0.001 HIS A 352 PHE 0.021 0.001 PHE A 547 TYR 0.019 0.001 TYR A 550 ARG 0.009 0.001 ARG A 256 Details of bonding type rmsd hydrogen bonds : bond 0.06374 ( 631) hydrogen bonds : angle 4.00192 ( 1875) covalent geometry : bond 0.00298 (10308) covalent geometry : angle 0.56358 (14088) Misc. bond : bond 0.00004 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 346 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7868 (mt-10) REVERT: A 456 SER cc_start: 0.8082 (t) cc_final: 0.7814 (p) REVERT: A 546 TRP cc_start: 0.8418 (m100) cc_final: 0.8126 (m100) REVERT: A 614 MET cc_start: 0.5051 (mpp) cc_final: 0.4419 (mpp) REVERT: A 621 LEU cc_start: 0.7498 (tp) cc_final: 0.7157 (mp) REVERT: A 635 LEU cc_start: 0.7036 (tp) cc_final: 0.6693 (mt) REVERT: A 710 MET cc_start: 0.6793 (tpt) cc_final: 0.6043 (mtm) REVERT: A 765 ILE cc_start: 0.6706 (OUTLIER) cc_final: 0.6424 (tp) REVERT: A 779 ILE cc_start: 0.7917 (mt) cc_final: 0.7407 (mm) REVERT: B 346 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7828 (mt-10) REVERT: B 383 LEU cc_start: 0.8222 (tp) cc_final: 0.7982 (tt) REVERT: B 456 SER cc_start: 0.8229 (t) cc_final: 0.7950 (p) REVERT: B 546 TRP cc_start: 0.8458 (m100) cc_final: 0.8163 (m100) REVERT: B 558 PHE cc_start: 0.6718 (OUTLIER) cc_final: 0.6255 (m-80) REVERT: B 614 MET cc_start: 0.4833 (mpp) cc_final: 0.4220 (mpp) REVERT: B 621 LEU cc_start: 0.6531 (OUTLIER) cc_final: 0.6107 (mp) REVERT: B 635 LEU cc_start: 0.7198 (tp) cc_final: 0.6849 (mt) REVERT: B 701 GLN cc_start: 0.5949 (OUTLIER) cc_final: 0.5747 (mm-40) REVERT: B 765 ILE cc_start: 0.6621 (OUTLIER) cc_final: 0.6398 (tp) REVERT: B 779 ILE cc_start: 0.7874 (mt) cc_final: 0.7267 (mm) outliers start: 32 outliers final: 4 residues processed: 143 average time/residue: 1.2929 time to fit residues: 198.0946 Evaluate side-chains 97 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain B residue 558 PHE Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain B residue 701 GLN Chi-restraints excluded: chain B residue 765 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 62 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 101 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 chunk 34 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 706 HIS B 316 GLN B 706 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.176009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.134376 restraints weight = 15383.712| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 2.66 r_work: 0.3794 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3780 r_free = 0.3780 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3780 r_free = 0.3780 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10310 Z= 0.134 Angle : 0.555 6.693 14088 Z= 0.287 Chirality : 0.037 0.141 1650 Planarity : 0.004 0.036 1676 Dihedral : 8.276 59.314 2728 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.10 % Allowed : 13.40 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.25), residues: 1178 helix: 2.46 (0.19), residues: 790 sheet: -1.35 (0.64), residues: 66 loop : -1.58 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 434 HIS 0.010 0.001 HIS B 706 PHE 0.024 0.001 PHE B 547 TYR 0.010 0.001 TYR A 424 ARG 0.010 0.001 ARG B 589 Details of bonding type rmsd hydrogen bonds : bond 0.05831 ( 631) hydrogen bonds : angle 3.88323 ( 1875) covalent geometry : bond 0.00277 (10308) covalent geometry : angle 0.55475 (14088) Misc. bond : bond 0.00013 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 1.100 Fit side-chains revert: symmetry clash REVERT: A 346 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7823 (mt-10) REVERT: A 558 PHE cc_start: 0.6750 (OUTLIER) cc_final: 0.6249 (m-80) REVERT: A 569 LYS cc_start: 0.7456 (mttt) cc_final: 0.6925 (mmtt) REVERT: A 614 MET cc_start: 0.4871 (mpp) cc_final: 0.4483 (mpp) REVERT: A 635 LEU cc_start: 0.6947 (tp) cc_final: 0.6643 (mt) REVERT: A 654 ILE cc_start: 0.5849 (OUTLIER) cc_final: 0.5385 (pt) REVERT: A 656 GLN cc_start: 0.7133 (OUTLIER) cc_final: 0.6905 (pm20) REVERT: A 779 ILE cc_start: 0.7905 (mt) cc_final: 0.7379 (mm) REVERT: B 346 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7846 (mt-10) REVERT: B 383 LEU cc_start: 0.8225 (tp) cc_final: 0.7945 (tt) REVERT: B 456 SER cc_start: 0.8173 (t) cc_final: 0.7871 (p) REVERT: B 614 MET cc_start: 0.4715 (mpp) cc_final: 0.4294 (mpp) REVERT: B 635 LEU cc_start: 0.7062 (tp) cc_final: 0.6718 (mt) REVERT: B 779 ILE cc_start: 0.7887 (mt) cc_final: 0.7400 (mm) outliers start: 31 outliers final: 6 residues processed: 122 average time/residue: 1.2276 time to fit residues: 161.2138 Evaluate side-chains 91 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 654 ILE Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 656 GLN Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain B residue 655 SER Chi-restraints excluded: chain B residue 659 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 33 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 36 optimal weight: 0.0030 chunk 6 optimal weight: 0.8980 chunk 49 optimal weight: 0.0970 chunk 102 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN A 523 GLN B 523 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.177482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.134814 restraints weight = 14851.737| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 2.68 r_work: 0.3771 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3798 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3798 r_free = 0.3798 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3797 r_free = 0.3797 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10310 Z= 0.126 Angle : 0.532 5.967 14088 Z= 0.275 Chirality : 0.037 0.141 1650 Planarity : 0.003 0.029 1676 Dihedral : 8.124 59.507 2728 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.70 % Allowed : 14.10 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.26), residues: 1178 helix: 2.56 (0.19), residues: 788 sheet: -1.28 (0.64), residues: 66 loop : -1.59 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 434 HIS 0.005 0.001 HIS B 706 PHE 0.026 0.001 PHE B 547 TYR 0.013 0.001 TYR A 550 ARG 0.008 0.001 ARG B 552 Details of bonding type rmsd hydrogen bonds : bond 0.05429 ( 631) hydrogen bonds : angle 3.79008 ( 1875) covalent geometry : bond 0.00256 (10308) covalent geometry : angle 0.53165 (14088) Misc. bond : bond 0.00023 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 97 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 346 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7817 (mt-10) REVERT: A 558 PHE cc_start: 0.6690 (OUTLIER) cc_final: 0.6240 (m-80) REVERT: A 569 LYS cc_start: 0.7403 (mttt) cc_final: 0.7131 (mttp) REVERT: A 614 MET cc_start: 0.4774 (mpp) cc_final: 0.4434 (mpp) REVERT: A 635 LEU cc_start: 0.6727 (tp) cc_final: 0.6430 (mt) REVERT: A 706 HIS cc_start: 0.7283 (p-80) cc_final: 0.6616 (t70) REVERT: A 710 MET cc_start: 0.6545 (tpp) cc_final: 0.5682 (mtm) REVERT: A 779 ILE cc_start: 0.7810 (mt) cc_final: 0.7323 (mm) REVERT: B 346 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7805 (mt-10) REVERT: B 383 LEU cc_start: 0.8167 (tp) cc_final: 0.7961 (tt) REVERT: B 456 SER cc_start: 0.8169 (t) cc_final: 0.7813 (p) REVERT: B 558 PHE cc_start: 0.6667 (OUTLIER) cc_final: 0.6177 (m-80) REVERT: B 614 MET cc_start: 0.4554 (mpp) cc_final: 0.4263 (mpp) REVERT: B 635 LEU cc_start: 0.6898 (tp) cc_final: 0.6595 (mt) REVERT: B 779 ILE cc_start: 0.7799 (mt) cc_final: 0.7367 (mm) outliers start: 37 outliers final: 9 residues processed: 126 average time/residue: 1.1035 time to fit residues: 151.0213 Evaluate side-chains 96 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain B residue 558 PHE Chi-restraints excluded: chain B residue 655 SER Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 781 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 24 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 109 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 671 GLN ** B 706 HIS ** 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 = 0.4329 r_free = 0.4329 target = 0.174220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.131514 restraints weight = 14758.955| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 2.65 r_work: 0.3732 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3768 r_free = 0.3768 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3768 r_free = 0.3768 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10310 Z= 0.152 Angle : 0.561 7.341 14088 Z= 0.288 Chirality : 0.038 0.148 1650 Planarity : 0.003 0.032 1676 Dihedral : 8.146 59.714 2728 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.90 % Allowed : 15.90 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.25), residues: 1178 helix: 2.53 (0.18), residues: 800 sheet: -1.91 (0.63), residues: 56 loop : -1.50 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 434 HIS 0.006 0.001 HIS B 706 PHE 0.026 0.001 PHE A 547 TYR 0.014 0.002 TYR B 550 ARG 0.010 0.001 ARG B 375 Details of bonding type rmsd hydrogen bonds : bond 0.06016 ( 631) hydrogen bonds : angle 3.83433 ( 1875) covalent geometry : bond 0.00337 (10308) covalent geometry : angle 0.56101 (14088) Misc. bond : bond 0.00002 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 90 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: A 346 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7800 (mt-10) REVERT: A 439 ARG cc_start: 0.7871 (tmm-80) cc_final: 0.7631 (ttp80) REVERT: A 442 MET cc_start: 0.7124 (OUTLIER) cc_final: 0.6844 (ttm) REVERT: A 456 SER cc_start: 0.8182 (t) cc_final: 0.7822 (p) REVERT: A 558 PHE cc_start: 0.6718 (OUTLIER) cc_final: 0.6239 (m-80) REVERT: A 569 LYS cc_start: 0.7340 (mttt) cc_final: 0.6914 (mmtm) REVERT: A 614 MET cc_start: 0.4782 (mpp) cc_final: 0.4363 (mpp) REVERT: A 635 LEU cc_start: 0.6900 (tp) cc_final: 0.6545 (mt) REVERT: A 656 GLN cc_start: 0.7257 (OUTLIER) cc_final: 0.6285 (pm20) REVERT: A 710 MET cc_start: 0.6486 (tpp) cc_final: 0.5813 (mtp) REVERT: A 779 ILE cc_start: 0.7828 (mt) cc_final: 0.7368 (mm) REVERT: B 346 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7763 (mt-10) REVERT: B 383 LEU cc_start: 0.8158 (tp) cc_final: 0.7909 (tt) REVERT: B 456 SER cc_start: 0.8245 (t) cc_final: 0.7881 (p) REVERT: B 569 LYS cc_start: 0.7401 (mttt) cc_final: 0.6941 (mmtt) REVERT: B 614 MET cc_start: 0.4536 (mpp) cc_final: 0.4199 (mpp) REVERT: B 635 LEU cc_start: 0.7076 (tp) cc_final: 0.6642 (mt) REVERT: B 654 ILE cc_start: 0.5994 (OUTLIER) cc_final: 0.5536 (pt) REVERT: B 779 ILE cc_start: 0.7934 (mt) cc_final: 0.7488 (mm) outliers start: 39 outliers final: 20 residues processed: 117 average time/residue: 1.0038 time to fit residues: 128.3411 Evaluate side-chains 100 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 656 GLN Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 671 GLN Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 706 HIS Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 655 SER Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 781 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 5 optimal weight: 1.9990 chunk 59 optimal weight: 20.0000 chunk 21 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 50 optimal weight: 0.0980 chunk 3 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN B 328 ASN B 671 GLN ** B 706 HIS ** 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 = 0.4321 r_free = 0.4321 target = 0.173569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.130549 restraints weight = 14947.162| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.67 r_work: 0.3721 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3748 r_free = 0.3748 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3748 r_free = 0.3748 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10310 Z= 0.152 Angle : 0.564 6.408 14088 Z= 0.289 Chirality : 0.038 0.149 1650 Planarity : 0.004 0.049 1676 Dihedral : 8.121 59.737 2728 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.00 % Allowed : 18.30 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.25), residues: 1178 helix: 2.51 (0.18), residues: 800 sheet: -1.79 (0.64), residues: 56 loop : -1.51 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 434 HIS 0.005 0.001 HIS B 706 PHE 0.029 0.001 PHE B 547 TYR 0.013 0.002 TYR B 550 ARG 0.014 0.001 ARG A 552 Details of bonding type rmsd hydrogen bonds : bond 0.06110 ( 631) hydrogen bonds : angle 3.83648 ( 1875) covalent geometry : bond 0.00337 (10308) covalent geometry : angle 0.56360 (14088) Misc. bond : bond 0.00009 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 89 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 346 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7792 (mt-10) REVERT: A 442 MET cc_start: 0.7132 (OUTLIER) cc_final: 0.6779 (ttm) REVERT: A 456 SER cc_start: 0.8204 (t) cc_final: 0.7835 (p) REVERT: A 558 PHE cc_start: 0.6731 (OUTLIER) cc_final: 0.6257 (m-80) REVERT: A 614 MET cc_start: 0.4761 (mpp) cc_final: 0.4342 (mpp) REVERT: A 635 LEU cc_start: 0.7013 (tp) cc_final: 0.6621 (mt) REVERT: A 656 GLN cc_start: 0.7245 (OUTLIER) cc_final: 0.6268 (pm20) REVERT: A 706 HIS cc_start: 0.7250 (p-80) cc_final: 0.6613 (t70) REVERT: A 710 MET cc_start: 0.6478 (tpp) cc_final: 0.5722 (mtm) REVERT: A 779 ILE cc_start: 0.7871 (mt) cc_final: 0.7401 (mm) REVERT: B 346 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7737 (mt-10) REVERT: B 383 LEU cc_start: 0.8194 (tp) cc_final: 0.7990 (tt) REVERT: B 558 PHE cc_start: 0.6697 (OUTLIER) cc_final: 0.6196 (m-80) REVERT: B 569 LYS cc_start: 0.7301 (mttt) cc_final: 0.6891 (mmtt) REVERT: B 614 MET cc_start: 0.4553 (mpp) cc_final: 0.4190 (mpp) REVERT: B 635 LEU cc_start: 0.7106 (tp) cc_final: 0.6686 (mt) REVERT: B 654 ILE cc_start: 0.6046 (OUTLIER) cc_final: 0.5616 (pt) REVERT: B 710 MET cc_start: 0.6666 (OUTLIER) cc_final: 0.5702 (mtt) REVERT: B 779 ILE cc_start: 0.7964 (mt) cc_final: 0.7531 (mm) outliers start: 40 outliers final: 19 residues processed: 115 average time/residue: 1.0614 time to fit residues: 132.9420 Evaluate side-chains 104 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 656 GLN Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 671 GLN Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 558 PHE Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 655 SER Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 710 MET Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 781 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 7 optimal weight: 0.3980 chunk 90 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.174762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.132172 restraints weight = 14957.238| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.66 r_work: 0.3741 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3768 r_free = 0.3768 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3768 r_free = 0.3768 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10310 Z= 0.134 Angle : 0.549 6.183 14088 Z= 0.283 Chirality : 0.037 0.148 1650 Planarity : 0.004 0.054 1676 Dihedral : 7.938 58.697 2728 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.60 % Allowed : 19.60 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.25), residues: 1178 helix: 2.61 (0.18), residues: 800 sheet: -1.82 (0.64), residues: 56 loop : -1.46 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 434 HIS 0.002 0.001 HIS B 706 PHE 0.030 0.001 PHE A 547 TYR 0.011 0.001 TYR B 550 ARG 0.013 0.001 ARG A 552 Details of bonding type rmsd hydrogen bonds : bond 0.05689 ( 631) hydrogen bonds : angle 3.74943 ( 1875) covalent geometry : bond 0.00282 (10308) covalent geometry : angle 0.54870 (14088) Misc. bond : bond 0.00010 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 91 time to evaluate : 1.082 Fit side-chains REVERT: A 346 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7747 (mt-10) REVERT: A 439 ARG cc_start: 0.7905 (tmm-80) cc_final: 0.7674 (ttp80) REVERT: A 558 PHE cc_start: 0.6719 (OUTLIER) cc_final: 0.6247 (m-80) REVERT: A 569 LYS cc_start: 0.7352 (mttt) cc_final: 0.6785 (mmtt) REVERT: A 614 MET cc_start: 0.4704 (mpp) cc_final: 0.4333 (mpp) REVERT: A 635 LEU cc_start: 0.6938 (tp) cc_final: 0.6589 (mt) REVERT: A 656 GLN cc_start: 0.7251 (OUTLIER) cc_final: 0.6257 (pm20) REVERT: A 706 HIS cc_start: 0.7307 (OUTLIER) cc_final: 0.7011 (t70) REVERT: A 710 MET cc_start: 0.6594 (tpp) cc_final: 0.5762 (mtm) REVERT: A 779 ILE cc_start: 0.7887 (mt) cc_final: 0.7423 (mm) REVERT: B 346 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7744 (mt-10) REVERT: B 383 LEU cc_start: 0.8183 (tp) cc_final: 0.7961 (tt) REVERT: B 456 SER cc_start: 0.8219 (t) cc_final: 0.7839 (p) REVERT: B 569 LYS cc_start: 0.7283 (mttt) cc_final: 0.6877 (mmtt) REVERT: B 614 MET cc_start: 0.4497 (mpp) cc_final: 0.4266 (mpp) REVERT: B 635 LEU cc_start: 0.7027 (tp) cc_final: 0.6636 (mt) REVERT: B 710 MET cc_start: 0.6592 (OUTLIER) cc_final: 0.5727 (mtt) REVERT: B 779 ILE cc_start: 0.7881 (mt) cc_final: 0.7435 (mm) outliers start: 36 outliers final: 15 residues processed: 116 average time/residue: 1.2177 time to fit residues: 154.0231 Evaluate side-chains 102 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 656 GLN Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 706 HIS Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 655 SER Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 710 MET Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 781 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 62 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 GLN A 706 HIS ** B 706 HIS ** 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 = 0.4314 r_free = 0.4314 target = 0.173108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.129895 restraints weight = 15048.269| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.68 r_work: 0.3713 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3738 r_free = 0.3738 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3738 r_free = 0.3738 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10310 Z= 0.155 Angle : 0.584 7.091 14088 Z= 0.300 Chirality : 0.038 0.150 1650 Planarity : 0.004 0.047 1676 Dihedral : 8.049 58.567 2728 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.10 % Allowed : 20.30 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.25), residues: 1178 helix: 2.54 (0.18), residues: 798 sheet: -1.89 (0.64), residues: 56 loop : -1.44 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 434 HIS 0.003 0.001 HIS B 706 PHE 0.030 0.001 PHE B 547 TYR 0.013 0.002 TYR B 424 ARG 0.010 0.001 ARG A 552 Details of bonding type rmsd hydrogen bonds : bond 0.06065 ( 631) hydrogen bonds : angle 3.79745 ( 1875) covalent geometry : bond 0.00346 (10308) covalent geometry : angle 0.58418 (14088) Misc. bond : bond 0.00005 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 87 time to evaluate : 0.969 Fit side-chains REVERT: A 346 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7738 (mt-10) REVERT: A 442 MET cc_start: 0.7129 (OUTLIER) cc_final: 0.6794 (ttm) REVERT: A 558 PHE cc_start: 0.6711 (OUTLIER) cc_final: 0.6247 (m-80) REVERT: A 569 LYS cc_start: 0.7357 (mttt) cc_final: 0.6770 (mmtt) REVERT: A 614 MET cc_start: 0.4716 (mpp) cc_final: 0.4365 (mpp) REVERT: A 635 LEU cc_start: 0.7059 (tp) cc_final: 0.6651 (mt) REVERT: A 656 GLN cc_start: 0.7284 (OUTLIER) cc_final: 0.6238 (pm20) REVERT: A 706 HIS cc_start: 0.7313 (OUTLIER) cc_final: 0.6867 (t70) REVERT: A 710 MET cc_start: 0.6498 (tpp) cc_final: 0.5489 (mtm) REVERT: A 779 ILE cc_start: 0.7911 (mt) cc_final: 0.7446 (mm) REVERT: B 346 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7733 (mt-10) REVERT: B 383 LEU cc_start: 0.8165 (tp) cc_final: 0.7926 (tt) REVERT: B 569 LYS cc_start: 0.7290 (mttt) cc_final: 0.6886 (mmtt) REVERT: B 614 MET cc_start: 0.4533 (mpp) cc_final: 0.4310 (mpp) REVERT: B 635 LEU cc_start: 0.6974 (tp) cc_final: 0.6554 (mt) REVERT: B 710 MET cc_start: 0.6572 (OUTLIER) cc_final: 0.5743 (mtt) REVERT: B 779 ILE cc_start: 0.7940 (mt) cc_final: 0.7438 (mm) outliers start: 31 outliers final: 17 residues processed: 109 average time/residue: 1.0894 time to fit residues: 128.9853 Evaluate side-chains 99 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 656 GLN Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 706 HIS Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 558 PHE Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 655 SER Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 710 MET Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 781 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 63 optimal weight: 0.2980 chunk 57 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 78 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 8 optimal weight: 0.0010 chunk 58 optimal weight: 5.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.174860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.131845 restraints weight = 14937.798| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.67 r_work: 0.3744 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3749 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3749 r_free = 0.3749 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3749 r_free = 0.3749 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3749 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10310 Z= 0.130 Angle : 0.562 6.744 14088 Z= 0.290 Chirality : 0.037 0.147 1650 Planarity : 0.003 0.033 1676 Dihedral : 7.878 58.473 2728 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.70 % Allowed : 21.00 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.25), residues: 1178 helix: 2.64 (0.18), residues: 798 sheet: -1.87 (0.64), residues: 56 loop : -1.37 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 434 HIS 0.008 0.001 HIS A 706 PHE 0.028 0.001 PHE B 547 TYR 0.009 0.001 TYR A 471 ARG 0.009 0.001 ARG B 552 Details of bonding type rmsd hydrogen bonds : bond 0.05598 ( 631) hydrogen bonds : angle 3.72055 ( 1875) covalent geometry : bond 0.00268 (10308) covalent geometry : angle 0.56202 (14088) Misc. bond : bond 0.00015 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 0.985 Fit side-chains REVERT: A 346 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7755 (mt-10) REVERT: A 558 PHE cc_start: 0.6702 (OUTLIER) cc_final: 0.6233 (m-80) REVERT: A 569 LYS cc_start: 0.7334 (mttt) cc_final: 0.6765 (mmtt) REVERT: A 614 MET cc_start: 0.4765 (mpp) cc_final: 0.4386 (mpp) REVERT: A 619 LEU cc_start: 0.6030 (OUTLIER) cc_final: 0.5472 (mp) REVERT: A 635 LEU cc_start: 0.7034 (tp) cc_final: 0.6649 (mt) REVERT: A 656 GLN cc_start: 0.7322 (OUTLIER) cc_final: 0.6334 (pm20) REVERT: A 710 MET cc_start: 0.6516 (tpp) cc_final: 0.5610 (mtm) REVERT: A 779 ILE cc_start: 0.7902 (mt) cc_final: 0.7483 (mm) REVERT: B 346 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7751 (mt-10) REVERT: B 558 PHE cc_start: 0.6660 (OUTLIER) cc_final: 0.6151 (m-80) REVERT: B 569 LYS cc_start: 0.7317 (mttt) cc_final: 0.7071 (mttp) REVERT: B 614 MET cc_start: 0.4471 (mpp) cc_final: 0.4217 (mpp) REVERT: B 635 LEU cc_start: 0.7048 (tp) cc_final: 0.6648 (mt) REVERT: B 710 MET cc_start: 0.6521 (tpp) cc_final: 0.5703 (mtt) REVERT: B 779 ILE cc_start: 0.7959 (mt) cc_final: 0.7467 (mm) outliers start: 27 outliers final: 16 residues processed: 102 average time/residue: 1.2008 time to fit residues: 134.0063 Evaluate side-chains 100 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 656 GLN Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 558 PHE Chi-restraints excluded: chain B residue 655 SER Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 781 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 32 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 93 optimal weight: 0.0270 chunk 91 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 114 optimal weight: 0.2980 chunk 39 optimal weight: 0.7980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.176753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.133667 restraints weight = 14867.925| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 2.67 r_work: 0.3760 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3791 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3791 r_free = 0.3791 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3791 r_free = 0.3791 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3791 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10310 Z= 0.125 Angle : 0.558 7.845 14088 Z= 0.288 Chirality : 0.037 0.147 1650 Planarity : 0.003 0.029 1676 Dihedral : 7.720 59.728 2728 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.50 % Allowed : 21.20 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.25), residues: 1178 helix: 2.70 (0.18), residues: 800 sheet: -0.39 (0.61), residues: 82 loop : -1.71 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 434 HIS 0.003 0.001 HIS A 706 PHE 0.030 0.001 PHE B 547 TYR 0.009 0.001 TYR A 471 ARG 0.009 0.001 ARG B 371 Details of bonding type rmsd hydrogen bonds : bond 0.05195 ( 631) hydrogen bonds : angle 3.63130 ( 1875) covalent geometry : bond 0.00258 (10308) covalent geometry : angle 0.55833 (14088) Misc. bond : bond 0.00024 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.994 Fit side-chains revert: symmetry clash REVERT: A 346 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7765 (mt-10) REVERT: A 558 PHE cc_start: 0.6629 (OUTLIER) cc_final: 0.6158 (m-80) REVERT: A 575 LYS cc_start: 0.7540 (pptt) cc_final: 0.7275 (pptt) REVERT: A 614 MET cc_start: 0.4648 (mpp) cc_final: 0.4363 (mpp) REVERT: A 619 LEU cc_start: 0.6062 (OUTLIER) cc_final: 0.5456 (mp) REVERT: A 635 LEU cc_start: 0.6868 (tp) cc_final: 0.6495 (mt) REVERT: A 656 GLN cc_start: 0.7174 (OUTLIER) cc_final: 0.6245 (pm20) REVERT: A 779 ILE cc_start: 0.7856 (mt) cc_final: 0.7357 (mm) REVERT: B 346 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7724 (mt-10) REVERT: B 355 GLU cc_start: 0.7522 (tp30) cc_final: 0.6603 (tt0) REVERT: B 542 MET cc_start: 0.8511 (ttp) cc_final: 0.8236 (ttm) REVERT: B 569 LYS cc_start: 0.7284 (mttt) cc_final: 0.7013 (mttp) REVERT: B 635 LEU cc_start: 0.6897 (tp) cc_final: 0.6493 (mt) REVERT: B 779 ILE cc_start: 0.7875 (mt) cc_final: 0.7385 (mm) outliers start: 25 outliers final: 13 residues processed: 104 average time/residue: 1.0733 time to fit residues: 121.4380 Evaluate side-chains 95 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 656 GLN Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 655 SER Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 783 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 46 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 74 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 94 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.174747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.132284 restraints weight = 14848.543| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.64 r_work: 0.3744 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3769 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3769 r_free = 0.3769 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3769 r_free = 0.3769 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3769 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10310 Z= 0.140 Angle : 0.597 12.432 14088 Z= 0.301 Chirality : 0.038 0.147 1650 Planarity : 0.003 0.030 1676 Dihedral : 7.802 59.996 2728 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.40 % Allowed : 21.60 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.12 (0.25), residues: 1178 helix: 2.66 (0.18), residues: 800 sheet: -0.37 (0.61), residues: 82 loop : -1.76 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 434 HIS 0.008 0.001 HIS A 706 PHE 0.027 0.001 PHE A 547 TYR 0.021 0.001 TYR A 550 ARG 0.016 0.001 ARG B 371 Details of bonding type rmsd hydrogen bonds : bond 0.05555 ( 631) hydrogen bonds : angle 3.68457 ( 1875) covalent geometry : bond 0.00309 (10308) covalent geometry : angle 0.59701 (14088) Misc. bond : bond 0.00016 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7130.76 seconds wall clock time: 124 minutes 36.52 seconds (7476.52 seconds total)