Starting phenix.real_space_refine on Sun Dec 29 07:21:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dbq_46724/12_2024/9dbq_46724.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dbq_46724/12_2024/9dbq_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_46724/12_2024/9dbq_46724.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dbq_46724/12_2024/9dbq_46724.map" model { file = "/net/cci-nas-00/data/ceres_data/9dbq_46724/12_2024/9dbq_46724.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dbq_46724/12_2024/9dbq_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-5532/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: 5.64, per 1000 atoms: 0.56 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: 2.79 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: 1.01 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: 3.08 Time building geometry restraints manager: 3.12 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: 0.00 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: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.460 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 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:14.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.770 ------------------------------------------------------------------------------- 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 10308 Z= 0.201 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 *********************** 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 : 1.144 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: 1.5001 time to fit residues: 340.8396 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 : 1.074 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 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 10308 Z= 0.194 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 *********************** 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 : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 346 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7723 (mt-10) REVERT: A 456 SER cc_start: 0.8086 (t) cc_final: 0.7809 (p) REVERT: A 546 TRP cc_start: 0.8411 (m100) cc_final: 0.8129 (m100) REVERT: A 614 MET cc_start: 0.5055 (mpp) cc_final: 0.4434 (mpp) REVERT: A 621 LEU cc_start: 0.7465 (tp) cc_final: 0.7127 (mp) REVERT: A 635 LEU cc_start: 0.6948 (tp) cc_final: 0.6591 (mt) REVERT: A 710 MET cc_start: 0.6775 (tpt) cc_final: 0.6034 (mtm) REVERT: A 765 ILE cc_start: 0.6668 (OUTLIER) cc_final: 0.6401 (tp) REVERT: A 779 ILE cc_start: 0.7881 (mt) cc_final: 0.7371 (mm) REVERT: B 346 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7700 (mt-10) REVERT: B 383 LEU cc_start: 0.8080 (tp) cc_final: 0.7856 (tt) REVERT: B 456 SER cc_start: 0.8242 (t) cc_final: 0.7958 (p) REVERT: B 546 TRP cc_start: 0.8429 (m100) cc_final: 0.8132 (m100) REVERT: B 558 PHE cc_start: 0.6580 (OUTLIER) cc_final: 0.6127 (m-80) REVERT: B 614 MET cc_start: 0.4797 (mpp) cc_final: 0.4201 (mpp) REVERT: B 621 LEU cc_start: 0.6416 (OUTLIER) cc_final: 0.6024 (mp) REVERT: B 635 LEU cc_start: 0.7110 (tp) cc_final: 0.6740 (mt) REVERT: B 701 GLN cc_start: 0.5891 (OUTLIER) cc_final: 0.5689 (mm-40) REVERT: B 765 ILE cc_start: 0.6593 (OUTLIER) cc_final: 0.6383 (tp) REVERT: B 779 ILE cc_start: 0.7830 (mt) cc_final: 0.7228 (mm) outliers start: 32 outliers final: 4 residues processed: 143 average time/residue: 1.3160 time to fit residues: 201.9472 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 : 1.377 ------------------------------------------------------------------------------- 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 59 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 107 optimal weight: 0.0030 chunk 115 optimal weight: 0.8980 chunk 95 optimal weight: 8.9990 chunk 106 optimal weight: 0.0970 chunk 36 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10308 Z= 0.189 Angle : 0.558 6.674 14088 Z= 0.289 Chirality : 0.037 0.142 1650 Planarity : 0.004 0.037 1676 Dihedral : 8.312 59.108 2728 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.20 % Allowed : 13.40 % Favored : 83.40 % 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: 1.76 (0.25), residues: 1178 helix: 2.44 (0.19), residues: 790 sheet: -2.04 (0.63), residues: 56 loop : -1.51 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 434 HIS 0.006 0.001 HIS B 706 PHE 0.023 0.001 PHE B 547 TYR 0.010 0.001 TYR A 424 ARG 0.009 0.001 ARG B 589 *********************** 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: 32 poor density : 98 time to evaluate : 1.092 Fit side-chains revert: symmetry clash REVERT: A 346 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7710 (mt-10) REVERT: A 456 SER cc_start: 0.8106 (t) cc_final: 0.7818 (p) REVERT: A 558 PHE cc_start: 0.6644 (OUTLIER) cc_final: 0.6158 (m-80) REVERT: A 569 LYS cc_start: 0.7476 (mttt) cc_final: 0.6930 (mmtt) REVERT: A 614 MET cc_start: 0.4880 (mpp) cc_final: 0.4461 (mpp) REVERT: A 635 LEU cc_start: 0.6872 (tp) cc_final: 0.6534 (mt) REVERT: A 654 ILE cc_start: 0.5825 (OUTLIER) cc_final: 0.5341 (pt) REVERT: A 779 ILE cc_start: 0.7873 (mt) cc_final: 0.7354 (mm) REVERT: B 346 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7722 (mt-10) REVERT: B 383 LEU cc_start: 0.8090 (tp) cc_final: 0.7812 (tt) REVERT: B 456 SER cc_start: 0.8223 (t) cc_final: 0.7915 (p) REVERT: B 614 MET cc_start: 0.4689 (mpp) cc_final: 0.4259 (mpp) REVERT: B 635 LEU cc_start: 0.7036 (tp) cc_final: 0.6665 (mt) REVERT: B 654 ILE cc_start: 0.5809 (OUTLIER) cc_final: 0.5376 (pt) REVERT: B 779 ILE cc_start: 0.7860 (mt) cc_final: 0.7375 (mm) outliers start: 32 outliers final: 6 residues processed: 121 average time/residue: 1.2947 time to fit residues: 168.3594 Evaluate side-chains 94 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 1.143 ------------------------------------------------------------------------------- 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 662 LEU Chi-restraints excluded: chain B residue 654 ILE 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 106 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 107 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 30 optimal weight: 0.3980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN A 701 GLN B 523 GLN B 706 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10308 Z= 0.250 Angle : 0.590 7.346 14088 Z= 0.302 Chirality : 0.039 0.148 1650 Planarity : 0.004 0.031 1676 Dihedral : 8.408 58.080 2728 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.60 % Allowed : 14.20 % Favored : 81.20 % 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: 1.67 (0.25), residues: 1178 helix: 2.34 (0.19), residues: 800 sheet: -2.05 (0.61), residues: 56 loop : -1.60 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 434 HIS 0.012 0.001 HIS B 706 PHE 0.025 0.002 PHE B 547 TYR 0.013 0.002 TYR A 424 ARG 0.011 0.001 ARG B 375 *********************** 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 139 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 93 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 346 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7738 (mt-10) REVERT: A 456 SER cc_start: 0.8257 (t) cc_final: 0.7928 (p) REVERT: A 558 PHE cc_start: 0.6678 (OUTLIER) cc_final: 0.6211 (m-80) REVERT: A 569 LYS cc_start: 0.7462 (mttt) cc_final: 0.7141 (mttp) REVERT: A 614 MET cc_start: 0.4908 (mpp) cc_final: 0.4514 (mpp) REVERT: A 635 LEU cc_start: 0.7024 (tp) cc_final: 0.6629 (mt) REVERT: A 654 ILE cc_start: 0.5891 (OUTLIER) cc_final: 0.5426 (pt) REVERT: A 710 MET cc_start: 0.6515 (tpp) cc_final: 0.5731 (mtm) REVERT: A 776 ARG cc_start: 0.5829 (OUTLIER) cc_final: 0.5037 (tpp80) REVERT: A 779 ILE cc_start: 0.7870 (mt) cc_final: 0.7395 (mm) REVERT: B 346 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7701 (mt-10) REVERT: B 383 LEU cc_start: 0.8103 (tp) cc_final: 0.7868 (tt) REVERT: B 558 PHE cc_start: 0.6615 (OUTLIER) cc_final: 0.6156 (m-80) REVERT: B 614 MET cc_start: 0.4644 (mpp) cc_final: 0.4301 (mpp) REVERT: B 635 LEU cc_start: 0.7190 (tp) cc_final: 0.6739 (mt) REVERT: B 654 ILE cc_start: 0.5966 (OUTLIER) cc_final: 0.5510 (pt) REVERT: B 779 ILE cc_start: 0.7953 (mt) cc_final: 0.7536 (mm) outliers start: 46 outliers final: 18 residues processed: 130 average time/residue: 1.2031 time to fit residues: 169.2996 Evaluate side-chains 105 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 1.243 ------------------------------------------------------------------------------- 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 613 VAL 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 662 LEU Chi-restraints excluded: chain A residue 671 GLN Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 776 ARG Chi-restraints excluded: chain A residue 781 VAL 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 659 GLN Chi-restraints excluded: chain B residue 671 GLN Chi-restraints excluded: chain B residue 679 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 706 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10308 Z= 0.253 Angle : 0.600 7.827 14088 Z= 0.306 Chirality : 0.039 0.152 1650 Planarity : 0.004 0.045 1676 Dihedral : 8.374 59.175 2728 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.30 % Allowed : 16.60 % Favored : 79.10 % 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: 1.64 (0.25), residues: 1178 helix: 2.33 (0.18), residues: 800 sheet: -1.94 (0.63), residues: 56 loop : -1.65 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 434 HIS 0.012 0.001 HIS B 706 PHE 0.028 0.002 PHE A 547 TYR 0.014 0.002 TYR A 550 ARG 0.011 0.001 ARG A 552 *********************** 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 137 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 94 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7570 (tt0) cc_final: 0.6910 (tm-30) REVERT: A 346 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7684 (mt-10) REVERT: A 558 PHE cc_start: 0.6682 (OUTLIER) cc_final: 0.6202 (m-80) REVERT: A 569 LYS cc_start: 0.7393 (mttt) cc_final: 0.6907 (mmtm) REVERT: A 614 MET cc_start: 0.4903 (mpp) cc_final: 0.4552 (mpp) REVERT: A 635 LEU cc_start: 0.7113 (tp) cc_final: 0.6639 (mt) REVERT: A 656 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.6383 (pm20) REVERT: A 706 HIS cc_start: 0.7321 (OUTLIER) cc_final: 0.6596 (t70) REVERT: A 710 MET cc_start: 0.6442 (tpp) cc_final: 0.5705 (mtm) REVERT: A 779 ILE cc_start: 0.7898 (mt) cc_final: 0.7444 (mm) REVERT: B 346 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7678 (mt-10) REVERT: B 383 LEU cc_start: 0.8091 (tp) cc_final: 0.7800 (tt) REVERT: B 569 LYS cc_start: 0.7347 (mttt) cc_final: 0.6925 (mmtt) REVERT: B 614 MET cc_start: 0.4595 (mpp) cc_final: 0.4266 (mpp) REVERT: B 654 ILE cc_start: 0.5878 (OUTLIER) cc_final: 0.5412 (pt) REVERT: B 779 ILE cc_start: 0.8001 (mt) cc_final: 0.7581 (mm) outliers start: 43 outliers final: 23 residues processed: 127 average time/residue: 1.2224 time to fit residues: 167.4034 Evaluate side-chains 108 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 81 time to evaluate : 1.144 ------------------------------------------------------------------------------- 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 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 679 THR 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 765 ILE 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 659 GLN 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 38 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 20.0000 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 706 HIS B 671 GLN B 701 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10308 Z= 0.233 Angle : 0.592 6.747 14088 Z= 0.302 Chirality : 0.039 0.153 1650 Planarity : 0.004 0.050 1676 Dihedral : 8.261 59.865 2728 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.30 % Allowed : 17.10 % Favored : 78.60 % 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: 1.70 (0.25), residues: 1178 helix: 2.38 (0.18), residues: 800 sheet: -1.96 (0.63), residues: 56 loop : -1.63 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 434 HIS 0.006 0.001 HIS B 706 PHE 0.027 0.002 PHE A 547 TYR 0.012 0.002 TYR B 424 ARG 0.012 0.001 ARG A 552 *********************** 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 134 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 91 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7573 (tt0) cc_final: 0.6913 (tm-30) REVERT: A 346 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7647 (mt-10) REVERT: A 355 GLU cc_start: 0.7818 (tp30) cc_final: 0.7376 (pt0) REVERT: A 439 ARG cc_start: 0.7836 (tmm-80) cc_final: 0.7612 (ttp80) REVERT: A 558 PHE cc_start: 0.6670 (OUTLIER) cc_final: 0.6194 (m-80) REVERT: A 614 MET cc_start: 0.4843 (mpp) cc_final: 0.4494 (mpp) REVERT: A 635 LEU cc_start: 0.7096 (tp) cc_final: 0.6642 (mt) REVERT: A 656 GLN cc_start: 0.7259 (OUTLIER) cc_final: 0.6330 (pm20) REVERT: A 706 HIS cc_start: 0.7122 (OUTLIER) cc_final: 0.6549 (t70) REVERT: A 710 MET cc_start: 0.6420 (tpp) cc_final: 0.5692 (mtm) REVERT: A 779 ILE cc_start: 0.7836 (mt) cc_final: 0.7385 (mm) REVERT: B 346 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7639 (mt-10) REVERT: B 383 LEU cc_start: 0.8097 (tp) cc_final: 0.7853 (tt) REVERT: B 569 LYS cc_start: 0.7370 (mttt) cc_final: 0.6949 (mmtt) REVERT: B 614 MET cc_start: 0.4558 (mpp) cc_final: 0.4246 (mpp) REVERT: B 654 ILE cc_start: 0.5893 (OUTLIER) cc_final: 0.5420 (pt) REVERT: B 779 ILE cc_start: 0.8034 (mt) cc_final: 0.7565 (mm) outliers start: 43 outliers final: 21 residues processed: 120 average time/residue: 1.1682 time to fit residues: 151.8119 Evaluate side-chains 105 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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 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 671 GLN 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 765 ILE Chi-restraints excluded: chain A residue 781 VAL 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 659 GLN Chi-restraints excluded: chain B residue 662 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 96 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 113 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN B 328 ASN ** B 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10308 Z= 0.192 Angle : 0.573 6.982 14088 Z= 0.295 Chirality : 0.038 0.151 1650 Planarity : 0.003 0.059 1676 Dihedral : 8.119 59.626 2728 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.40 % Allowed : 19.30 % Favored : 77.30 % 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: 1.84 (0.25), residues: 1178 helix: 2.49 (0.18), residues: 800 sheet: -1.99 (0.62), residues: 56 loop : -1.56 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 434 HIS 0.005 0.001 HIS A 706 PHE 0.010 0.001 PHE A 639 TYR 0.010 0.001 TYR B 424 ARG 0.013 0.000 ARG A 552 *********************** 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 123 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 89 time to evaluate : 1.071 Fit side-chains revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7615 (tt0) cc_final: 0.6967 (tm-30) REVERT: A 346 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7648 (mt-10) REVERT: A 558 PHE cc_start: 0.6688 (OUTLIER) cc_final: 0.6211 (m-80) REVERT: A 569 LYS cc_start: 0.7389 (mttt) cc_final: 0.6861 (mmtm) REVERT: A 614 MET cc_start: 0.4779 (mpp) cc_final: 0.4387 (mpp) REVERT: A 635 LEU cc_start: 0.7069 (tp) cc_final: 0.6654 (mt) REVERT: A 656 GLN cc_start: 0.7300 (OUTLIER) cc_final: 0.6402 (pm20) REVERT: A 779 ILE cc_start: 0.7866 (mt) cc_final: 0.7426 (mm) REVERT: B 346 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7637 (mt-10) REVERT: B 383 LEU cc_start: 0.8147 (tp) cc_final: 0.7918 (tt) REVERT: B 552 ARG cc_start: 0.8570 (ttp80) cc_final: 0.8314 (ttp80) REVERT: B 569 LYS cc_start: 0.7337 (mttt) cc_final: 0.6923 (mmtt) REVERT: B 614 MET cc_start: 0.4551 (mpp) cc_final: 0.4221 (mpp) REVERT: B 635 LEU cc_start: 0.6925 (tp) cc_final: 0.6519 (mt) REVERT: B 779 ILE cc_start: 0.8018 (mt) cc_final: 0.7548 (mm) outliers start: 34 outliers final: 18 residues processed: 114 average time/residue: 1.1228 time to fit residues: 139.1097 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 : 1.080 ------------------------------------------------------------------------------- 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 643 SER Chi-restraints excluded: chain A residue 656 GLN Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 709 ILE 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 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 765 ILE 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 70 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 72 optimal weight: 7.9990 chunk 77 optimal weight: 0.7980 chunk 56 optimal weight: 0.1980 chunk 10 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 706 HIS B 706 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10308 Z= 0.177 Angle : 0.560 6.586 14088 Z= 0.289 Chirality : 0.037 0.148 1650 Planarity : 0.003 0.040 1676 Dihedral : 7.945 58.722 2728 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.10 % Allowed : 19.50 % Favored : 77.40 % 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: 1.99 (0.25), residues: 1178 helix: 2.59 (0.18), residues: 800 sheet: -1.98 (0.62), residues: 56 loop : -1.46 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 434 HIS 0.005 0.001 HIS B 706 PHE 0.029 0.001 PHE B 547 TYR 0.009 0.001 TYR A 471 ARG 0.009 0.000 ARG A 552 *********************** 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 122 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 91 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7625 (tt0) cc_final: 0.6956 (tm-30) REVERT: A 346 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7652 (mt-10) REVERT: A 355 GLU cc_start: 0.7650 (tp30) cc_final: 0.7128 (pt0) REVERT: A 558 PHE cc_start: 0.6696 (OUTLIER) cc_final: 0.6227 (m-80) REVERT: A 614 MET cc_start: 0.4767 (mpp) cc_final: 0.4495 (mpp) REVERT: A 635 LEU cc_start: 0.7028 (tp) cc_final: 0.6648 (mt) REVERT: A 656 GLN cc_start: 0.7267 (OUTLIER) cc_final: 0.6370 (pm20) REVERT: A 709 ILE cc_start: 0.3393 (OUTLIER) cc_final: 0.3147 (pt) REVERT: A 710 MET cc_start: 0.6439 (tpp) cc_final: 0.5771 (ppp) REVERT: A 779 ILE cc_start: 0.7870 (mt) cc_final: 0.7470 (mm) REVERT: B 346 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7639 (mt-10) REVERT: B 383 LEU cc_start: 0.8139 (tp) cc_final: 0.7912 (tt) REVERT: B 552 ARG cc_start: 0.8555 (ttp80) cc_final: 0.8298 (ttp80) REVERT: B 569 LYS cc_start: 0.7347 (mttt) cc_final: 0.6936 (mmtt) REVERT: B 618 THR cc_start: 0.4510 (OUTLIER) cc_final: 0.4101 (t) REVERT: B 635 LEU cc_start: 0.7019 (tp) cc_final: 0.6618 (mt) REVERT: B 779 ILE cc_start: 0.7878 (mt) cc_final: 0.7436 (mm) outliers start: 31 outliers final: 15 residues processed: 113 average time/residue: 1.1028 time to fit residues: 135.4086 Evaluate side-chains 99 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 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 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 618 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 63 optimal weight: 0.4980 chunk 46 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 701 GLN A 706 HIS B 706 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10308 Z= 0.198 Angle : 0.591 12.641 14088 Z= 0.302 Chirality : 0.038 0.148 1650 Planarity : 0.003 0.031 1676 Dihedral : 7.942 59.654 2728 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.70 % Allowed : 20.40 % Favored : 76.90 % 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: 2.00 (0.25), residues: 1178 helix: 2.58 (0.18), residues: 800 sheet: -0.93 (0.61), residues: 72 loop : -1.67 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 434 HIS 0.010 0.001 HIS A 706 PHE 0.009 0.001 PHE A 639 TYR 0.010 0.001 TYR B 424 ARG 0.008 0.000 ARG A 552 *********************** 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 110 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 1.074 Fit side-chains REVERT: A 346 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7653 (mt-10) REVERT: A 542 MET cc_start: 0.8418 (ttp) cc_final: 0.8183 (ttm) REVERT: A 558 PHE cc_start: 0.6635 (OUTLIER) cc_final: 0.6154 (m-80) REVERT: A 569 LYS cc_start: 0.7392 (mttt) cc_final: 0.6684 (mmtm) REVERT: A 614 MET cc_start: 0.4759 (mpp) cc_final: 0.4483 (mpp) REVERT: A 635 LEU cc_start: 0.7059 (tp) cc_final: 0.6671 (mt) REVERT: A 656 GLN cc_start: 0.7257 (OUTLIER) cc_final: 0.6393 (pm20) REVERT: A 710 MET cc_start: 0.6384 (tpp) cc_final: 0.5612 (mtm) REVERT: A 779 ILE cc_start: 0.7894 (mt) cc_final: 0.7435 (mm) REVERT: B 346 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7641 (mt-10) REVERT: B 383 LEU cc_start: 0.8138 (tp) cc_final: 0.7926 (tt) REVERT: B 542 MET cc_start: 0.8408 (ttp) cc_final: 0.8090 (ttm) REVERT: B 552 ARG cc_start: 0.8546 (ttp80) cc_final: 0.8288 (ttp80) REVERT: B 569 LYS cc_start: 0.7288 (mttt) cc_final: 0.6889 (mmtt) REVERT: B 618 THR cc_start: 0.4517 (OUTLIER) cc_final: 0.4061 (t) REVERT: B 635 LEU cc_start: 0.6946 (tp) cc_final: 0.6540 (mt) REVERT: B 706 HIS cc_start: 0.5088 (t-170) cc_final: 0.4755 (t-90) REVERT: B 710 MET cc_start: 0.6233 (tpp) cc_final: 0.5655 (mtm) REVERT: B 779 ILE cc_start: 0.7891 (mt) cc_final: 0.7454 (mm) outliers start: 27 outliers final: 17 residues processed: 104 average time/residue: 1.1544 time to fit residues: 130.6219 Evaluate side-chains 101 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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 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 718 THR 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 618 THR Chi-restraints excluded: chain B residue 643 SER 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 68 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 93 optimal weight: 0.2980 chunk 9 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 701 GLN A 706 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10308 Z= 0.193 Angle : 0.594 12.246 14088 Z= 0.303 Chirality : 0.038 0.148 1650 Planarity : 0.003 0.030 1676 Dihedral : 7.899 59.949 2728 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.10 % Allowed : 21.30 % 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: 1.99 (0.25), residues: 1178 helix: 2.58 (0.18), residues: 800 sheet: -0.94 (0.61), residues: 72 loop : -1.68 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 434 HIS 0.009 0.001 HIS A 706 PHE 0.029 0.001 PHE A 547 TYR 0.010 0.001 TYR A 424 ARG 0.010 0.001 ARG A 371 ********************** 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 104 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 1.065 Fit side-chains REVERT: A 346 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7653 (mt-10) REVERT: A 355 GLU cc_start: 0.7666 (tp30) cc_final: 0.6866 (tt0) REVERT: A 542 MET cc_start: 0.8413 (ttp) cc_final: 0.8177 (ttm) REVERT: A 558 PHE cc_start: 0.6643 (OUTLIER) cc_final: 0.6165 (m-80) REVERT: A 569 LYS cc_start: 0.7410 (mttt) cc_final: 0.6948 (mmtm) REVERT: A 635 LEU cc_start: 0.7056 (tp) cc_final: 0.6670 (mt) REVERT: A 656 GLN cc_start: 0.7313 (OUTLIER) cc_final: 0.6445 (pm20) REVERT: A 779 ILE cc_start: 0.7880 (mt) cc_final: 0.7462 (mm) REVERT: B 346 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7641 (mt-10) REVERT: B 355 GLU cc_start: 0.7701 (tp30) cc_final: 0.6833 (tt0) REVERT: B 383 LEU cc_start: 0.8103 (tp) cc_final: 0.7900 (tt) REVERT: B 542 MET cc_start: 0.8399 (ttp) cc_final: 0.8079 (ttm) REVERT: B 552 ARG cc_start: 0.8534 (ttp80) cc_final: 0.8277 (ttp80) REVERT: B 569 LYS cc_start: 0.7299 (mttt) cc_final: 0.6769 (mmtt) REVERT: B 618 THR cc_start: 0.4508 (OUTLIER) cc_final: 0.4054 (t) REVERT: B 635 LEU cc_start: 0.6949 (tp) cc_final: 0.6545 (mt) REVERT: B 779 ILE cc_start: 0.7900 (mt) cc_final: 0.7464 (mm) outliers start: 21 outliers final: 14 residues processed: 100 average time/residue: 1.2188 time to fit residues: 132.0706 Evaluate side-chains 96 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 1.131 ------------------------------------------------------------------------------- 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 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 718 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain B residue 558 PHE Chi-restraints excluded: chain B residue 618 THR 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 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 28 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 13 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 96 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 659 GLN B 706 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.174274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.131054 restraints weight = 14794.207| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 2.66 r_work: 0.3731 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3758 r_free = 0.3758 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3754 r_free = 0.3754 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10308 Z= 0.202 Angle : 0.615 12.613 14088 Z= 0.310 Chirality : 0.038 0.149 1650 Planarity : 0.003 0.032 1676 Dihedral : 7.888 59.994 2728 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.40 % Allowed : 21.40 % Favored : 76.20 % 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: 1.98 (0.25), residues: 1178 helix: 2.57 (0.18), residues: 800 sheet: -0.93 (0.61), residues: 72 loop : -1.70 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 434 HIS 0.011 0.001 HIS A 706 PHE 0.029 0.001 PHE B 547 TYR 0.010 0.001 TYR B 424 ARG 0.015 0.001 ARG B 371 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3420.46 seconds wall clock time: 62 minutes 4.07 seconds (3724.07 seconds total)