Starting phenix.real_space_refine on Sat Dec 28 21:37:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ty7_26168/12_2024/7ty7_26168.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ty7_26168/12_2024/7ty7_26168.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ty7_26168/12_2024/7ty7_26168.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ty7_26168/12_2024/7ty7_26168.map" model { file = "/net/cci-nas-00/data/ceres_data/7ty7_26168/12_2024/7ty7_26168.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ty7_26168/12_2024/7ty7_26168.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 36 5.16 5 C 5757 2.51 5 N 1312 2.21 5 O 1431 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 8538 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4075 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 29, 'TRANS': 486} Chain breaks: 1 Chain: "B" Number of atoms: 4075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4075 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 29, 'TRANS': 486} Chain breaks: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 170 Unusual residues: {'BCT': 1, 'CLR': 4, 'PC1': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 142 Unusual residues: {'BCT': 1, 'CLR': 3, 'PC1': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Time building chain proxies: 6.00, per 1000 atoms: 0.70 Number of scatterers: 8538 At special positions: 0 Unit cell: (121.588, 89.308, 85.004, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 2 15.00 O 1431 8.00 N 1312 7.00 C 5757 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=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG C 1 " - " ASN A 642 " " NAG D 1 " - " ASN B 642 " Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 1.1 seconds 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1920 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 2 sheets defined 73.4% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 379 through 390 Processing helix chain 'A' and resid 392 through 400 removed outlier: 3.623A pdb=" N ALA A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 431 removed outlier: 3.692A pdb=" N LEU A 406 " --> pdb=" O SER A 402 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) Proline residue: A 419 - end of helix removed outlier: 3.585A pdb=" N GLY A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 455 Processing helix chain 'A' and resid 465 through 483 Processing helix chain 'A' and resid 485 through 508 removed outlier: 3.691A pdb=" N VAL A 491 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TRP A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 516 Processing helix chain 'A' and resid 517 through 547 removed outlier: 3.706A pdb=" N LEU A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 593 removed outlier: 3.535A pdb=" N LEU A 573 " --> pdb=" O ASN A 569 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 608 removed outlier: 3.561A pdb=" N ARG A 603 " --> pdb=" O GLY A 599 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A 604 " --> pdb=" O LYS A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 624 removed outlier: 3.511A pdb=" N ILE A 624 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 666 removed outlier: 4.082A pdb=" N MET A 664 " --> pdb=" O PRO A 660 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 665 " --> pdb=" O ILE A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 690 removed outlier: 3.562A pdb=" N LEU A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR A 685 " --> pdb=" O GLU A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 719 removed outlier: 4.016A pdb=" N LEU A 718 " --> pdb=" O GLY A 714 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE A 719 " --> pdb=" O VAL A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 739 Processing helix chain 'A' and resid 760 through 772 Processing helix chain 'A' and resid 773 through 775 No H-bonds generated for 'chain 'A' and resid 773 through 775' Processing helix chain 'A' and resid 776 through 781 Processing helix chain 'A' and resid 784 through 799 removed outlier: 3.887A pdb=" N LEU A 788 " --> pdb=" O PRO A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 812 Processing helix chain 'A' and resid 822 through 827 Processing helix chain 'A' and resid 829 through 853 Processing helix chain 'A' and resid 858 through 865 Processing helix chain 'A' and resid 865 through 872 removed outlier: 3.599A pdb=" N LEU A 869 " --> pdb=" O LEU A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 878 removed outlier: 3.766A pdb=" N LEU A 876 " --> pdb=" O VAL A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 887 removed outlier: 3.519A pdb=" N LEU A 883 " --> pdb=" O ARG A 879 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N CYS A 885 " --> pdb=" O VAL A 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 390 Processing helix chain 'B' and resid 392 through 400 removed outlier: 3.622A pdb=" N ALA B 400 " --> pdb=" O ASP B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 431 removed outlier: 3.694A pdb=" N LEU B 406 " --> pdb=" O SER B 402 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE B 414 " --> pdb=" O ILE B 410 " (cutoff:3.500A) Proline residue: B 419 - end of helix removed outlier: 3.585A pdb=" N GLY B 424 " --> pdb=" O ALA B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 455 Processing helix chain 'B' and resid 465 through 483 Processing helix chain 'B' and resid 485 through 508 removed outlier: 3.692A pdb=" N VAL B 491 " --> pdb=" O ILE B 487 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TRP B 492 " --> pdb=" O VAL B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 516 Processing helix chain 'B' and resid 517 through 547 removed outlier: 3.706A pdb=" N LEU B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 593 removed outlier: 3.534A pdb=" N LEU B 573 " --> pdb=" O ASN B 569 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN B 593 " --> pdb=" O ARG B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 608 removed outlier: 3.560A pdb=" N ARG B 603 " --> pdb=" O GLY B 599 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL B 604 " --> pdb=" O LYS B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 624 removed outlier: 3.511A pdb=" N ILE B 624 " --> pdb=" O VAL B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 666 removed outlier: 4.083A pdb=" N MET B 664 " --> pdb=" O PRO B 660 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE B 665 " --> pdb=" O ILE B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 690 removed outlier: 3.562A pdb=" N LEU B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR B 685 " --> pdb=" O GLU B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 719 removed outlier: 4.016A pdb=" N LEU B 718 " --> pdb=" O GLY B 714 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE B 719 " --> pdb=" O VAL B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 739 Processing helix chain 'B' and resid 760 through 772 Processing helix chain 'B' and resid 773 through 775 No H-bonds generated for 'chain 'B' and resid 773 through 775' Processing helix chain 'B' and resid 776 through 781 Processing helix chain 'B' and resid 784 through 799 removed outlier: 3.885A pdb=" N LEU B 788 " --> pdb=" O PRO B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 812 Processing helix chain 'B' and resid 822 through 827 Processing helix chain 'B' and resid 829 through 853 Processing helix chain 'B' and resid 858 through 865 Processing helix chain 'B' and resid 865 through 872 removed outlier: 3.598A pdb=" N LEU B 869 " --> pdb=" O LEU B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 878 removed outlier: 3.765A pdb=" N LEU B 876 " --> pdb=" O VAL B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 887 removed outlier: 3.518A pdb=" N LEU B 883 " --> pdb=" O ARG B 879 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N CYS B 885 " --> pdb=" O VAL B 881 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 461 through 463 removed outlier: 4.798A pdb=" N VAL A 461 " --> pdb=" O THR A 727 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 461 through 463 removed outlier: 4.798A pdb=" N VAL B 461 " --> pdb=" O THR B 727 " (cutoff:3.500A) 508 hydrogen bonds defined for protein. 1488 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.37 Time building geometry restraints manager: 2.79 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: 1323 1.32 - 1.45: 2194 1.45 - 1.57: 5154 1.57 - 1.69: 4 1.69 - 1.82: 66 Bond restraints: 8741 Sorted by residual: bond pdb=" N ILE A 783 " pdb=" CA ILE A 783 " ideal model delta sigma weight residual 1.460 1.497 -0.038 7.50e-03 1.78e+04 2.50e+01 bond pdb=" N ILE B 783 " pdb=" CA ILE B 783 " ideal model delta sigma weight residual 1.460 1.496 -0.037 7.50e-03 1.78e+04 2.42e+01 bond pdb=" N HIS B 819 " pdb=" CA HIS B 819 " ideal model delta sigma weight residual 1.453 1.492 -0.038 8.30e-03 1.45e+04 2.14e+01 bond pdb=" N HIS A 819 " pdb=" CA HIS A 819 " ideal model delta sigma weight residual 1.453 1.491 -0.038 8.30e-03 1.45e+04 2.07e+01 bond pdb=" N VAL A 634 " pdb=" CA VAL A 634 " ideal model delta sigma weight residual 1.461 1.496 -0.035 8.70e-03 1.32e+04 1.65e+01 ... (remaining 8736 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 8031 1.70 - 3.39: 3032 3.39 - 5.09: 745 5.09 - 6.79: 88 6.79 - 8.48: 4 Bond angle restraints: 11900 Sorted by residual: angle pdb=" N LEU B 680 " pdb=" CA LEU B 680 " pdb=" C LEU B 680 " ideal model delta sigma weight residual 111.36 105.56 5.80 1.09e+00 8.42e-01 2.83e+01 angle pdb=" N LEU A 680 " pdb=" CA LEU A 680 " pdb=" C LEU A 680 " ideal model delta sigma weight residual 111.36 105.58 5.78 1.09e+00 8.42e-01 2.81e+01 angle pdb=" C THR A 837 " pdb=" N GLY A 838 " pdb=" CA GLY A 838 " ideal model delta sigma weight residual 119.98 125.81 -5.83 1.11e+00 8.12e-01 2.76e+01 angle pdb=" C THR B 837 " pdb=" N GLY B 838 " pdb=" CA GLY B 838 " ideal model delta sigma weight residual 119.98 125.80 -5.82 1.11e+00 8.12e-01 2.75e+01 angle pdb=" C LEU A 427 " pdb=" N GLY A 428 " pdb=" CA GLY A 428 " ideal model delta sigma weight residual 119.94 125.58 -5.64 1.11e+00 8.12e-01 2.58e+01 ... (remaining 11895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.43: 5287 25.43 - 50.86: 245 50.86 - 76.29: 26 76.29 - 101.71: 2 101.71 - 127.14: 3 Dihedral angle restraints: 5563 sinusoidal: 2587 harmonic: 2976 Sorted by residual: dihedral pdb=" C1 NAG C 2 " pdb=" C5 NAG C 2 " pdb=" O5 NAG C 2 " pdb=" C6 NAG C 2 " ideal model delta sinusoidal sigma weight residual 171.16 -61.70 -127.14 1 3.00e+01 1.11e-03 1.71e+01 dihedral pdb=" C1 NAG C 2 " pdb=" C5 NAG C 2 " pdb=" O5 NAG C 2 " pdb=" C4 NAG C 2 " ideal model delta sinusoidal sigma weight residual -64.11 61.63 -125.74 1 3.00e+01 1.11e-03 1.69e+01 dihedral pdb=" CA GLN A 625 " pdb=" C GLN A 625 " pdb=" N ASP A 626 " pdb=" CA ASP A 626 " ideal model delta harmonic sigma weight residual -180.00 -159.49 -20.51 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 5560 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 602 0.058 - 0.116: 509 0.116 - 0.174: 285 0.174 - 0.231: 28 0.231 - 0.289: 4 Chirality restraints: 1428 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-02 2.50e+03 2.09e+02 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-02 2.50e+03 1.66e+02 chirality pdb=" CA LEU B 680 " pdb=" N LEU B 680 " pdb=" C LEU B 680 " pdb=" CB LEU B 680 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.38e+00 ... (remaining 1425 not shown) Planarity restraints: 1404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " 0.350 2.00e-02 2.50e+03 3.01e-01 1.13e+03 pdb=" C7 NAG C 1 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " 0.147 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " -0.535 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " 0.123 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.345 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG D 1 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.091 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.530 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " -0.174 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.337 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" C7 NAG D 2 " 0.077 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " -0.043 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.509 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " -0.205 2.00e-02 2.50e+03 ... (remaining 1401 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1264 2.82 - 3.34: 9215 3.34 - 3.86: 13300 3.86 - 4.38: 17762 4.38 - 4.90: 28719 Nonbonded interactions: 70260 Sorted by model distance: nonbonded pdb=" O PRO A 561 " pdb=" CG LYS A 562 " model vdw 2.304 3.440 nonbonded pdb=" O PRO B 561 " pdb=" CG LYS B 562 " model vdw 2.305 3.440 nonbonded pdb=" O LEU A 577 " pdb=" OG1 THR A 581 " model vdw 2.412 3.040 nonbonded pdb=" O LEU B 577 " pdb=" OG1 THR B 581 " model vdw 2.412 3.040 nonbonded pdb=" NH2 ARG B 832 " pdb=" OE1 GLU B 882 " model vdw 2.457 3.120 ... (remaining 70255 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 369 through 891 or resid 2101 through 2103)) selection = (chain 'B' and (resid 369 through 891 or resid 2101 through 2103)) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.740 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 22.650 Find NCS groups from input model: 0.390 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: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 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 : 0.013 0.081 8741 Z= 0.853 Angle : 1.814 8.482 11900 Z= 1.380 Chirality : 0.088 0.289 1428 Planarity : 0.014 0.301 1402 Dihedral : 13.973 127.141 3643 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.45 % Allowed : 4.57 % Favored : 94.99 % 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: -3.03 (0.21), residues: 1024 helix: -1.79 (0.16), residues: 678 sheet: None (None), residues: 0 loop : -2.14 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 492 HIS 0.006 0.002 HIS B 834 PHE 0.014 0.002 PHE A 471 TYR 0.017 0.002 TYR B 824 ARG 0.006 0.001 ARG A 827 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 137 time to evaluate : 1.050 Fit side-chains REVERT: A 479 CYS cc_start: 0.8762 (m) cc_final: 0.8481 (m) REVERT: A 626 ASP cc_start: 0.8246 (m-30) cc_final: 0.7950 (m-30) REVERT: A 821 ASP cc_start: 0.8875 (t0) cc_final: 0.8625 (t0) REVERT: B 479 CYS cc_start: 0.8730 (m) cc_final: 0.8473 (m) REVERT: B 626 ASP cc_start: 0.8182 (m-30) cc_final: 0.7895 (m-30) REVERT: B 821 ASP cc_start: 0.8901 (t0) cc_final: 0.8643 (t0) outliers start: 4 outliers final: 0 residues processed: 139 average time/residue: 0.1457 time to fit residues: 31.6689 Evaluate side-chains 74 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 GLN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8741 Z= 0.221 Angle : 0.657 10.390 11900 Z= 0.317 Chirality : 0.043 0.330 1428 Planarity : 0.005 0.041 1402 Dihedral : 9.969 97.302 1737 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.89 % Allowed : 9.58 % Favored : 88.53 % 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: 0.33 (0.25), residues: 1024 helix: 0.86 (0.19), residues: 688 sheet: None (None), residues: 0 loop : -1.03 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 831 HIS 0.005 0.001 HIS A 819 PHE 0.021 0.001 PHE B 411 TYR 0.014 0.001 TYR A 824 ARG 0.005 0.001 ARG B 490 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.952 Fit side-chains REVERT: A 626 ASP cc_start: 0.8244 (m-30) cc_final: 0.7963 (m-30) REVERT: A 696 MET cc_start: 0.8731 (mmm) cc_final: 0.8497 (mmm) REVERT: A 805 LEU cc_start: 0.9596 (tp) cc_final: 0.9336 (tp) REVERT: A 821 ASP cc_start: 0.8935 (t0) cc_final: 0.8724 (t0) REVERT: A 880 ASN cc_start: 0.9425 (p0) cc_final: 0.9032 (t0) REVERT: B 626 ASP cc_start: 0.8221 (m-30) cc_final: 0.7954 (m-30) REVERT: B 696 MET cc_start: 0.8766 (mmm) cc_final: 0.8525 (mmm) REVERT: B 805 LEU cc_start: 0.9595 (tp) cc_final: 0.9330 (tp) REVERT: B 821 ASP cc_start: 0.9009 (t0) cc_final: 0.8777 (t0) REVERT: B 880 ASN cc_start: 0.9413 (p0) cc_final: 0.8982 (t0) outliers start: 17 outliers final: 8 residues processed: 92 average time/residue: 0.1473 time to fit residues: 21.7599 Evaluate side-chains 68 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 765 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 74 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8741 Z= 0.195 Angle : 0.607 11.329 11900 Z= 0.282 Chirality : 0.040 0.212 1428 Planarity : 0.005 0.041 1402 Dihedral : 9.154 82.406 1737 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.12 % Allowed : 10.36 % Favored : 87.53 % 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: 1.24 (0.26), residues: 1024 helix: 1.69 (0.19), residues: 686 sheet: None (None), residues: 0 loop : -1.00 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 492 HIS 0.003 0.001 HIS B 819 PHE 0.016 0.001 PHE A 471 TYR 0.015 0.001 TYR B 824 ARG 0.003 0.000 ARG A 490 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 1.121 Fit side-chains REVERT: A 626 ASP cc_start: 0.8217 (m-30) cc_final: 0.7963 (m-30) REVERT: A 696 MET cc_start: 0.8781 (mmm) cc_final: 0.8559 (mmm) REVERT: A 805 LEU cc_start: 0.9640 (tp) cc_final: 0.9395 (tp) REVERT: A 821 ASP cc_start: 0.8991 (t0) cc_final: 0.8746 (t0) REVERT: A 833 MET cc_start: 0.9092 (ppp) cc_final: 0.8877 (tmm) REVERT: A 880 ASN cc_start: 0.9425 (p0) cc_final: 0.8938 (t0) REVERT: B 559 MET cc_start: 0.9281 (mpp) cc_final: 0.9033 (mmp) REVERT: B 626 ASP cc_start: 0.8224 (m-30) cc_final: 0.7958 (m-30) REVERT: B 696 MET cc_start: 0.8806 (mmm) cc_final: 0.8582 (mmm) REVERT: B 805 LEU cc_start: 0.9626 (tp) cc_final: 0.9379 (tp) REVERT: B 821 ASP cc_start: 0.9019 (t0) cc_final: 0.8767 (t0) REVERT: B 833 MET cc_start: 0.9119 (ppp) cc_final: 0.8891 (tmm) REVERT: B 880 ASN cc_start: 0.9396 (p0) cc_final: 0.8911 (t0) outliers start: 19 outliers final: 7 residues processed: 80 average time/residue: 0.1581 time to fit residues: 20.3841 Evaluate side-chains 70 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 843 CYS Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 587 MET Chi-restraints excluded: chain B residue 842 ILE Chi-restraints excluded: chain B residue 843 CYS Chi-restraints excluded: chain B residue 850 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 44 optimal weight: 0.3980 chunk 62 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 82 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN A 683 GLN ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 683 GLN ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8741 Z= 0.183 Angle : 0.575 10.473 11900 Z= 0.269 Chirality : 0.039 0.212 1428 Planarity : 0.005 0.043 1402 Dihedral : 8.318 59.565 1737 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.00 % Allowed : 11.92 % Favored : 86.08 % 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: 1.43 (0.26), residues: 1024 helix: 1.83 (0.19), residues: 696 sheet: None (None), residues: 0 loop : -0.99 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 492 HIS 0.002 0.001 HIS B 819 PHE 0.015 0.001 PHE A 471 TYR 0.014 0.001 TYR A 824 ARG 0.003 0.000 ARG A 490 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: A 626 ASP cc_start: 0.8176 (m-30) cc_final: 0.7908 (m-30) REVERT: A 696 MET cc_start: 0.8781 (mmm) cc_final: 0.8532 (mmm) REVERT: A 805 LEU cc_start: 0.9644 (tp) cc_final: 0.9406 (tp) REVERT: A 821 ASP cc_start: 0.8986 (t0) cc_final: 0.8738 (t0) REVERT: A 833 MET cc_start: 0.9141 (ppp) cc_final: 0.8912 (tmm) REVERT: A 880 ASN cc_start: 0.9440 (p0) cc_final: 0.8967 (t0) REVERT: B 559 MET cc_start: 0.9306 (mpp) cc_final: 0.9074 (mmp) REVERT: B 626 ASP cc_start: 0.8155 (m-30) cc_final: 0.7895 (m-30) REVERT: B 805 LEU cc_start: 0.9644 (tp) cc_final: 0.9410 (tp) REVERT: B 821 ASP cc_start: 0.9021 (t0) cc_final: 0.8767 (t0) REVERT: B 880 ASN cc_start: 0.9426 (p0) cc_final: 0.8945 (t0) outliers start: 18 outliers final: 8 residues processed: 83 average time/residue: 0.1448 time to fit residues: 19.3908 Evaluate side-chains 70 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 587 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 842 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 40 optimal weight: 0.0270 chunk 84 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.7444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8741 Z= 0.289 Angle : 0.615 9.351 11900 Z= 0.286 Chirality : 0.040 0.211 1428 Planarity : 0.005 0.042 1402 Dihedral : 8.150 58.853 1737 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.78 % Allowed : 11.36 % Favored : 85.86 % 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 (0.27), residues: 1024 helix: 2.01 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -0.82 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 492 HIS 0.003 0.001 HIS B 819 PHE 0.014 0.001 PHE A 471 TYR 0.013 0.001 TYR A 824 ARG 0.003 0.000 ARG A 490 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 61 time to evaluate : 0.936 Fit side-chains REVERT: A 626 ASP cc_start: 0.8187 (m-30) cc_final: 0.7922 (m-30) REVERT: A 696 MET cc_start: 0.8810 (mmm) cc_final: 0.8546 (mmm) REVERT: A 821 ASP cc_start: 0.9001 (t0) cc_final: 0.8781 (t0) REVERT: A 833 MET cc_start: 0.9222 (ppp) cc_final: 0.8973 (tmm) REVERT: A 880 ASN cc_start: 0.9490 (p0) cc_final: 0.9030 (t0) REVERT: B 559 MET cc_start: 0.9354 (mpp) cc_final: 0.9109 (mmp) REVERT: B 626 ASP cc_start: 0.8198 (m-30) cc_final: 0.7937 (m-30) REVERT: B 821 ASP cc_start: 0.8973 (t0) cc_final: 0.8712 (t0) REVERT: B 833 MET cc_start: 0.9201 (ppp) cc_final: 0.8995 (tmm) REVERT: B 880 ASN cc_start: 0.9461 (p0) cc_final: 0.8993 (t0) outliers start: 25 outliers final: 11 residues processed: 78 average time/residue: 0.1588 time to fit residues: 19.6826 Evaluate side-chains 71 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain A residue 843 CYS Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 587 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 842 ILE Chi-restraints excluded: chain B residue 843 CYS Chi-restraints excluded: chain B residue 850 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 95 optimal weight: 0.0170 chunk 11 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 834 HIS ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8741 Z= 0.163 Angle : 0.568 9.497 11900 Z= 0.262 Chirality : 0.039 0.217 1428 Planarity : 0.005 0.044 1402 Dihedral : 7.850 59.208 1737 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.45 % Allowed : 13.36 % Favored : 85.19 % 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: 1.81 (0.27), residues: 1024 helix: 2.05 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -0.66 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 831 HIS 0.001 0.000 HIS A 703 PHE 0.014 0.001 PHE A 471 TYR 0.015 0.001 TYR A 824 ARG 0.002 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 1.006 Fit side-chains REVERT: A 587 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8471 (mmm) REVERT: A 626 ASP cc_start: 0.8176 (m-30) cc_final: 0.7907 (m-30) REVERT: A 821 ASP cc_start: 0.8925 (t0) cc_final: 0.8703 (t0) REVERT: A 833 MET cc_start: 0.9237 (ppp) cc_final: 0.9029 (tmm) REVERT: A 880 ASN cc_start: 0.9418 (p0) cc_final: 0.8989 (t0) REVERT: B 626 ASP cc_start: 0.8180 (m-30) cc_final: 0.7916 (m-30) REVERT: B 821 ASP cc_start: 0.8900 (t0) cc_final: 0.8642 (t0) REVERT: B 833 MET cc_start: 0.9173 (ppp) cc_final: 0.8959 (tmm) REVERT: B 880 ASN cc_start: 0.9398 (p0) cc_final: 0.8977 (t0) outliers start: 13 outliers final: 8 residues processed: 76 average time/residue: 0.1520 time to fit residues: 18.4369 Evaluate side-chains 74 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain A residue 843 CYS Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 587 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 843 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8741 Z= 0.223 Angle : 0.605 9.410 11900 Z= 0.277 Chirality : 0.040 0.216 1428 Planarity : 0.004 0.042 1402 Dihedral : 7.763 58.314 1737 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.34 % Allowed : 13.81 % Favored : 83.85 % 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: 1.94 (0.27), residues: 1024 helix: 2.12 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -0.56 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 492 HIS 0.002 0.001 HIS A 819 PHE 0.015 0.001 PHE A 471 TYR 0.013 0.001 TYR A 824 ARG 0.003 0.000 ARG A 760 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.954 Fit side-chains REVERT: A 587 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8467 (mmm) REVERT: A 626 ASP cc_start: 0.8181 (m-30) cc_final: 0.7906 (m-30) REVERT: A 821 ASP cc_start: 0.8883 (t0) cc_final: 0.8648 (t0) REVERT: A 880 ASN cc_start: 0.9419 (p0) cc_final: 0.9026 (t0) REVERT: B 587 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8500 (mmm) REVERT: B 626 ASP cc_start: 0.8147 (m-30) cc_final: 0.7876 (m-30) REVERT: B 821 ASP cc_start: 0.8911 (t0) cc_final: 0.8668 (t0) REVERT: B 880 ASN cc_start: 0.9420 (p0) cc_final: 0.9014 (t0) outliers start: 21 outliers final: 12 residues processed: 78 average time/residue: 0.1499 time to fit residues: 18.7000 Evaluate side-chains 77 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain A residue 843 CYS Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain B residue 486 TYR Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 587 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 842 ILE Chi-restraints excluded: chain B residue 843 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 651 HIS ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 HIS ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8741 Z= 0.217 Angle : 0.622 9.420 11900 Z= 0.281 Chirality : 0.040 0.217 1428 Planarity : 0.004 0.041 1402 Dihedral : 7.696 58.839 1737 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.23 % Allowed : 14.25 % Favored : 83.52 % 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: 1.96 (0.27), residues: 1024 helix: 2.15 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -0.58 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 492 HIS 0.003 0.001 HIS B 651 PHE 0.014 0.001 PHE A 471 TYR 0.013 0.001 TYR A 824 ARG 0.002 0.000 ARG B 490 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.851 Fit side-chains REVERT: A 587 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8525 (mmm) REVERT: A 626 ASP cc_start: 0.8146 (m-30) cc_final: 0.7856 (m-30) REVERT: A 821 ASP cc_start: 0.8878 (t0) cc_final: 0.8626 (t0) REVERT: A 833 MET cc_start: 0.9275 (ppp) cc_final: 0.9039 (tmm) REVERT: A 880 ASN cc_start: 0.9423 (p0) cc_final: 0.9045 (t0) REVERT: B 587 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8550 (mmm) REVERT: B 626 ASP cc_start: 0.8102 (m-30) cc_final: 0.7814 (m-30) REVERT: B 821 ASP cc_start: 0.8872 (t0) cc_final: 0.8622 (t0) REVERT: B 880 ASN cc_start: 0.9423 (p0) cc_final: 0.9030 (t0) outliers start: 20 outliers final: 13 residues processed: 77 average time/residue: 0.1492 time to fit residues: 18.2867 Evaluate side-chains 80 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain A residue 843 CYS Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain B residue 486 TYR Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 587 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 842 ILE Chi-restraints excluded: chain B residue 843 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 91 optimal weight: 0.0370 chunk 60 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8741 Z= 0.176 Angle : 0.616 9.499 11900 Z= 0.277 Chirality : 0.039 0.219 1428 Planarity : 0.004 0.039 1402 Dihedral : 7.561 59.705 1737 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.34 % Allowed : 14.14 % Favored : 83.52 % 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: 1.94 (0.27), residues: 1024 helix: 2.12 (0.20), residues: 698 sheet: None (None), residues: 0 loop : -0.55 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 496 HIS 0.001 0.000 HIS A 703 PHE 0.013 0.001 PHE A 471 TYR 0.013 0.001 TYR A 824 ARG 0.002 0.000 ARG B 490 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.980 Fit side-chains REVERT: A 587 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8536 (mmm) REVERT: A 672 LEU cc_start: 0.9546 (tp) cc_final: 0.9345 (pp) REVERT: A 821 ASP cc_start: 0.8828 (t0) cc_final: 0.8584 (t0) REVERT: A 880 ASN cc_start: 0.9418 (p0) cc_final: 0.9053 (t0) REVERT: B 587 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.8517 (mmm) REVERT: B 672 LEU cc_start: 0.9548 (tp) cc_final: 0.9344 (pp) REVERT: B 821 ASP cc_start: 0.8831 (t0) cc_final: 0.8578 (t0) REVERT: B 880 ASN cc_start: 0.9409 (p0) cc_final: 0.9033 (t0) outliers start: 21 outliers final: 14 residues processed: 84 average time/residue: 0.1593 time to fit residues: 21.9114 Evaluate side-chains 82 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain A residue 843 CYS Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain B residue 486 TYR Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 587 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 842 ILE Chi-restraints excluded: chain B residue 843 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 0.5980 chunk 93 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8741 Z= 0.192 Angle : 0.658 10.772 11900 Z= 0.293 Chirality : 0.040 0.220 1428 Planarity : 0.004 0.037 1402 Dihedral : 7.524 59.523 1737 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.78 % Allowed : 15.70 % Favored : 82.52 % 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 (0.27), residues: 1024 helix: 2.10 (0.20), residues: 698 sheet: None (None), residues: 0 loop : -0.49 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 662 HIS 0.001 0.000 HIS A 703 PHE 0.013 0.001 PHE A 471 TYR 0.013 0.001 TYR A 824 ARG 0.001 0.000 ARG B 389 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.947 Fit side-chains REVERT: A 587 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8535 (mmm) REVERT: A 672 LEU cc_start: 0.9547 (tp) cc_final: 0.9345 (pp) REVERT: A 712 MET cc_start: 0.8754 (mtp) cc_final: 0.8410 (mtm) REVERT: A 821 ASP cc_start: 0.8825 (t0) cc_final: 0.8583 (t0) REVERT: A 880 ASN cc_start: 0.9422 (p0) cc_final: 0.9071 (t0) REVERT: B 587 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8519 (mmm) REVERT: B 672 LEU cc_start: 0.9549 (tp) cc_final: 0.9344 (pp) REVERT: B 821 ASP cc_start: 0.8828 (t0) cc_final: 0.8578 (t0) REVERT: B 880 ASN cc_start: 0.9410 (p0) cc_final: 0.9046 (t0) outliers start: 16 outliers final: 14 residues processed: 79 average time/residue: 0.1477 time to fit residues: 18.6280 Evaluate side-chains 83 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain A residue 843 CYS Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain B residue 486 TYR Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 587 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 842 ILE Chi-restraints excluded: chain B residue 843 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 83 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 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 = 0.2932 r_free = 0.2932 target = 0.050330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.043810 restraints weight = 37428.120| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 3.70 r_work: 0.2613 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8741 Z= 0.329 Angle : 0.716 11.643 11900 Z= 0.324 Chirality : 0.041 0.216 1428 Planarity : 0.005 0.036 1402 Dihedral : 7.657 59.798 1737 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.23 % Allowed : 15.48 % Favored : 82.29 % 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: 2.04 (0.27), residues: 1024 helix: 2.17 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -0.44 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 662 HIS 0.003 0.001 HIS B 819 PHE 0.014 0.001 PHE A 471 TYR 0.012 0.001 TYR A 824 ARG 0.002 0.000 ARG B 602 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1717.21 seconds wall clock time: 32 minutes 46.05 seconds (1966.05 seconds total)