Starting phenix.real_space_refine on Sun Jun 8 02:21:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ty7_26168/06_2025/7ty7_26168.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ty7_26168/06_2025/7ty7_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_26168/06_2025/7ty7_26168.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ty7_26168/06_2025/7ty7_26168.map" model { file = "/net/cci-nas-00/data/ceres_data/7ty7_26168/06_2025/7ty7_26168.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ty7_26168/06_2025/7ty7_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-5710/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: 6.11, per 1000 atoms: 0.72 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: 2.26 Conformation dependent library (CDL) restraints added in 925.4 milliseconds 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: 0.97 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: 2.33 Time building geometry restraints manager: 2.62 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: 2.800 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: 23.220 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.850 ------------------------------------------------------------------------------- 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 8745 Z= 1.013 Angle : 1.815 8.482 11912 Z= 1.379 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00151 ( 2) link_NAG-ASN : angle 2.05971 ( 6) link_BETA1-4 : bond 0.00389 ( 2) link_BETA1-4 : angle 1.73622 ( 6) hydrogen bonds : bond 0.25099 ( 508) hydrogen bonds : angle 8.53976 ( 1488) covalent geometry : bond 0.01318 ( 8741) covalent geometry : angle 1.81443 (11900) *********************** 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 : 0.899 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: 0.1422 time to fit residues: 30.6025 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 : 0.898 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.052448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.045979 restraints weight = 36556.453| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 3.64 r_work: 0.2659 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8745 Z= 0.150 Angle : 0.660 10.387 11912 Z= 0.318 Chirality : 0.043 0.329 1428 Planarity : 0.005 0.041 1402 Dihedral : 9.968 97.292 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00267 ( 2) link_NAG-ASN : angle 1.79962 ( 6) link_BETA1-4 : bond 0.00677 ( 2) link_BETA1-4 : angle 1.95176 ( 6) hydrogen bonds : bond 0.04904 ( 508) hydrogen bonds : angle 4.49706 ( 1488) covalent geometry : bond 0.00335 ( 8741) covalent geometry : angle 0.65732 (11900) *********************** 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 : 0.924 Fit side-chains REVERT: A 479 CYS cc_start: 0.9260 (m) cc_final: 0.9042 (m) REVERT: A 626 ASP cc_start: 0.8474 (m-30) cc_final: 0.8160 (m-30) REVERT: A 696 MET cc_start: 0.8918 (mmm) cc_final: 0.8708 (mmm) REVERT: A 776 MET cc_start: 0.9442 (ptp) cc_final: 0.9114 (ptp) REVERT: A 805 LEU cc_start: 0.9361 (tp) cc_final: 0.9119 (tp) REVERT: A 821 ASP cc_start: 0.9147 (t0) cc_final: 0.8931 (t0) REVERT: A 880 ASN cc_start: 0.9431 (p0) cc_final: 0.8993 (t0) REVERT: B 617 MET cc_start: 0.9462 (mmm) cc_final: 0.9261 (mmm) REVERT: B 626 ASP cc_start: 0.8449 (m-30) cc_final: 0.8157 (m-30) REVERT: B 696 MET cc_start: 0.8955 (mmm) cc_final: 0.8743 (mmm) REVERT: B 805 LEU cc_start: 0.9365 (tp) cc_final: 0.9119 (tp) REVERT: B 821 ASP cc_start: 0.9233 (t0) cc_final: 0.8998 (t0) REVERT: B 880 ASN cc_start: 0.9411 (p0) cc_final: 0.8937 (t0) outliers start: 17 outliers final: 8 residues processed: 92 average time/residue: 0.1529 time to fit residues: 22.6917 Evaluate side-chains 69 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 1.670 ------------------------------------------------------------------------------- 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 90 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 651 HIS ** 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 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.048552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.042277 restraints weight = 39572.681| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 3.71 r_work: 0.2563 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 8745 Z= 0.311 Angle : 0.725 10.761 11912 Z= 0.343 Chirality : 0.043 0.208 1428 Planarity : 0.005 0.040 1402 Dihedral : 9.560 85.505 1737 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.34 % Allowed : 10.02 % Favored : 86.64 % 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: 1.17 (0.27), residues: 1024 helix: 1.57 (0.19), residues: 696 sheet: None (None), residues: 0 loop : -0.94 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 492 HIS 0.006 0.002 HIS B 819 PHE 0.015 0.002 PHE A 471 TYR 0.014 0.001 TYR A 824 ARG 0.005 0.001 ARG A 490 Details of bonding type rmsd link_NAG-ASN : bond 0.00280 ( 2) link_NAG-ASN : angle 2.24953 ( 6) link_BETA1-4 : bond 0.00459 ( 2) link_BETA1-4 : angle 1.87271 ( 6) hydrogen bonds : bond 0.04582 ( 508) hydrogen bonds : angle 4.34127 ( 1488) covalent geometry : bond 0.00709 ( 8741) covalent geometry : angle 0.72233 (11900) *********************** 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 91 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 61 time to evaluate : 1.104 Fit side-chains REVERT: A 617 MET cc_start: 0.9507 (mmm) cc_final: 0.9100 (mmm) REVERT: A 626 ASP cc_start: 0.8568 (m-30) cc_final: 0.8281 (m-30) REVERT: A 821 ASP cc_start: 0.9238 (t0) cc_final: 0.8999 (t0) REVERT: A 833 MET cc_start: 0.9299 (ppp) cc_final: 0.8985 (tmm) REVERT: B 626 ASP cc_start: 0.8559 (m-30) cc_final: 0.8284 (m-30) REVERT: B 821 ASP cc_start: 0.9259 (t0) cc_final: 0.9015 (t0) REVERT: B 833 MET cc_start: 0.9318 (ppp) cc_final: 0.8995 (tmm) outliers start: 30 outliers final: 18 residues processed: 85 average time/residue: 0.1686 time to fit residues: 23.2207 Evaluate side-chains 71 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 1.364 ------------------------------------------------------------------------------- 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 450 LEU Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain A residue 843 CYS Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 453 LEU 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 846 VAL 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 98 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 683 GLN ** A 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 GLN ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.050359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.043867 restraints weight = 37672.687| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 3.73 r_work: 0.2606 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8745 Z= 0.128 Angle : 0.600 11.654 11912 Z= 0.279 Chirality : 0.039 0.215 1428 Planarity : 0.005 0.043 1402 Dihedral : 8.783 59.872 1737 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % 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: 1.41 (0.26), residues: 1024 helix: 1.80 (0.19), residues: 700 sheet: None (None), residues: 0 loop : -1.01 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 831 HIS 0.003 0.001 HIS B 819 PHE 0.016 0.001 PHE A 471 TYR 0.015 0.001 TYR A 824 ARG 0.002 0.000 ARG B 389 Details of bonding type rmsd link_NAG-ASN : bond 0.00052 ( 2) link_NAG-ASN : angle 1.20751 ( 6) link_BETA1-4 : bond 0.00393 ( 2) link_BETA1-4 : angle 2.56201 ( 6) hydrogen bonds : bond 0.03936 ( 508) hydrogen bonds : angle 4.06069 ( 1488) covalent geometry : bond 0.00301 ( 8741) covalent geometry : angle 0.59708 (11900) *********************** 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 84 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.934 Fit side-chains REVERT: A 559 MET cc_start: 0.9394 (mpp) cc_final: 0.9043 (mmp) REVERT: A 617 MET cc_start: 0.9526 (mmm) cc_final: 0.9222 (mmm) REVERT: A 626 ASP cc_start: 0.8487 (m-30) cc_final: 0.8198 (m-30) REVERT: A 821 ASP cc_start: 0.9210 (t0) cc_final: 0.8983 (t0) REVERT: A 833 MET cc_start: 0.9346 (ppp) cc_final: 0.9037 (tmm) REVERT: A 880 ASN cc_start: 0.9485 (p0) cc_final: 0.8980 (t0) REVERT: B 559 MET cc_start: 0.9357 (mpp) cc_final: 0.9042 (mmp) REVERT: B 617 MET cc_start: 0.9523 (mmm) cc_final: 0.9207 (mmm) REVERT: B 626 ASP cc_start: 0.8449 (m-30) cc_final: 0.8173 (m-30) REVERT: B 821 ASP cc_start: 0.9284 (t0) cc_final: 0.9042 (t0) REVERT: B 833 MET cc_start: 0.9356 (ppp) cc_final: 0.9038 (tmm) REVERT: B 880 ASN cc_start: 0.9444 (p0) cc_final: 0.8919 (t0) outliers start: 18 outliers final: 9 residues processed: 76 average time/residue: 0.1428 time to fit residues: 17.4652 Evaluate side-chains 67 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 842 ILE Chi-restraints excluded: chain B residue 843 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 53 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.049889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.043532 restraints weight = 38075.566| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 3.81 r_work: 0.2604 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8745 Z= 0.128 Angle : 0.587 9.486 11912 Z= 0.270 Chirality : 0.039 0.217 1428 Planarity : 0.005 0.043 1402 Dihedral : 8.253 59.839 1737 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.56 % Allowed : 13.03 % Favored : 84.41 % 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: 1.63 (0.26), residues: 1024 helix: 1.99 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -0.94 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 848 HIS 0.002 0.000 HIS B 819 PHE 0.014 0.001 PHE A 471 TYR 0.014 0.001 TYR A 824 ARG 0.002 0.000 ARG B 490 Details of bonding type rmsd link_NAG-ASN : bond 0.00077 ( 2) link_NAG-ASN : angle 0.81984 ( 6) link_BETA1-4 : bond 0.00657 ( 2) link_BETA1-4 : angle 1.52724 ( 6) hydrogen bonds : bond 0.03666 ( 508) hydrogen bonds : angle 3.95450 ( 1488) covalent geometry : bond 0.00302 ( 8741) covalent geometry : angle 0.58580 (11900) *********************** 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 88 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 0.941 Fit side-chains REVERT: A 557 VAL cc_start: 0.8934 (OUTLIER) cc_final: 0.8591 (m) REVERT: A 617 MET cc_start: 0.9546 (mmm) cc_final: 0.9268 (mmm) REVERT: A 626 ASP cc_start: 0.8397 (m-30) cc_final: 0.8094 (m-30) REVERT: A 821 ASP cc_start: 0.9087 (t0) cc_final: 0.8836 (t0) REVERT: A 833 MET cc_start: 0.9396 (ppp) cc_final: 0.9042 (tmm) REVERT: B 559 MET cc_start: 0.9344 (mpp) cc_final: 0.9053 (mmp) REVERT: B 626 ASP cc_start: 0.8396 (m-30) cc_final: 0.8107 (m-30) REVERT: B 821 ASP cc_start: 0.9137 (t0) cc_final: 0.8888 (t0) REVERT: B 833 MET cc_start: 0.9408 (ppp) cc_final: 0.9055 (tmm) outliers start: 23 outliers final: 13 residues processed: 79 average time/residue: 0.1538 time to fit residues: 19.5028 Evaluate side-chains 74 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 587 MET 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 850 VAL 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 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 3 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.050582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.044092 restraints weight = 36968.639| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 3.68 r_work: 0.2622 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8745 Z= 0.126 Angle : 0.593 9.477 11912 Z= 0.272 Chirality : 0.039 0.217 1428 Planarity : 0.004 0.043 1402 Dihedral : 7.970 58.735 1737 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.56 % Allowed : 12.58 % Favored : 84.86 % 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: 1.78 (0.27), residues: 1024 helix: 2.09 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -0.86 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 492 HIS 0.001 0.000 HIS A 819 PHE 0.015 0.001 PHE A 471 TYR 0.014 0.001 TYR A 824 ARG 0.002 0.000 ARG B 490 Details of bonding type rmsd link_NAG-ASN : bond 0.00014 ( 2) link_NAG-ASN : angle 0.81381 ( 6) link_BETA1-4 : bond 0.00414 ( 2) link_BETA1-4 : angle 1.55246 ( 6) hydrogen bonds : bond 0.03544 ( 508) hydrogen bonds : angle 3.89106 ( 1488) covalent geometry : bond 0.00302 ( 8741) covalent geometry : angle 0.59231 (11900) *********************** 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 91 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 1.124 Fit side-chains REVERT: A 559 MET cc_start: 0.9347 (mpp) cc_final: 0.8910 (mmp) REVERT: A 626 ASP cc_start: 0.8348 (m-30) cc_final: 0.8052 (m-30) REVERT: A 821 ASP cc_start: 0.9078 (t0) cc_final: 0.8823 (t0) REVERT: A 833 MET cc_start: 0.9389 (ppp) cc_final: 0.9024 (tmm) REVERT: A 880 ASN cc_start: 0.9486 (p0) cc_final: 0.9101 (t0) REVERT: B 557 VAL cc_start: 0.9003 (OUTLIER) cc_final: 0.8704 (m) REVERT: B 617 MET cc_start: 0.9581 (mmm) cc_final: 0.9368 (mmm) REVERT: B 626 ASP cc_start: 0.8345 (m-30) cc_final: 0.8056 (m-30) REVERT: B 821 ASP cc_start: 0.9113 (t0) cc_final: 0.8861 (t0) REVERT: B 833 MET cc_start: 0.9406 (ppp) cc_final: 0.9049 (tmm) REVERT: B 880 ASN cc_start: 0.9453 (p0) cc_final: 0.9061 (t0) outliers start: 23 outliers final: 14 residues processed: 81 average time/residue: 0.1816 time to fit residues: 24.1652 Evaluate side-chains 81 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 1.074 ------------------------------------------------------------------------------- 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 850 VAL 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 557 VAL 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 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 65 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 564 GLN ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.050548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.044256 restraints weight = 38513.533| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 3.82 r_work: 0.2622 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8745 Z= 0.128 Angle : 0.601 9.448 11912 Z= 0.272 Chirality : 0.039 0.219 1428 Planarity : 0.004 0.043 1402 Dihedral : 7.815 59.275 1737 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.78 % Allowed : 12.92 % Favored : 84.30 % 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: 1.85 (0.27), residues: 1024 helix: 2.19 (0.20), residues: 686 sheet: None (None), residues: 0 loop : -0.85 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 492 HIS 0.002 0.000 HIS A 819 PHE 0.015 0.001 PHE A 471 TYR 0.013 0.001 TYR B 824 ARG 0.002 0.000 ARG B 490 Details of bonding type rmsd link_NAG-ASN : bond 0.00012 ( 2) link_NAG-ASN : angle 0.78831 ( 6) link_BETA1-4 : bond 0.00400 ( 2) link_BETA1-4 : angle 1.26395 ( 6) hydrogen bonds : bond 0.03490 ( 508) hydrogen bonds : angle 3.87282 ( 1488) covalent geometry : bond 0.00305 ( 8741) covalent geometry : angle 0.59987 (11900) *********************** 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 90 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 65 time to evaluate : 1.005 Fit side-chains REVERT: A 617 MET cc_start: 0.9539 (mmm) cc_final: 0.9277 (mmm) REVERT: A 626 ASP cc_start: 0.8424 (m-30) cc_final: 0.8139 (m-30) REVERT: A 821 ASP cc_start: 0.9125 (t0) cc_final: 0.8885 (t0) REVERT: A 833 MET cc_start: 0.9381 (ppp) cc_final: 0.9000 (tmm) REVERT: A 880 ASN cc_start: 0.9464 (p0) cc_final: 0.9067 (t0) REVERT: B 617 MET cc_start: 0.9571 (mmm) cc_final: 0.9306 (mmm) REVERT: B 626 ASP cc_start: 0.8431 (m-30) cc_final: 0.8167 (m-30) REVERT: B 821 ASP cc_start: 0.9139 (t0) cc_final: 0.8900 (t0) REVERT: B 833 MET cc_start: 0.9413 (ppp) cc_final: 0.9041 (tmm) REVERT: B 880 ASN cc_start: 0.9430 (p0) cc_final: 0.9013 (t0) outliers start: 25 outliers final: 17 residues processed: 80 average time/residue: 0.1485 time to fit residues: 19.1402 Evaluate side-chains 82 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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 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 850 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 77 optimal weight: 4.9990 chunk 45 optimal weight: 0.0570 chunk 57 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 3 optimal weight: 0.1980 chunk 41 optimal weight: 0.5980 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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** A 834 HIS B 651 HIS ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.051619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.045390 restraints weight = 38078.122| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 3.61 r_work: 0.2690 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8745 Z= 0.108 Angle : 0.596 9.525 11912 Z= 0.269 Chirality : 0.039 0.220 1428 Planarity : 0.004 0.042 1402 Dihedral : 7.598 58.942 1737 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.12 % Allowed : 14.03 % 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: 1.90 (0.27), residues: 1024 helix: 2.24 (0.20), residues: 686 sheet: None (None), residues: 0 loop : -0.84 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 496 HIS 0.002 0.000 HIS A 703 PHE 0.013 0.001 PHE A 471 TYR 0.014 0.001 TYR A 824 ARG 0.002 0.000 ARG B 389 Details of bonding type rmsd link_NAG-ASN : bond 0.00075 ( 2) link_NAG-ASN : angle 0.53704 ( 6) link_BETA1-4 : bond 0.00325 ( 2) link_BETA1-4 : angle 1.25395 ( 6) hydrogen bonds : bond 0.03312 ( 508) hydrogen bonds : angle 3.81485 ( 1488) covalent geometry : bond 0.00251 ( 8741) covalent geometry : angle 0.59540 (11900) *********************** 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 93 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 1.028 Fit side-chains REVERT: A 435 MET cc_start: 0.8906 (mmm) cc_final: 0.8663 (tpt) REVERT: A 587 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8591 (mmm) REVERT: A 617 MET cc_start: 0.9566 (mmm) cc_final: 0.9288 (mmm) REVERT: A 626 ASP cc_start: 0.8222 (m-30) cc_final: 0.7919 (m-30) REVERT: A 672 LEU cc_start: 0.9510 (tp) cc_final: 0.9297 (pp) REVERT: A 821 ASP cc_start: 0.8892 (t0) cc_final: 0.8616 (t0) REVERT: A 833 MET cc_start: 0.9451 (ppp) cc_final: 0.9093 (tmm) REVERT: A 880 ASN cc_start: 0.9431 (p0) cc_final: 0.9049 (t0) REVERT: B 587 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8564 (mmm) REVERT: B 617 MET cc_start: 0.9599 (mmm) cc_final: 0.9276 (mmm) REVERT: B 626 ASP cc_start: 0.8206 (m-30) cc_final: 0.7912 (m-30) REVERT: B 672 LEU cc_start: 0.9509 (tp) cc_final: 0.9293 (pp) REVERT: B 776 MET cc_start: 0.9644 (ptp) cc_final: 0.9440 (ptp) REVERT: B 821 ASP cc_start: 0.8878 (t0) cc_final: 0.8618 (t0) REVERT: B 833 MET cc_start: 0.9427 (ppp) cc_final: 0.9063 (tmm) REVERT: B 843 CYS cc_start: 0.9524 (OUTLIER) cc_final: 0.9196 (t) REVERT: B 880 ASN cc_start: 0.9402 (p0) cc_final: 0.9002 (t0) outliers start: 19 outliers final: 11 residues processed: 85 average time/residue: 0.1501 time to fit residues: 20.3870 Evaluate side-chains 82 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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 640 VAL Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain A residue 842 ILE 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 842 ILE Chi-restraints excluded: chain B residue 843 CYS Chi-restraints excluded: chain B residue 850 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 18 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 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 834 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.050739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.044617 restraints weight = 37864.110| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 3.52 r_work: 0.2674 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8745 Z= 0.142 Angle : 0.639 9.678 11912 Z= 0.286 Chirality : 0.039 0.218 1428 Planarity : 0.004 0.037 1402 Dihedral : 7.529 58.816 1737 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.23 % Allowed : 14.48 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.27), residues: 1024 helix: 2.31 (0.20), residues: 686 sheet: None (None), residues: 0 loop : -0.76 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 662 HIS 0.002 0.001 HIS A 819 PHE 0.014 0.001 PHE A 471 TYR 0.013 0.001 TYR A 824 ARG 0.002 0.000 ARG B 490 Details of bonding type rmsd link_NAG-ASN : bond 0.00048 ( 2) link_NAG-ASN : angle 0.75478 ( 6) link_BETA1-4 : bond 0.00311 ( 2) link_BETA1-4 : angle 1.20929 ( 6) hydrogen bonds : bond 0.03415 ( 508) hydrogen bonds : angle 3.81417 ( 1488) covalent geometry : bond 0.00339 ( 8741) covalent geometry : angle 0.63812 (11900) *********************** 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 88 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 1.027 Fit side-chains REVERT: A 587 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8569 (mmm) REVERT: A 617 MET cc_start: 0.9588 (mmm) cc_final: 0.9293 (mmm) REVERT: A 626 ASP cc_start: 0.8215 (m-30) cc_final: 0.7907 (m-30) REVERT: A 821 ASP cc_start: 0.8855 (t0) cc_final: 0.8597 (t0) REVERT: A 833 MET cc_start: 0.9468 (ppp) cc_final: 0.9100 (tmm) REVERT: A 880 ASN cc_start: 0.9448 (p0) cc_final: 0.9059 (t0) REVERT: B 587 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8552 (mmm) REVERT: B 626 ASP cc_start: 0.8189 (m-30) cc_final: 0.7884 (m-30) REVERT: B 821 ASP cc_start: 0.8845 (t0) cc_final: 0.8587 (t0) REVERT: B 833 MET cc_start: 0.9466 (ppp) cc_final: 0.9107 (tmm) REVERT: B 843 CYS cc_start: 0.9532 (OUTLIER) cc_final: 0.9200 (t) REVERT: B 880 ASN cc_start: 0.9431 (p0) cc_final: 0.9023 (t0) outliers start: 20 outliers final: 12 residues processed: 81 average time/residue: 0.1490 time to fit residues: 19.4190 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 : 0.975 ------------------------------------------------------------------------------- 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 640 VAL 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 842 ILE Chi-restraints excluded: chain B residue 843 CYS Chi-restraints excluded: chain B residue 850 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 23 optimal weight: 0.8980 chunk 53 optimal weight: 0.0870 chunk 24 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.7358 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.051385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.045347 restraints weight = 37430.803| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 3.51 r_work: 0.2694 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8745 Z= 0.119 Angle : 0.648 9.631 11912 Z= 0.286 Chirality : 0.039 0.220 1428 Planarity : 0.004 0.037 1402 Dihedral : 7.422 59.406 1737 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.78 % Allowed : 14.92 % Favored : 83.30 % 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: 1.96 (0.27), residues: 1024 helix: 2.26 (0.20), residues: 686 sheet: None (None), residues: 0 loop : -0.75 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 662 HIS 0.002 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00038 ( 2) link_NAG-ASN : angle 0.55558 ( 6) link_BETA1-4 : bond 0.00285 ( 2) link_BETA1-4 : angle 1.16659 ( 6) hydrogen bonds : bond 0.03365 ( 508) hydrogen bonds : angle 3.81305 ( 1488) covalent geometry : bond 0.00283 ( 8741) covalent geometry : angle 0.64753 (11900) ********************** 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 84 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.892 Fit side-chains REVERT: A 435 MET cc_start: 0.8937 (mmm) cc_final: 0.8680 (tpt) REVERT: A 587 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8559 (mmm) REVERT: A 617 MET cc_start: 0.9577 (mmm) cc_final: 0.9269 (mmm) REVERT: A 821 ASP cc_start: 0.8837 (t0) cc_final: 0.8579 (t0) REVERT: A 833 MET cc_start: 0.9469 (ppp) cc_final: 0.9102 (tmm) REVERT: A 880 ASN cc_start: 0.9446 (p0) cc_final: 0.9060 (t0) REVERT: B 587 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8550 (mmm) REVERT: B 721 MET cc_start: 0.8637 (mtp) cc_final: 0.8377 (mmm) REVERT: B 821 ASP cc_start: 0.8812 (t0) cc_final: 0.8555 (t0) REVERT: B 833 MET cc_start: 0.9468 (ppp) cc_final: 0.9101 (tmm) REVERT: B 843 CYS cc_start: 0.9526 (OUTLIER) cc_final: 0.9195 (t) REVERT: B 880 ASN cc_start: 0.9415 (p0) cc_final: 0.9021 (t0) outliers start: 16 outliers final: 11 residues processed: 77 average time/residue: 0.1529 time to fit residues: 18.7058 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 : 1.032 ------------------------------------------------------------------------------- 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 640 VAL 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 842 ILE Chi-restraints excluded: chain B residue 843 CYS Chi-restraints excluded: chain B residue 850 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 37 optimal weight: 0.0470 chunk 69 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 88 optimal weight: 0.0470 chunk 44 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 70 optimal weight: 0.4980 overall best weight: 0.4576 ------------------------------------------------------------------------------- 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 736 ASN ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.052124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.046093 restraints weight = 37689.742| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 3.53 r_work: 0.2714 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8745 Z= 0.110 Angle : 0.646 9.610 11912 Z= 0.286 Chirality : 0.039 0.222 1428 Planarity : 0.004 0.038 1402 Dihedral : 7.247 59.728 1737 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.45 % Allowed : 16.04 % 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: 1.99 (0.27), residues: 1024 helix: 2.26 (0.20), residues: 686 sheet: None (None), residues: 0 loop : -0.68 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 662 HIS 0.002 0.000 HIS B 703 PHE 0.013 0.001 PHE A 471 TYR 0.013 0.001 TYR A 824 ARG 0.003 0.000 ARG B 432 Details of bonding type rmsd link_NAG-ASN : bond 0.00097 ( 2) link_NAG-ASN : angle 0.42352 ( 6) link_BETA1-4 : bond 0.00350 ( 2) link_BETA1-4 : angle 1.17190 ( 6) hydrogen bonds : bond 0.03265 ( 508) hydrogen bonds : angle 3.78731 ( 1488) covalent geometry : bond 0.00260 ( 8741) covalent geometry : angle 0.64559 (11900) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3600.99 seconds wall clock time: 64 minutes 4.61 seconds (3844.61 seconds total)