Starting phenix.real_space_refine on Wed Feb 14 03:31:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ty7_26168/02_2024/7ty7_26168_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ty7_26168/02_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ty7_26168/02_2024/7ty7_26168.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ty7_26168/02_2024/7ty7_26168.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ty7_26168/02_2024/7ty7_26168_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ty7_26168/02_2024/7ty7_26168_updated.pdb" } 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 Residue "A GLU 473": "OE1" <-> "OE2" Residue "A GLU 508": "OE1" <-> "OE2" Residue "A GLU 758": "OE1" <-> "OE2" Residue "A TYR 818": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 473": "OE1" <-> "OE2" Residue "B GLU 508": "OE1" <-> "OE2" Residue "B GLU 758": "OE1" <-> "OE2" Residue "B TYR 818": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 5.16, per 1000 atoms: 0.60 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 - 3.50 Amino acid : False - 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: 3.72 Conformation dependent library (CDL) restraints added in 1.7 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... running ksdssp... Secondary structure from input PDB file: 43 helices and 0 sheets defined 65.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 380 through 399 Proline residue: A 391 - end of helix removed outlier: 5.033A pdb=" N LEU A 394 " --> pdb=" O TYR A 390 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N SER A 395 " --> pdb=" O PRO A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 430 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 437 through 452 Processing helix chain 'A' and resid 466 through 482 Processing helix chain 'A' and resid 486 through 507 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 515 Processing helix chain 'A' and resid 518 through 546 removed outlier: 3.706A pdb=" N LEU A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 592 Processing helix chain 'A' and resid 599 through 607 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 609 through 623 Processing helix chain 'A' and resid 661 through 689 removed outlier: 3.558A pdb=" N PHE A 665 " --> pdb=" O ILE A 661 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ALA A 668 " --> pdb=" O MET A 664 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N LEU A 669 " --> pdb=" O PHE A 665 " (cutoff:3.500A) Proline residue: A 670 - end of helix 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 702 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 738 Processing helix chain 'A' and resid 761 through 771 Processing helix chain 'A' and resid 777 through 782 removed outlier: 4.163A pdb=" N ARG A 782 " --> pdb=" O PRO A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 800 removed outlier: 3.976A pdb=" N LEU A 800 " --> pdb=" O GLY A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 811 Processing helix chain 'A' and resid 823 through 826 No H-bonds generated for 'chain 'A' and resid 823 through 826' Processing helix chain 'A' and resid 830 through 852 Processing helix chain 'A' and resid 859 through 871 removed outlier: 3.803A pdb=" N THR A 866 " --> pdb=" O VAL A 862 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL A 867 " --> pdb=" O LEU A 863 " (cutoff:3.500A) Proline residue: A 868 - end of helix Processing helix chain 'A' and resid 873 through 877 Processing helix chain 'A' and resid 880 through 886 removed outlier: 3.875A pdb=" N CYS A 885 " --> pdb=" O VAL A 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 399 Proline residue: B 391 - end of helix removed outlier: 5.032A pdb=" N LEU B 394 " --> pdb=" O TYR B 390 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N SER B 395 " --> pdb=" O PRO B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 430 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 437 through 452 Processing helix chain 'B' and resid 466 through 482 Processing helix chain 'B' and resid 486 through 507 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 515 Processing helix chain 'B' and resid 518 through 546 removed outlier: 3.706A pdb=" N LEU B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 592 Processing helix chain 'B' and resid 599 through 607 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 609 through 623 Processing helix chain 'B' and resid 661 through 689 removed outlier: 3.559A pdb=" N PHE B 665 " --> pdb=" O ILE B 661 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ALA B 668 " --> pdb=" O MET B 664 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N LEU B 669 " --> pdb=" O PHE B 665 " (cutoff:3.500A) Proline residue: B 670 - end of helix 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 702 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 738 Processing helix chain 'B' and resid 761 through 771 Processing helix chain 'B' and resid 777 through 782 removed outlier: 4.166A pdb=" N ARG B 782 " --> pdb=" O PRO B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 800 removed outlier: 3.976A pdb=" N LEU B 800 " --> pdb=" O GLY B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 811 Processing helix chain 'B' and resid 823 through 826 No H-bonds generated for 'chain 'B' and resid 823 through 826' Processing helix chain 'B' and resid 830 through 852 Processing helix chain 'B' and resid 859 through 877 removed outlier: 3.803A pdb=" N THR B 866 " --> pdb=" O VAL B 862 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL B 867 " --> pdb=" O LEU B 863 " (cutoff:3.500A) Proline residue: B 868 - end of helix removed outlier: 4.807A pdb=" N LEU B 874 " --> pdb=" O ARG B 870 " (cutoff:3.500A) Proline residue: B 875 - end of helix Processing helix chain 'B' and resid 880 through 886 removed outlier: 3.878A pdb=" N CYS B 885 " --> pdb=" O VAL B 881 " (cutoff:3.500A) 435 hydrogen bonds defined for protein. 1281 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: 2.31 Time building geometry restraints manager: 3.89 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: 98.72 - 105.86: 294 105.86 - 112.99: 4583 112.99 - 120.13: 3835 120.13 - 127.26: 3143 127.26 - 134.39: 45 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: 1280 2.82 - 3.34: 9265 3.34 - 3.86: 13392 3.86 - 4.38: 17882 4.38 - 4.90: 28733 Nonbonded interactions: 70552 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 2.440 nonbonded pdb=" O LEU B 577 " pdb=" OG1 THR B 581 " model vdw 2.412 2.440 nonbonded pdb=" NH2 ARG B 832 " pdb=" OE1 GLU B 882 " model vdw 2.457 2.520 ... (remaining 70547 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 2.080 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: 8.090 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 26.640 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.270 ------------------------------------------------------------------------------- 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= 0.855 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 fitting. rotamer outliers: 4 poor density : 137 time to evaluate : 1.005 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: 0.1472 time to fit residues: 31.4337 Evaluate side-chains 74 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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: 0.0050 chunk 42 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.7396 ------------------------------------------------------------------------------- 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: 0.8550 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8741 Z= 0.207 Angle : 0.635 10.562 11900 Z= 0.304 Chirality : 0.041 0.255 1428 Planarity : 0.005 0.033 1402 Dihedral : 9.814 87.604 1737 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.67 % Allowed : 10.02 % Favored : 88.31 % 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: 0.23 (0.26), residues: 1024 helix: 0.91 (0.19), residues: 668 sheet: None (None), residues: 0 loop : -1.24 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 831 HIS 0.005 0.001 HIS A 819 PHE 0.020 0.001 PHE B 411 TYR 0.013 0.001 TYR B 824 ARG 0.005 0.001 ARG A 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 90 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 75 time to evaluate : 0.994 Fit side-chains REVERT: A 626 ASP cc_start: 0.8260 (m-30) cc_final: 0.7954 (m-30) REVERT: A 696 MET cc_start: 0.8756 (mmm) cc_final: 0.8521 (mmm) REVERT: A 805 LEU cc_start: 0.9556 (tp) cc_final: 0.9268 (tp) REVERT: A 821 ASP cc_start: 0.9002 (t0) cc_final: 0.8779 (t0) REVERT: A 880 ASN cc_start: 0.9373 (p0) cc_final: 0.9005 (t0) REVERT: B 626 ASP cc_start: 0.8261 (m-30) cc_final: 0.7996 (m-30) REVERT: B 696 MET cc_start: 0.8773 (mmm) cc_final: 0.8542 (mmm) REVERT: B 805 LEU cc_start: 0.9551 (tp) cc_final: 0.9255 (tp) REVERT: B 821 ASP cc_start: 0.9022 (t0) cc_final: 0.8787 (t0) REVERT: B 880 ASN cc_start: 0.9386 (p0) cc_final: 0.8993 (t0) outliers start: 15 outliers final: 4 residues processed: 85 average time/residue: 0.1466 time to fit residues: 19.9238 Evaluate side-chains 66 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 62 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain B residue 386 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: 2.9990 chunk 77 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 651 HIS ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8741 Z= 0.246 Angle : 0.602 11.171 11900 Z= 0.278 Chirality : 0.040 0.221 1428 Planarity : 0.005 0.041 1402 Dihedral : 8.759 59.718 1737 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.67 % Allowed : 9.80 % 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: 1.33 (0.27), residues: 1024 helix: 1.85 (0.19), residues: 670 sheet: None (None), residues: 0 loop : -1.02 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 492 HIS 0.004 0.001 HIS B 819 PHE 0.015 0.001 PHE B 411 TYR 0.015 0.001 TYR B 824 ARG 0.004 0.000 ARG B 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 92 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 68 time to evaluate : 1.039 Fit side-chains REVERT: A 626 ASP cc_start: 0.8242 (m-30) cc_final: 0.7971 (m-30) REVERT: A 805 LEU cc_start: 0.9593 (tp) cc_final: 0.9329 (tp) REVERT: A 821 ASP cc_start: 0.9010 (t0) cc_final: 0.8794 (t0) REVERT: B 626 ASP cc_start: 0.8208 (m-30) cc_final: 0.7927 (m-30) REVERT: B 805 LEU cc_start: 0.9591 (tp) cc_final: 0.9321 (tp) REVERT: B 821 ASP cc_start: 0.8997 (t0) cc_final: 0.8792 (t0) outliers start: 24 outliers final: 15 residues processed: 86 average time/residue: 0.1427 time to fit residues: 19.8088 Evaluate side-chains 72 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 57 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 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 450 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 69 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8741 Z= 0.210 Angle : 0.564 9.404 11900 Z= 0.263 Chirality : 0.039 0.212 1428 Planarity : 0.004 0.044 1402 Dihedral : 8.366 58.809 1737 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.34 % Allowed : 10.91 % Favored : 86.75 % 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: 1.60 (0.27), residues: 1024 helix: 2.02 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -0.87 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 492 HIS 0.003 0.001 HIS B 819 PHE 0.014 0.001 PHE A 471 TYR 0.015 0.001 TYR A 824 ARG 0.002 0.000 ARG B 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 85 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 64 time to evaluate : 0.917 Fit side-chains REVERT: A 512 LEU cc_start: 0.9573 (mt) cc_final: 0.9313 (tt) REVERT: A 626 ASP cc_start: 0.8218 (m-30) cc_final: 0.7921 (m-30) REVERT: A 805 LEU cc_start: 0.9603 (tp) cc_final: 0.9355 (tp) REVERT: A 880 ASN cc_start: 0.9416 (p0) cc_final: 0.9028 (t0) REVERT: B 559 MET cc_start: 0.9333 (mpp) cc_final: 0.9072 (mmp) REVERT: B 626 ASP cc_start: 0.8205 (m-30) cc_final: 0.7921 (m-30) REVERT: B 805 LEU cc_start: 0.9598 (tp) cc_final: 0.9341 (tp) REVERT: B 880 ASN cc_start: 0.9383 (p0) cc_final: 0.9012 (t0) outliers start: 21 outliers final: 11 residues processed: 81 average time/residue: 0.1527 time to fit residues: 19.7609 Evaluate side-chains 72 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 61 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 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 B residue 450 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 88 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8741 Z= 0.184 Angle : 0.560 9.461 11900 Z= 0.259 Chirality : 0.038 0.215 1428 Planarity : 0.004 0.045 1402 Dihedral : 8.074 59.723 1737 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.45 % Allowed : 10.36 % Favored : 87.19 % 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: 1.77 (0.27), residues: 1024 helix: 2.21 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -0.87 (0.35), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 492 HIS 0.002 0.001 HIS B 819 PHE 0.013 0.001 PHE A 471 TYR 0.014 0.001 TYR A 824 ARG 0.002 0.000 ARG B 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 88 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 66 time to evaluate : 1.000 Fit side-chains REVERT: A 626 ASP cc_start: 0.8166 (m-30) cc_final: 0.7896 (m-30) REVERT: A 805 LEU cc_start: 0.9607 (tp) cc_final: 0.9360 (tp) REVERT: A 880 ASN cc_start: 0.9416 (p0) cc_final: 0.9014 (t0) REVERT: B 559 MET cc_start: 0.9368 (mpp) cc_final: 0.9118 (mmp) REVERT: B 626 ASP cc_start: 0.8171 (m-30) cc_final: 0.7879 (m-30) REVERT: B 805 LEU cc_start: 0.9601 (tp) cc_final: 0.9354 (tp) outliers start: 22 outliers final: 18 residues processed: 81 average time/residue: 0.1543 time to fit residues: 19.9980 Evaluate side-chains 79 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 61 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 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 740 VAL Chi-restraints excluded: chain A residue 837 THR 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 450 LEU 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 740 VAL Chi-restraints excluded: chain B residue 837 THR 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: 4.9990 chunk 24 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 95 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8741 Z= 0.200 Angle : 0.582 9.445 11900 Z= 0.266 Chirality : 0.038 0.214 1428 Planarity : 0.004 0.045 1402 Dihedral : 7.899 59.323 1737 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.78 % Allowed : 11.80 % Favored : 85.41 % 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: 1.91 (0.27), residues: 1024 helix: 2.30 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -0.78 (0.35), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 A 490 *********************** 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 fitting. rotamer outliers: 25 poor density : 60 time to evaluate : 0.995 Fit side-chains REVERT: A 587 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8483 (mmm) REVERT: A 626 ASP cc_start: 0.8227 (m-30) cc_final: 0.7938 (m-30) REVERT: A 880 ASN cc_start: 0.9452 (p0) cc_final: 0.9069 (t0) REVERT: B 559 MET cc_start: 0.9349 (mpp) cc_final: 0.9082 (mmp) REVERT: B 587 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8495 (mmm) REVERT: B 617 MET cc_start: 0.9265 (mmm) cc_final: 0.9024 (mmt) REVERT: B 626 ASP cc_start: 0.8106 (m-30) cc_final: 0.7843 (m-30) outliers start: 25 outliers final: 15 residues processed: 76 average time/residue: 0.1474 time to fit residues: 18.1867 Evaluate side-chains 76 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 59 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 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 837 THR 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 450 LEU 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=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: 0.9980 chunk 61 optimal weight: 5.9990 chunk 59 optimal weight: 0.0670 chunk 45 optimal weight: 4.9990 chunk 60 optimal weight: 0.0270 chunk 39 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 overall best weight: 0.5776 ------------------------------------------------------------------------------- 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 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 HIS ** 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: 0.8598 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8741 Z= 0.163 Angle : 0.576 9.878 11900 Z= 0.261 Chirality : 0.038 0.217 1428 Planarity : 0.004 0.046 1402 Dihedral : 7.743 59.069 1737 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.78 % Allowed : 13.03 % 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: 1.92 (0.27), residues: 1024 helix: 2.31 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -0.77 (0.35), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 831 HIS 0.003 0.001 HIS B 651 PHE 0.013 0.001 PHE A 471 TYR 0.012 0.001 TYR B 824 ARG 0.001 0.000 ARG A 389 *********************** 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 80 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 64 time to evaluate : 1.099 Fit side-chains REVERT: A 587 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8502 (mmm) REVERT: A 626 ASP cc_start: 0.8177 (m-30) cc_final: 0.7856 (m-30) REVERT: A 880 ASN cc_start: 0.9430 (p0) cc_final: 0.9052 (t0) REVERT: B 559 MET cc_start: 0.9353 (mpp) cc_final: 0.9118 (mmp) REVERT: B 587 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8519 (mmm) REVERT: B 626 ASP cc_start: 0.8158 (m-30) cc_final: 0.7836 (m-30) REVERT: B 880 ASN cc_start: 0.9396 (p0) cc_final: 0.9068 (t0) outliers start: 16 outliers final: 11 residues processed: 74 average time/residue: 0.1476 time to fit residues: 17.6087 Evaluate side-chains 70 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 57 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain A residue 837 THR 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 450 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 587 MET Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 837 THR 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: 0.7980 chunk 62 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8741 Z= 0.186 Angle : 0.588 9.468 11900 Z= 0.268 Chirality : 0.038 0.216 1428 Planarity : 0.004 0.041 1402 Dihedral : 7.607 59.180 1737 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.23 % Allowed : 12.58 % 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: 2.02 (0.27), residues: 1024 helix: 2.36 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -0.66 (0.35), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 492 HIS 0.002 0.001 HIS A 703 PHE 0.013 0.001 PHE A 471 TYR 0.012 0.001 TYR A 824 ARG 0.001 0.000 ARG B 432 *********************** 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 78 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 58 time to evaluate : 1.105 Fit side-chains REVERT: A 587 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8526 (mmm) REVERT: A 626 ASP cc_start: 0.8162 (m-30) cc_final: 0.7850 (m-30) REVERT: A 880 ASN cc_start: 0.9440 (p0) cc_final: 0.9073 (t0) REVERT: B 559 MET cc_start: 0.9353 (mpp) cc_final: 0.9121 (mmp) REVERT: B 587 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8519 (mmm) REVERT: B 626 ASP cc_start: 0.8200 (m-30) cc_final: 0.7901 (m-30) REVERT: B 880 ASN cc_start: 0.9417 (p0) cc_final: 0.9091 (t0) outliers start: 20 outliers final: 13 residues processed: 71 average time/residue: 0.1557 time to fit residues: 17.7892 Evaluate side-chains 74 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 59 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 LEU 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 837 THR 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 450 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 587 MET Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 837 THR 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: 2.9990 chunk 71 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 86 optimal weight: 0.1980 chunk 91 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 96 optimal weight: 6.9990 chunk 59 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 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 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: 0.8602 moved from start: 0.3601 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 : 0.597 9.562 11900 Z= 0.271 Chirality : 0.038 0.217 1428 Planarity : 0.004 0.036 1402 Dihedral : 7.442 59.793 1737 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.89 % Allowed : 13.59 % Favored : 84.52 % 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: 2.05 (0.27), residues: 1024 helix: 2.38 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -0.58 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 492 HIS 0.002 0.000 HIS A 703 PHE 0.012 0.001 PHE A 471 TYR 0.011 0.001 TYR A 824 ARG 0.001 0.000 ARG A 589 *********************** 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 75 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 58 time to evaluate : 0.989 Fit side-chains REVERT: A 587 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8519 (mmm) REVERT: A 626 ASP cc_start: 0.8243 (m-30) cc_final: 0.7926 (m-30) REVERT: A 880 ASN cc_start: 0.9432 (p0) cc_final: 0.9049 (t0) REVERT: B 587 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8525 (mmm) REVERT: B 617 MET cc_start: 0.9089 (mmm) cc_final: 0.8829 (mmm) REVERT: B 626 ASP cc_start: 0.8195 (m-30) cc_final: 0.7856 (m-30) REVERT: B 880 ASN cc_start: 0.9413 (p0) cc_final: 0.9076 (t0) outliers start: 17 outliers final: 13 residues processed: 69 average time/residue: 0.1478 time to fit residues: 16.5398 Evaluate side-chains 73 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 58 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 LEU 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 837 THR 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 450 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 587 MET Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 837 THR 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: 1.9990 chunk 93 optimal weight: 3.9990 chunk 80 optimal weight: 0.3980 chunk 8 optimal weight: 0.1980 chunk 62 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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: 0.8610 moved from start: 0.3699 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= 0.189 Angle : 0.608 9.575 11900 Z= 0.275 Chirality : 0.038 0.216 1428 Planarity : 0.004 0.036 1402 Dihedral : 7.344 59.740 1737 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.78 % Allowed : 13.92 % 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: 2.07 (0.27), residues: 1024 helix: 2.38 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -0.60 (0.35), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 492 HIS 0.002 0.001 HIS A 703 PHE 0.013 0.001 PHE A 471 TYR 0.013 0.001 TYR B 824 ARG 0.002 0.000 ARG B 589 ********************** 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 73 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 57 time to evaluate : 1.047 Fit side-chains REVERT: A 587 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8540 (mmm) REVERT: A 626 ASP cc_start: 0.8222 (m-30) cc_final: 0.7906 (m-30) REVERT: A 880 ASN cc_start: 0.9437 (p0) cc_final: 0.9064 (t0) REVERT: B 435 MET cc_start: 0.8482 (mmm) cc_final: 0.8249 (tpt) REVERT: B 587 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8530 (mmm) REVERT: B 617 MET cc_start: 0.9142 (mmm) cc_final: 0.8842 (mmm) REVERT: B 626 ASP cc_start: 0.8200 (m-30) cc_final: 0.7877 (m-30) REVERT: B 880 ASN cc_start: 0.9406 (p0) cc_final: 0.9072 (t0) outliers start: 16 outliers final: 14 residues processed: 67 average time/residue: 0.1532 time to fit residues: 16.5875 Evaluate side-chains 73 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 57 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 837 THR 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 450 LEU 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 837 THR 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: 4.9990 chunk 33 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.2942 r_free = 0.2942 target = 0.050114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.043717 restraints weight = 38119.656| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 3.65 r_work: 0.2627 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8741 Z= 0.253 Angle : 0.638 9.629 11900 Z= 0.289 Chirality : 0.039 0.218 1428 Planarity : 0.004 0.035 1402 Dihedral : 7.329 59.463 1737 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.23 % Allowed : 13.47 % 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: 2.08 (0.28), residues: 1024 helix: 2.39 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -0.62 (0.35), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 662 HIS 0.002 0.001 HIS A 819 PHE 0.013 0.001 PHE A 471 TYR 0.011 0.001 TYR A 824 ARG 0.002 0.000 ARG A 602 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1825.47 seconds wall clock time: 33 minutes 59.34 seconds (2039.34 seconds total)