Starting phenix.real_space_refine on Wed Feb 14 04:14:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ty8_26169/02_2024/7ty8_26169_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ty8_26169/02_2024/7ty8_26169.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ty8_26169/02_2024/7ty8_26169.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ty8_26169/02_2024/7ty8_26169.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ty8_26169/02_2024/7ty8_26169_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ty8_26169/02_2024/7ty8_26169_updated.pdb" } resolution = 3.18 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= 0.029 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 36 5.16 5 C 5800 2.51 5 N 1314 2.21 5 O 1433 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 472": "OE1" <-> "OE2" Residue "A GLU 758": "OE1" <-> "OE2" Residue "B GLU 472": "OE1" <-> "OE2" Residue "B GLU 758": "OE1" <-> "OE2" 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: 8591 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4067 Classifications: {'peptide': 515} Link IDs: {'PTRANS': 29, 'TRANS': 485} Chain breaks: 1 Chain: "B" Number of atoms: 4067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4067 Classifications: {'peptide': 515} Link IDs: {'PTRANS': 29, 'TRANS': 485} 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: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 186 Unusual residues: {'CLR': 4, 'NFL': 1, 'PC1': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 186 Unusual residues: {'CLR': 4, 'NFL': 1, 'PC1': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Time building chain proxies: 5.32, per 1000 atoms: 0.62 Number of scatterers: 8591 At special positions: 0 Unit cell: (125.892, 85.004, 83.928, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 2 15.00 F 6 9.00 O 1433 8.00 N 1314 7.00 C 5800 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: 3.75 Conformation dependent library (CDL) restraints added in 1.8 seconds 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1916 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 0 sheets defined 66.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.18 Creating SS restraints... Processing helix chain 'A' and resid 380 through 392 Proline residue: A 391 - end of helix Processing helix chain 'A' and resid 395 through 398 No H-bonds generated for 'chain 'A' and resid 395 through 398' Processing helix chain 'A' and resid 403 through 431 removed outlier: 3.529A pdb=" N PHE A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) Proline residue: A 419 - end of helix Processing helix chain 'A' and resid 437 through 454 Processing helix chain 'A' and resid 466 through 482 removed outlier: 3.711A pdb=" N THR A 481 " --> pdb=" O SER A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 506 removed outlier: 4.143A pdb=" N VAL A 491 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TRP A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL A 502 " --> pdb=" O ILE A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 515 removed outlier: 3.527A pdb=" N VAL A 513 " --> pdb=" O SER A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 546 removed outlier: 3.901A pdb=" N ILE A 543 " --> pdb=" O LYS A 539 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 592 Processing helix chain 'A' and resid 599 through 607 removed outlier: 3.737A pdb=" N VAL A 604 " --> pdb=" O LYS A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 622 removed outlier: 3.526A pdb=" N MET A 617 " --> pdb=" O SER A 613 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP A 621 " --> pdb=" O MET A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 689 removed outlier: 3.581A pdb=" N PHE A 665 " --> pdb=" O ILE A 661 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ALA A 668 " --> pdb=" O MET A 664 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N LEU A 669 " --> pdb=" O PHE A 665 " (cutoff:3.500A) Proline residue: A 670 - end of helix removed outlier: 3.741A pdb=" N ILE A 684 " --> pdb=" O LEU A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 719 removed outlier: 3.966A pdb=" N LEU A 718 " --> pdb=" O GLY A 714 " (cutoff:3.500A) removed outlier: 4.041A 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 772 removed outlier: 3.584A pdb=" N ALA A 767 " --> pdb=" O GLY A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 782 removed outlier: 4.327A pdb=" N ARG A 782 " --> pdb=" O PRO A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 800 removed outlier: 3.560A pdb=" N ILE A 791 " --> pdb=" O VAL A 787 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 800 " --> pdb=" O GLY A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 813 removed outlier: 3.798A pdb=" N LEU A 811 " --> pdb=" O ASP A 807 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 812 " --> pdb=" O ARG A 808 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE A 813 " --> pdb=" O ILE A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 818 No H-bonds generated for 'chain 'A' and resid 816 through 818' 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 removed outlier: 3.604A pdb=" N LEU A 835 " --> pdb=" O TRP A 831 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 852 " --> pdb=" O TRP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 863 Processing helix chain 'A' and resid 865 through 871 removed outlier: 3.559A pdb=" N LEU A 869 " --> pdb=" O LEU A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 877 Processing helix chain 'A' and resid 880 through 886 Processing helix chain 'B' and resid 380 through 392 Proline residue: B 391 - end of helix Processing helix chain 'B' and resid 395 through 398 No H-bonds generated for 'chain 'B' and resid 395 through 398' Processing helix chain 'B' and resid 403 through 431 removed outlier: 3.528A pdb=" N PHE B 414 " --> pdb=" O ILE B 410 " (cutoff:3.500A) Proline residue: B 419 - end of helix Processing helix chain 'B' and resid 437 through 454 Processing helix chain 'B' and resid 466 through 482 removed outlier: 3.711A pdb=" N THR B 481 " --> pdb=" O SER B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 506 removed outlier: 4.157A pdb=" N VAL B 491 " --> pdb=" O ILE B 487 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TRP B 492 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL B 502 " --> pdb=" O ILE B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 515 removed outlier: 3.528A pdb=" N VAL B 513 " --> pdb=" O SER B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 546 removed outlier: 3.903A pdb=" N ILE B 543 " --> pdb=" O LYS B 539 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE B 544 " --> pdb=" O LEU B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 592 Processing helix chain 'B' and resid 599 through 607 removed outlier: 3.737A pdb=" N VAL B 604 " --> pdb=" O LYS B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 622 removed outlier: 3.525A pdb=" N MET B 617 " --> pdb=" O SER B 613 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP B 621 " --> pdb=" O MET B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 689 removed outlier: 3.581A pdb=" N PHE B 665 " --> pdb=" O ILE B 661 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ALA B 668 " --> pdb=" O MET B 664 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LEU B 669 " --> pdb=" O PHE B 665 " (cutoff:3.500A) Proline residue: B 670 - end of helix removed outlier: 3.743A pdb=" N ILE B 684 " --> pdb=" O LEU B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 719 removed outlier: 3.964A pdb=" N LEU B 718 " --> pdb=" O GLY B 714 " (cutoff:3.500A) removed outlier: 4.041A 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 772 removed outlier: 3.583A pdb=" N ALA B 767 " --> pdb=" O GLY B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 782 removed outlier: 4.327A pdb=" N ARG B 782 " --> pdb=" O PRO B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 800 removed outlier: 3.560A pdb=" N ILE B 791 " --> pdb=" O VAL B 787 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU B 800 " --> pdb=" O GLY B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 813 removed outlier: 3.799A pdb=" N LEU B 811 " --> pdb=" O ASP B 807 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 812 " --> pdb=" O ARG B 808 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE B 813 " --> pdb=" O ILE B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 818 No H-bonds generated for 'chain 'B' and resid 816 through 818' 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 removed outlier: 3.605A pdb=" N LEU B 835 " --> pdb=" O TRP B 831 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER B 852 " --> pdb=" O TRP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 859 through 863 Processing helix chain 'B' and resid 865 through 871 removed outlier: 3.556A pdb=" N LEU B 869 " --> pdb=" O LEU B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 877 Processing helix chain 'B' and resid 880 through 886 414 hydrogen bonds defined for protein. 1224 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: 4.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1392 1.33 - 1.45: 2156 1.45 - 1.58: 5174 1.58 - 1.70: 4 1.70 - 1.83: 66 Bond restraints: 8792 Sorted by residual: bond pdb=" N ILE B 783 " pdb=" CA ILE B 783 " ideal model delta sigma weight residual 1.460 1.497 -0.037 7.60e-03 1.73e+04 2.36e+01 bond pdb=" N ILE A 783 " pdb=" CA ILE A 783 " ideal model delta sigma weight residual 1.460 1.496 -0.036 7.60e-03 1.73e+04 2.24e+01 bond pdb=" N VAL B 634 " pdb=" CA VAL B 634 " ideal model delta sigma weight residual 1.461 1.496 -0.035 8.70e-03 1.32e+04 1.60e+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 1.60e+01 bond pdb=" N LEU A 669 " pdb=" CA LEU A 669 " ideal model delta sigma weight residual 1.462 1.492 -0.030 8.50e-03 1.38e+04 1.27e+01 ... (remaining 8787 not shown) Histogram of bond angle deviations from ideal: 100.03 - 106.91: 360 106.91 - 113.79: 4839 113.79 - 120.67: 3871 120.67 - 127.55: 2864 127.55 - 134.43: 46 Bond angle restraints: 11980 Sorted by residual: angle pdb=" C PRO B 598 " pdb=" N GLY B 599 " pdb=" CA GLY B 599 " ideal model delta sigma weight residual 120.03 125.80 -5.77 1.12e+00 7.97e-01 2.65e+01 angle pdb=" C PRO A 598 " pdb=" N GLY A 599 " pdb=" CA GLY A 599 " ideal model delta sigma weight residual 120.03 125.79 -5.76 1.12e+00 7.97e-01 2.65e+01 angle pdb=" C GLY B 380 " pdb=" N GLY B 381 " pdb=" CA GLY B 381 " ideal model delta sigma weight residual 120.00 125.62 -5.62 1.10e+00 8.26e-01 2.61e+01 angle pdb=" C GLY A 380 " pdb=" N GLY A 381 " pdb=" CA GLY A 381 " ideal model delta sigma weight residual 120.00 125.61 -5.61 1.10e+00 8.26e-01 2.60e+01 angle pdb=" N LEU A 873 " pdb=" CA LEU A 873 " pdb=" C LEU A 873 " ideal model delta sigma weight residual 111.07 116.05 -4.98 1.07e+00 8.73e-01 2.17e+01 ... (remaining 11975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 5094 17.32 - 34.64: 380 34.64 - 51.96: 106 51.96 - 69.28: 33 69.28 - 86.61: 13 Dihedral angle restraints: 5626 sinusoidal: 2656 harmonic: 2970 Sorted by residual: dihedral pdb=" CA ARG A 388 " pdb=" C ARG A 388 " pdb=" N ARG A 389 " pdb=" CA ARG A 389 " ideal model delta harmonic sigma weight residual -180.00 -160.60 -19.40 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA ARG B 388 " pdb=" C ARG B 388 " pdb=" N ARG B 389 " pdb=" CA ARG B 389 " ideal model delta harmonic sigma weight residual -180.00 -160.62 -19.38 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA TYR A 628 " pdb=" C TYR A 628 " pdb=" N THR A 629 " pdb=" CA THR A 629 " ideal model delta harmonic sigma weight residual 180.00 163.42 16.58 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 5623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 488 0.043 - 0.086: 398 0.086 - 0.129: 366 0.129 - 0.172: 163 0.172 - 0.215: 19 Chirality restraints: 1434 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 -2.33 -0.07 2.00e-02 2.50e+03 1.16e+01 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 -2.35 -0.05 2.00e-02 2.50e+03 7.08e+00 chirality pdb=" CA LEU B 484 " pdb=" N LEU B 484 " pdb=" C LEU B 484 " pdb=" CB LEU B 484 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 1431 not shown) Planarity restraints: 1404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " 0.305 2.00e-02 2.50e+03 2.57e-01 8.25e+02 pdb=" C7 NAG D 1 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " 0.189 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " -0.441 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " 0.304 2.00e-02 2.50e+03 2.56e-01 8.21e+02 pdb=" C7 NAG C 1 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " 0.189 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " -0.439 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 2 " -0.072 2.00e-02 2.50e+03 5.89e-02 4.33e+01 pdb=" C7 NAG C 2 " 0.019 2.00e-02 2.50e+03 pdb=" C8 NAG C 2 " -0.054 2.00e-02 2.50e+03 pdb=" N2 NAG C 2 " 0.093 2.00e-02 2.50e+03 pdb=" O7 NAG C 2 " 0.014 2.00e-02 2.50e+03 ... (remaining 1401 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 2725 2.91 - 3.40: 9467 3.40 - 3.90: 15239 3.90 - 4.40: 17349 4.40 - 4.90: 28451 Nonbonded interactions: 73231 Sorted by model distance: nonbonded pdb=" CD1 LEU B 874 " pdb=" CD2 PHE B 878 " model vdw 2.407 3.760 nonbonded pdb=" CD1 LEU A 874 " pdb=" CD2 PHE A 878 " model vdw 2.430 3.760 nonbonded pdb=" OH TYR A 555 " pdb=" OH TYR B 555 " model vdw 2.441 2.440 nonbonded pdb=" O VAL B 729 " pdb=" OG1 THR B 733 " model vdw 2.486 2.440 nonbonded pdb=" O VAL A 729 " pdb=" OG1 THR A 733 " model vdw 2.486 2.440 ... (remaining 73226 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' selection = chain 'B' } 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: 3.120 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: 8.220 Check model and map are aligned: 0.140 Set scattering table: 0.070 Process input model: 28.580 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 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 0.049 8792 Z= 0.858 Angle : 1.782 8.189 11980 Z= 1.347 Chirality : 0.085 0.215 1434 Planarity : 0.010 0.257 1402 Dihedral : 14.152 86.606 3710 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.78 % Allowed : 7.37 % Favored : 91.85 % 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: -3.38 (0.22), residues: 1022 helix: -2.25 (0.16), residues: 676 sheet: None (None), residues: 0 loop : -1.83 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 662 HIS 0.004 0.001 HIS A 819 PHE 0.016 0.002 PHE A 495 TYR 0.014 0.002 TYR B 628 ARG 0.004 0.001 ARG B 514 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 201 time to evaluate : 1.082 Fit side-chains REVERT: A 641 SER cc_start: 0.7642 (OUTLIER) cc_final: 0.7207 (p) REVERT: A 696 MET cc_start: 0.7845 (mmm) cc_final: 0.7568 (mmt) REVERT: A 833 MET cc_start: 0.8496 (tmm) cc_final: 0.8162 (tmm) REVERT: B 696 MET cc_start: 0.7842 (mmm) cc_final: 0.7557 (mmt) REVERT: B 833 MET cc_start: 0.8457 (tmm) cc_final: 0.8101 (tmm) outliers start: 7 outliers final: 2 residues processed: 208 average time/residue: 0.2116 time to fit residues: 59.8754 Evaluate side-chains 115 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 112 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain B residue 650 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 48 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 521 GLN A 550 GLN A 683 GLN B 521 GLN B 550 GLN B 683 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8792 Z= 0.231 Angle : 0.643 7.066 11980 Z= 0.313 Chirality : 0.041 0.164 1434 Planarity : 0.005 0.043 1402 Dihedral : 10.297 88.749 1813 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.01 % Allowed : 12.61 % Favored : 85.38 % 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: -0.32 (0.25), residues: 1022 helix: 0.33 (0.19), residues: 688 sheet: None (None), residues: 0 loop : -1.21 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 492 HIS 0.004 0.001 HIS B 651 PHE 0.022 0.002 PHE A 411 TYR 0.010 0.001 TYR A 486 ARG 0.007 0.001 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 133 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 812 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8879 (mp) outliers start: 18 outliers final: 9 residues processed: 145 average time/residue: 0.1543 time to fit residues: 34.4945 Evaluate side-chains 112 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 102 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 614 ILE 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: 0.9980 chunk 77 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 91 optimal weight: 0.1980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 834 HIS B 834 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8792 Z= 0.213 Angle : 0.579 7.441 11980 Z= 0.281 Chirality : 0.039 0.164 1434 Planarity : 0.005 0.048 1402 Dihedral : 9.861 85.950 1808 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.57 % Allowed : 13.84 % Favored : 82.59 % 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: 0.54 (0.25), residues: 1022 helix: 1.05 (0.19), residues: 678 sheet: None (None), residues: 0 loop : -0.98 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 662 HIS 0.002 0.001 HIS A 734 PHE 0.018 0.001 PHE A 411 TYR 0.020 0.001 TYR B 413 ARG 0.004 0.000 ARG B 694 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 113 time to evaluate : 1.062 Fit side-chains REVERT: A 558 LEU cc_start: 0.8838 (tp) cc_final: 0.8618 (tt) REVERT: A 664 MET cc_start: 0.7937 (mtm) cc_final: 0.7624 (mtp) REVERT: A 812 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8811 (mp) REVERT: A 833 MET cc_start: 0.7258 (tmm) cc_final: 0.7000 (ppp) REVERT: B 486 TYR cc_start: 0.7740 (t80) cc_final: 0.7490 (t80) REVERT: B 664 MET cc_start: 0.7970 (mtm) cc_final: 0.7655 (mtp) REVERT: B 833 MET cc_start: 0.7273 (tmm) cc_final: 0.7023 (ppp) outliers start: 32 outliers final: 18 residues processed: 132 average time/residue: 0.1598 time to fit residues: 32.3417 Evaluate side-chains 119 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 100 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 595 SER Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 681 GLU Chi-restraints excluded: chain B residue 809 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 26 optimal weight: 0.0770 chunk 82 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8792 Z= 0.197 Angle : 0.571 7.996 11980 Z= 0.274 Chirality : 0.039 0.164 1434 Planarity : 0.005 0.052 1402 Dihedral : 9.579 84.317 1808 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.46 % Allowed : 17.08 % Favored : 80.47 % 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: 0.99 (0.26), residues: 1022 helix: 1.40 (0.20), residues: 670 sheet: None (None), residues: 0 loop : -0.75 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 662 HIS 0.001 0.001 HIS B 734 PHE 0.014 0.001 PHE A 411 TYR 0.016 0.001 TYR B 413 ARG 0.005 0.000 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 111 time to evaluate : 1.019 Fit side-chains REVERT: A 399 ASP cc_start: 0.8814 (OUTLIER) cc_final: 0.8209 (t70) REVERT: A 486 TYR cc_start: 0.7679 (t80) cc_final: 0.7431 (t80) REVERT: A 664 MET cc_start: 0.7746 (mtm) cc_final: 0.7424 (mtp) REVERT: A 696 MET cc_start: 0.7868 (mmm) cc_final: 0.7560 (mmt) REVERT: A 820 PRO cc_start: 0.8802 (Cg_exo) cc_final: 0.8543 (Cg_endo) REVERT: A 833 MET cc_start: 0.7209 (tmm) cc_final: 0.6943 (ppp) REVERT: B 399 ASP cc_start: 0.8829 (OUTLIER) cc_final: 0.8213 (t70) REVERT: B 664 MET cc_start: 0.7758 (mtm) cc_final: 0.7432 (mtp) REVERT: B 696 MET cc_start: 0.8003 (mmm) cc_final: 0.7663 (mmt) REVERT: B 833 MET cc_start: 0.7257 (tmm) cc_final: 0.7054 (ppp) outliers start: 22 outliers final: 16 residues processed: 124 average time/residue: 0.1611 time to fit residues: 31.0389 Evaluate side-chains 120 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 102 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 595 SER Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 809 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 68 optimal weight: 0.0970 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 880 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8792 Z= 0.252 Angle : 0.582 9.161 11980 Z= 0.279 Chirality : 0.039 0.163 1434 Planarity : 0.005 0.053 1402 Dihedral : 9.402 83.158 1808 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.79 % Allowed : 17.19 % Favored : 80.02 % 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: 1.13 (0.26), residues: 1022 helix: 1.44 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -0.52 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 662 HIS 0.002 0.001 HIS B 547 PHE 0.016 0.001 PHE A 836 TYR 0.020 0.001 TYR B 486 ARG 0.003 0.000 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 106 time to evaluate : 1.008 Fit side-chains REVERT: A 664 MET cc_start: 0.7730 (mtm) cc_final: 0.7388 (mtp) REVERT: A 696 MET cc_start: 0.8151 (mmm) cc_final: 0.7826 (mmt) REVERT: A 820 PRO cc_start: 0.8693 (Cg_exo) cc_final: 0.8467 (Cg_endo) REVERT: A 833 MET cc_start: 0.7318 (tmm) cc_final: 0.7077 (ppp) REVERT: B 664 MET cc_start: 0.7738 (mtm) cc_final: 0.7392 (mtp) REVERT: B 696 MET cc_start: 0.8167 (mmm) cc_final: 0.7843 (mmt) REVERT: B 833 MET cc_start: 0.7337 (tmm) cc_final: 0.7096 (ppp) outliers start: 25 outliers final: 19 residues processed: 121 average time/residue: 0.1492 time to fit residues: 28.1299 Evaluate side-chains 122 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 103 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 595 SER Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 725 SER Chi-restraints excluded: chain B residue 809 ILE Chi-restraints excluded: chain B residue 831 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 0.4980 chunk 32 optimal weight: 0.5980 chunk 51 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 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 0.036 8792 Z= 0.217 Angle : 0.583 9.484 11980 Z= 0.275 Chirality : 0.039 0.163 1434 Planarity : 0.004 0.053 1402 Dihedral : 9.198 84.071 1808 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.34 % Allowed : 17.52 % Favored : 80.13 % 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: 1.30 (0.26), residues: 1022 helix: 1.57 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -0.42 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 662 HIS 0.002 0.001 HIS B 651 PHE 0.015 0.001 PHE B 451 TYR 0.024 0.002 TYR B 486 ARG 0.003 0.000 ARG B 694 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 106 time to evaluate : 0.984 Fit side-chains REVERT: A 664 MET cc_start: 0.7666 (mtm) cc_final: 0.7296 (mtp) REVERT: A 696 MET cc_start: 0.8179 (mmm) cc_final: 0.7890 (mmt) REVERT: A 820 PRO cc_start: 0.8700 (Cg_exo) cc_final: 0.8473 (Cg_endo) REVERT: A 833 MET cc_start: 0.7289 (tmm) cc_final: 0.6999 (ppp) REVERT: B 664 MET cc_start: 0.7675 (mtm) cc_final: 0.7305 (mtp) REVERT: B 820 PRO cc_start: 0.8633 (Cg_exo) cc_final: 0.8393 (Cg_endo) REVERT: B 833 MET cc_start: 0.7274 (tmm) cc_final: 0.6985 (ppp) outliers start: 21 outliers final: 20 residues processed: 119 average time/residue: 0.1389 time to fit residues: 26.1122 Evaluate side-chains 122 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 102 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 831 TRP Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 595 SER Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 725 SER Chi-restraints excluded: chain B residue 809 ILE Chi-restraints excluded: chain B residue 831 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 83 optimal weight: 0.0980 chunk 98 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 59 optimal weight: 0.1980 chunk 45 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8792 Z= 0.178 Angle : 0.567 10.350 11980 Z= 0.266 Chirality : 0.039 0.163 1434 Planarity : 0.004 0.053 1402 Dihedral : 8.911 83.517 1808 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.79 % Allowed : 18.86 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.26), residues: 1022 helix: 1.69 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -0.47 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 662 HIS 0.002 0.001 HIS A 834 PHE 0.013 0.001 PHE A 836 TYR 0.022 0.001 TYR B 486 ARG 0.003 0.000 ARG B 694 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 0.957 Fit side-chains REVERT: A 486 TYR cc_start: 0.7507 (t80) cc_final: 0.7260 (t80) REVERT: A 664 MET cc_start: 0.7577 (mtm) cc_final: 0.7228 (mtp) REVERT: A 820 PRO cc_start: 0.8666 (Cg_exo) cc_final: 0.8431 (Cg_endo) REVERT: A 833 MET cc_start: 0.7208 (tmm) cc_final: 0.6908 (ppp) REVERT: B 664 MET cc_start: 0.7590 (mtm) cc_final: 0.7236 (mtp) REVERT: B 820 PRO cc_start: 0.8641 (Cg_exo) cc_final: 0.8403 (Cg_endo) REVERT: B 833 MET cc_start: 0.7228 (tmm) cc_final: 0.6909 (ppp) outliers start: 16 outliers final: 13 residues processed: 116 average time/residue: 0.1365 time to fit residues: 25.2702 Evaluate side-chains 114 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 101 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 595 SER Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 831 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.2980 chunk 62 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 0.0870 chunk 9 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 94 optimal weight: 0.1980 chunk 85 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.4980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8792 Z= 0.170 Angle : 0.591 12.183 11980 Z= 0.273 Chirality : 0.038 0.163 1434 Planarity : 0.004 0.054 1402 Dihedral : 8.643 82.599 1808 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.67 % Allowed : 19.31 % Favored : 79.02 % 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: 1.51 (0.26), residues: 1022 helix: 1.74 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -0.42 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 662 HIS 0.002 0.001 HIS A 834 PHE 0.012 0.001 PHE A 836 TYR 0.023 0.001 TYR B 486 ARG 0.003 0.000 ARG B 694 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 106 time to evaluate : 0.994 Fit side-chains REVERT: A 664 MET cc_start: 0.7513 (mtm) cc_final: 0.7167 (mtp) REVERT: A 820 PRO cc_start: 0.8658 (Cg_exo) cc_final: 0.8429 (Cg_endo) REVERT: A 833 MET cc_start: 0.7237 (tmm) cc_final: 0.6952 (ppp) REVERT: B 664 MET cc_start: 0.7472 (mtm) cc_final: 0.7119 (mtp) REVERT: B 820 PRO cc_start: 0.8555 (Cg_exo) cc_final: 0.8329 (Cg_endo) REVERT: B 833 MET cc_start: 0.7245 (tmm) cc_final: 0.6926 (ppp) outliers start: 15 outliers final: 12 residues processed: 115 average time/residue: 0.1449 time to fit residues: 26.4330 Evaluate side-chains 112 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 100 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 831 TRP Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 831 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 28 optimal weight: 0.0980 chunk 82 optimal weight: 0.3980 chunk 86 optimal weight: 0.9980 chunk 91 optimal weight: 0.0170 chunk 60 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8792 Z= 0.179 Angle : 0.604 11.384 11980 Z= 0.276 Chirality : 0.039 0.164 1434 Planarity : 0.004 0.054 1402 Dihedral : 8.466 81.587 1808 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.45 % Allowed : 19.64 % Favored : 78.91 % 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: 1.56 (0.27), residues: 1022 helix: 1.76 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -0.35 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 662 HIS 0.002 0.001 HIS A 834 PHE 0.015 0.001 PHE B 524 TYR 0.028 0.002 TYR A 486 ARG 0.003 0.000 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 102 time to evaluate : 1.017 Fit side-chains REVERT: A 664 MET cc_start: 0.7373 (mtm) cc_final: 0.7061 (mtp) REVERT: A 820 PRO cc_start: 0.8663 (Cg_exo) cc_final: 0.8438 (Cg_endo) REVERT: A 833 MET cc_start: 0.7265 (tmm) cc_final: 0.6961 (ppp) REVERT: B 664 MET cc_start: 0.7455 (mtm) cc_final: 0.7133 (mtp) REVERT: B 820 PRO cc_start: 0.8560 (Cg_exo) cc_final: 0.8341 (Cg_endo) REVERT: B 833 MET cc_start: 0.7255 (tmm) cc_final: 0.6941 (ppp) outliers start: 13 outliers final: 11 residues processed: 110 average time/residue: 0.1425 time to fit residues: 24.8116 Evaluate side-chains 108 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 831 TRP Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 809 ILE Chi-restraints excluded: chain B residue 831 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 49 optimal weight: 0.4980 chunk 64 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 74 optimal weight: 0.0060 chunk 11 optimal weight: 1.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8792 Z= 0.186 Angle : 0.605 11.940 11980 Z= 0.278 Chirality : 0.039 0.199 1434 Planarity : 0.004 0.053 1402 Dihedral : 8.397 80.908 1808 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.23 % Allowed : 20.76 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.27), residues: 1022 helix: 1.80 (0.20), residues: 674 sheet: None (None), residues: 0 loop : -0.25 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 662 HIS 0.002 0.001 HIS A 834 PHE 0.015 0.001 PHE A 524 TYR 0.023 0.002 TYR A 486 ARG 0.003 0.000 ARG A 694 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 1.067 Fit side-chains REVERT: A 664 MET cc_start: 0.7429 (mtm) cc_final: 0.7129 (mtp) REVERT: A 820 PRO cc_start: 0.8580 (Cg_exo) cc_final: 0.8358 (Cg_endo) REVERT: A 833 MET cc_start: 0.7232 (tmm) cc_final: 0.6904 (ppp) REVERT: B 664 MET cc_start: 0.7384 (mtm) cc_final: 0.7085 (mtp) REVERT: B 820 PRO cc_start: 0.8567 (Cg_exo) cc_final: 0.8351 (Cg_endo) REVERT: B 833 MET cc_start: 0.7196 (tmm) cc_final: 0.6874 (ppp) outliers start: 11 outliers final: 11 residues processed: 104 average time/residue: 0.1489 time to fit residues: 24.6711 Evaluate side-chains 106 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 831 TRP Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 809 ILE Chi-restraints excluded: chain B residue 831 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 chunk 54 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.081794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.074120 restraints weight = 28392.301| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 3.35 r_work: 0.3232 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8792 Z= 0.203 Angle : 0.612 11.905 11980 Z= 0.281 Chirality : 0.040 0.190 1434 Planarity : 0.004 0.053 1402 Dihedral : 8.357 80.295 1808 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.45 % Allowed : 20.54 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.27), residues: 1022 helix: 1.77 (0.20), residues: 686 sheet: None (None), residues: 0 loop : -0.26 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 662 HIS 0.002 0.001 HIS A 834 PHE 0.016 0.001 PHE A 836 TYR 0.025 0.002 TYR A 486 ARG 0.002 0.000 ARG A 694 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1919.86 seconds wall clock time: 35 minutes 46.11 seconds (2146.11 seconds total)