Starting phenix.real_space_refine on Thu Aug 6 06:47:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j9x_36118/08_2026/8j9x_36118.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j9x_36118/08_2026/8j9x_36118.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j9x_36118/08_2026/8j9x_36118.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j9x_36118/08_2026/8j9x_36118.map" model { file = "/net/cci-nas-00/data/ceres_data/8j9x_36118/08_2026/8j9x_36118.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j9x_36118/08_2026/8j9x_36118.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.000 sd= 0.025 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 56 5.49 5 Mg 2 5.21 5 S 58 5.16 5 C 8716 2.51 5 N 2402 2.21 5 O 2656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13890 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 778, 6307 Classifications: {'peptide': 778} Link IDs: {'PTRANS': 30, 'TRANS': 747} Chain: "B" Number of atoms: 6307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 778, 6307 Classifications: {'peptide': 778} Link IDs: {'PTRANS': 30, 'TRANS': 747} Chain: "C" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 271 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "E" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 271 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "D" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 338 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Chain: "F" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 338 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'ASW': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'ASW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.46, per 1000 atoms: 0.25 Number of scatterers: 13890 At special positions: 0 Unit cell: (103.75, 120.35, 120.35, 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 58 16.00 P 56 15.00 Mg 2 11.99 O 2656 8.00 N 2402 7.00 C 8716 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 543.6 milliseconds 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2924 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 16 sheets defined 51.5% alpha, 9.8% beta 5 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 428 through 431 Processing helix chain 'A' and resid 439 through 453 removed outlier: 4.144A pdb=" N GLY A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 501 Processing helix chain 'A' and resid 502 through 513 Processing helix chain 'A' and resid 522 through 528 removed outlier: 3.693A pdb=" N ARG A 526 " --> pdb=" O THR A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 560 Processing helix chain 'A' and resid 560 through 566 removed outlier: 3.935A pdb=" N ILE A 564 " --> pdb=" O TRP A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 603 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 621 through 631 Processing helix chain 'A' and resid 644 through 653 removed outlier: 3.592A pdb=" N LEU A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 665 removed outlier: 3.750A pdb=" N GLU A 663 " --> pdb=" O LEU A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 682 Processing helix chain 'A' and resid 687 through 707 removed outlier: 3.783A pdb=" N THR A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LYS A 696 " --> pdb=" O GLN A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 732 removed outlier: 4.541A pdb=" N SER A 731 " --> pdb=" O LYS A 727 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASN A 732 " --> pdb=" O CYS A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 750 Processing helix chain 'A' and resid 755 through 767 Processing helix chain 'A' and resid 806 through 814 Processing helix chain 'A' and resid 815 through 822 Processing helix chain 'A' and resid 842 through 847 removed outlier: 3.722A pdb=" N MET A 846 " --> pdb=" O PRO A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 877 Processing helix chain 'A' and resid 881 through 893 removed outlier: 4.595A pdb=" N LEU A 885 " --> pdb=" O PRO A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 952 Processing helix chain 'A' and resid 955 through 959 removed outlier: 3.502A pdb=" N PHE A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 955 through 959' Processing helix chain 'A' and resid 981 through 991 removed outlier: 4.343A pdb=" N ARG A 985 " --> pdb=" O ASN A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1004 Processing helix chain 'A' and resid 1027 through 1075 removed outlier: 3.768A pdb=" N ILE A1031 " --> pdb=" O SER A1027 " (cutoff:3.500A) Proline residue: A1037 - end of helix removed outlier: 4.413A pdb=" N ALA A1072 " --> pdb=" O ILE A1068 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N GLU A1073 " --> pdb=" O ASN A1069 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASN A1075 " --> pdb=" O SER A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1092 Processing helix chain 'A' and resid 1098 through 1103 Processing helix chain 'A' and resid 1109 through 1118 Processing helix chain 'A' and resid 1122 through 1128 removed outlier: 3.764A pdb=" N LEU A1128 " --> pdb=" O TYR A1124 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1159 Processing helix chain 'A' and resid 1166 through 1187 Processing helix chain 'B' and resid 428 through 431 Processing helix chain 'B' and resid 439 through 453 removed outlier: 4.143A pdb=" N GLY B 453 " --> pdb=" O GLY B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 501 Processing helix chain 'B' and resid 502 through 513 Processing helix chain 'B' and resid 522 through 528 removed outlier: 3.693A pdb=" N ARG B 526 " --> pdb=" O THR B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 560 Processing helix chain 'B' and resid 560 through 566 removed outlier: 3.934A pdb=" N ILE B 564 " --> pdb=" O TRP B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 603 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 621 through 631 Processing helix chain 'B' and resid 644 through 653 removed outlier: 3.592A pdb=" N LEU B 648 " --> pdb=" O SER B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 665 removed outlier: 3.750A pdb=" N GLU B 663 " --> pdb=" O LEU B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 682 Processing helix chain 'B' and resid 687 through 707 removed outlier: 3.783A pdb=" N THR B 695 " --> pdb=" O LEU B 691 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LYS B 696 " --> pdb=" O GLN B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 732 removed outlier: 4.542A pdb=" N SER B 731 " --> pdb=" O LYS B 727 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASN B 732 " --> pdb=" O CYS B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 750 Processing helix chain 'B' and resid 755 through 767 Processing helix chain 'B' and resid 806 through 814 Processing helix chain 'B' and resid 815 through 822 Processing helix chain 'B' and resid 842 through 847 removed outlier: 3.721A pdb=" N MET B 846 " --> pdb=" O PRO B 842 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 877 Processing helix chain 'B' and resid 881 through 893 removed outlier: 4.594A pdb=" N LEU B 885 " --> pdb=" O PRO B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 944 through 952 Processing helix chain 'B' and resid 955 through 959 removed outlier: 3.501A pdb=" N PHE B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 955 through 959' Processing helix chain 'B' and resid 981 through 991 removed outlier: 4.343A pdb=" N ARG B 985 " --> pdb=" O ASN B 981 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1004 Processing helix chain 'B' and resid 1027 through 1075 removed outlier: 3.768A pdb=" N ILE B1031 " --> pdb=" O SER B1027 " (cutoff:3.500A) Proline residue: B1037 - end of helix removed outlier: 4.414A pdb=" N ALA B1072 " --> pdb=" O ILE B1068 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N GLU B1073 " --> pdb=" O ASN B1069 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASN B1075 " --> pdb=" O SER B1071 " (cutoff:3.500A) Processing helix chain 'B' and resid 1081 through 1092 Processing helix chain 'B' and resid 1098 through 1103 Processing helix chain 'B' and resid 1109 through 1118 Processing helix chain 'B' and resid 1122 through 1128 removed outlier: 3.764A pdb=" N LEU B1128 " --> pdb=" O TYR B1124 " (cutoff:3.500A) Processing helix chain 'B' and resid 1134 through 1159 Processing helix chain 'B' and resid 1166 through 1187 Processing sheet with id=AA1, first strand: chain 'A' and resid 468 through 469 removed outlier: 8.323A pdb=" N ILE A 468 " --> pdb=" O MET A 433 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU A 435 " --> pdb=" O ILE A 468 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LEU A 434 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N CYS A 537 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ALA A 436 " --> pdb=" O CYS A 537 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ILE A 534 " --> pdb=" O LYS A 570 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LEU A 572 " --> pdb=" O ILE A 534 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA A 536 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N VAL A 569 " --> pdb=" O PHE A 639 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 577 through 581 Processing sheet with id=AA3, first strand: chain 'A' and resid 736 through 737 Processing sheet with id=AA4, first strand: chain 'A' and resid 824 through 827 removed outlier: 4.451A pdb=" N VAL A 825 " --> pdb=" O ALA A 832 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 850 through 853 Processing sheet with id=AA6, first strand: chain 'A' and resid 909 through 913 Processing sheet with id=AA7, first strand: chain 'A' and resid 924 through 926 removed outlier: 3.528A pdb=" N SER A 926 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE A 932 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 974 " --> pdb=" O ILE A 934 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU A 975 " --> pdb=" O ILE A 963 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ILE A 963 " --> pdb=" O LEU A 975 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LYS A 977 " --> pdb=" O GLU A 961 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1013 through 1016 removed outlier: 4.405A pdb=" N LEU A1013 " --> pdb=" O PHE A1025 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 418 through 419 removed outlier: 6.076A pdb=" N LEU B 434 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N CYS B 537 " --> pdb=" O LEU B 434 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ALA B 436 " --> pdb=" O CYS B 537 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ILE B 534 " --> pdb=" O LYS B 570 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU B 572 " --> pdb=" O ILE B 534 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA B 536 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL B 569 " --> pdb=" O PHE B 639 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 577 through 581 Processing sheet with id=AB2, first strand: chain 'B' and resid 736 through 737 Processing sheet with id=AB3, first strand: chain 'B' and resid 824 through 827 removed outlier: 4.451A pdb=" N VAL B 825 " --> pdb=" O ALA B 832 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 850 through 853 Processing sheet with id=AB5, first strand: chain 'B' and resid 909 through 913 Processing sheet with id=AB6, first strand: chain 'B' and resid 924 through 926 removed outlier: 3.528A pdb=" N SER B 926 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE B 932 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE B 974 " --> pdb=" O ILE B 934 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU B 975 " --> pdb=" O ILE B 963 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ILE B 963 " --> pdb=" O LEU B 975 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LYS B 977 " --> pdb=" O GLU B 961 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1013 through 1016 removed outlier: 4.405A pdb=" N LEU B1013 " --> pdb=" O PHE B1025 " (cutoff:3.500A) 582 hydrogen bonds defined for protein. 1671 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 11 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 2.33 Time building geometry restraints manager: 1.27 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: 2258 1.32 - 1.44: 4159 1.44 - 1.57: 7716 1.57 - 1.69: 111 1.69 - 1.81: 90 Bond restraints: 14334 Sorted by residual: bond pdb=" O3' DG C 8 " pdb=" P DT C 9 " ideal model delta sigma weight residual 1.607 1.549 0.058 1.20e-02 6.94e+03 2.34e+01 bond pdb=" O3' DG C 11 " pdb=" P DG C 12 " ideal model delta sigma weight residual 1.607 1.552 0.055 1.20e-02 6.94e+03 2.07e+01 bond pdb=" N ILE B 707 " pdb=" CA ILE B 707 " ideal model delta sigma weight residual 1.460 1.492 -0.033 7.50e-03 1.78e+04 1.89e+01 bond pdb=" C3' DC D 6 " pdb=" C2' DC D 6 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.28e+01 bond pdb=" O3' DG C 12 " pdb=" P DC C 13 " ideal model delta sigma weight residual 1.607 1.565 0.042 1.20e-02 6.94e+03 1.25e+01 ... (remaining 14329 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 19255 2.09 - 4.18: 340 4.18 - 6.27: 21 6.27 - 8.36: 9 8.36 - 10.45: 3 Bond angle restraints: 19628 Sorted by residual: angle pdb=" C SER A 954 " pdb=" CA SER A 954 " pdb=" CB SER A 954 " ideal model delta sigma weight residual 117.23 109.53 7.70 1.36e+00 5.41e-01 3.21e+01 angle pdb=" C SER B 954 " pdb=" CA SER B 954 " pdb=" CB SER B 954 " ideal model delta sigma weight residual 117.23 109.56 7.67 1.36e+00 5.41e-01 3.18e+01 angle pdb=" O4' DA F 13 " pdb=" C4' DA F 13 " pdb=" C3' DA F 13 " ideal model delta sigma weight residual 106.00 103.25 2.75 6.00e-01 2.78e+00 2.10e+01 angle pdb=" O4' DA C 10 " pdb=" C4' DA C 10 " pdb=" C3' DA C 10 " ideal model delta sigma weight residual 106.00 103.29 2.71 6.00e-01 2.78e+00 2.04e+01 angle pdb=" O4' DA D 13 " pdb=" C4' DA D 13 " pdb=" C3' DA D 13 " ideal model delta sigma weight residual 106.00 103.30 2.70 6.00e-01 2.78e+00 2.02e+01 ... (remaining 19623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.25: 8055 35.25 - 70.49: 330 70.49 - 105.74: 16 105.74 - 140.99: 0 140.99 - 176.23: 3 Dihedral angle restraints: 8404 sinusoidal: 3842 harmonic: 4562 Sorted by residual: dihedral pdb=" C5 ASW D1301 " pdb=" N6 ASW D1301 " pdb=" S7 ASW D1301 " pdb=" O10 ASW D1301 " ideal model delta sinusoidal sigma weight residual -174.31 1.92 -176.23 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CA SER A 853 " pdb=" C SER A 853 " pdb=" N GLU A 854 " pdb=" CA GLU A 854 " ideal model delta harmonic sigma weight residual 180.00 158.32 21.68 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA SER B 853 " pdb=" C SER B 853 " pdb=" N GLU B 854 " pdb=" CA GLU B 854 " ideal model delta harmonic sigma weight residual 180.00 158.36 21.64 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 8401 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1395 0.036 - 0.071: 509 0.071 - 0.107: 175 0.107 - 0.142: 42 0.142 - 0.178: 13 Chirality restraints: 2134 Sorted by residual: chirality pdb=" C3' DT C 9 " pdb=" C4' DT C 9 " pdb=" O3' DT C 9 " pdb=" C2' DT C 9 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.89e-01 chirality pdb=" CA ILE B 707 " pdb=" N ILE B 707 " pdb=" C ILE B 707 " pdb=" CB ILE B 707 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.85e-01 chirality pdb=" CA ILE A 707 " pdb=" N ILE A 707 " pdb=" C ILE A 707 " pdb=" CB ILE A 707 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.47e-01 ... (remaining 2131 not shown) Planarity restraints: 2288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 937 " 0.029 5.00e-02 4.00e+02 4.45e-02 3.16e+00 pdb=" N PRO B 938 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 938 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 938 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 937 " -0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO A 938 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 938 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 938 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 586 " 0.020 5.00e-02 4.00e+02 3.00e-02 1.44e+00 pdb=" N PRO B 587 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO B 587 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 587 " 0.016 5.00e-02 4.00e+02 ... (remaining 2285 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2188 2.76 - 3.29: 13754 3.29 - 3.83: 24321 3.83 - 4.36: 28172 4.36 - 4.90: 46205 Nonbonded interactions: 114640 Sorted by model distance: nonbonded pdb=" OD2 ASP A 541 " pdb="MG MG A1301 " model vdw 2.224 2.170 nonbonded pdb=" NH1 ARG A 660 " pdb=" OP1 DA D 9 " model vdw 2.230 3.120 nonbonded pdb=" O PHE B1094 " pdb=" OH TYR B1122 " model vdw 2.231 3.040 nonbonded pdb=" O PHE A1094 " pdb=" OH TYR A1122 " model vdw 2.231 3.040 nonbonded pdb=" N7 DG C 8 " pdb=" O4 DT C 9 " model vdw 2.269 3.120 ... (remaining 114635 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.330 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: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.460 Find NCS groups from input model: 0.180 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: 0.000 Load rotamer database and sin/cos tables:7.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 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 : 0.004 0.058 14334 Z= 0.291 Angle : 0.621 10.448 19628 Z= 0.414 Chirality : 0.043 0.178 2134 Planarity : 0.003 0.044 2288 Dihedral : 17.549 176.234 5480 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.29 % Allowed : 0.73 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.22), residues: 1552 helix: 1.25 (0.21), residues: 700 sheet: -0.34 (0.40), residues: 192 loop : -0.49 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 863 TYR 0.010 0.001 TYR B 837 PHE 0.013 0.001 PHE A 739 TRP 0.011 0.001 TRP B 560 HIS 0.002 0.000 HIS A 566 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.29 (14334) covalent geometry : angle 0.62105 / 0.41 (19628) hydrogen bonds : bond 0.16200 / 10.44 ( 593) hydrogen bonds : angle 6.08936 / 4.37 ( 1693) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.619 Fit side-chains REVERT: A 537 CYS cc_start: 0.9145 (t) cc_final: 0.8912 (t) REVERT: A 756 MET cc_start: 0.8428 (tpp) cc_final: 0.8182 (tpp) REVERT: A 957 MET cc_start: 0.8838 (mmp) cc_final: 0.8530 (mpt) REVERT: B 635 MET cc_start: 0.8704 (ppp) cc_final: 0.8432 (ppp) REVERT: B 756 MET cc_start: 0.8464 (tpp) cc_final: 0.8256 (tpp) REVERT: B 957 MET cc_start: 0.8789 (mmp) cc_final: 0.8576 (mpt) outliers start: 4 outliers final: 2 residues processed: 70 average time/residue: 0.7535 time to fit residues: 57.4383 Evaluate side-chains 51 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 981 ASN Chi-restraints excluded: chain B residue 981 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.0270 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 476 ASN A 709 ASN A1014 ASN A1099 HIS A1114 ASN B1014 ASN B1114 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.062849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.048907 restraints weight = 69670.911| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 4.25 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14334 Z= 0.133 Angle : 0.598 11.231 19628 Z= 0.326 Chirality : 0.041 0.171 2134 Planarity : 0.004 0.043 2288 Dihedral : 18.599 174.069 2370 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.59 % Allowed : 7.39 % Favored : 92.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.22), residues: 1552 helix: 1.06 (0.20), residues: 712 sheet: -0.58 (0.37), residues: 198 loop : -0.46 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 660 TYR 0.012 0.001 TYR B1122 PHE 0.010 0.001 PHE A 739 TRP 0.009 0.001 TRP A 560 HIS 0.004 0.001 HIS A 887 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 (14334) covalent geometry : angle 0.59837 / 0.33 (19628) hydrogen bonds : bond 0.03927 / 2.63 ( 593) hydrogen bonds : angle 4.93182 / 3.50 ( 1693) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.473 Fit side-chains REVERT: A 635 MET cc_start: 0.8736 (ppp) cc_final: 0.8400 (ppp) REVERT: A 749 MET cc_start: 0.9256 (OUTLIER) cc_final: 0.8259 (mmm) REVERT: A 756 MET cc_start: 0.8622 (tpp) cc_final: 0.8381 (tpp) REVERT: A 957 MET cc_start: 0.9026 (mmp) cc_final: 0.8678 (mpt) REVERT: B 635 MET cc_start: 0.8788 (ppp) cc_final: 0.8373 (ppp) REVERT: B 756 MET cc_start: 0.8695 (tpp) cc_final: 0.8396 (tpp) REVERT: B 957 MET cc_start: 0.8983 (mmp) cc_final: 0.8682 (mpt) outliers start: 8 outliers final: 6 residues processed: 54 average time/residue: 0.6314 time to fit residues: 37.8420 Evaluate side-chains 50 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 981 ASN Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 840 VAL Chi-restraints excluded: chain B residue 981 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 40 optimal weight: 0.0270 chunk 75 optimal weight: 0.8980 chunk 11 optimal weight: 0.0970 chunk 83 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 41 optimal weight: 0.0070 chunk 9 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 17 optimal weight: 0.0980 overall best weight: 0.2254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 476 ASN ** B 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.063437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.049584 restraints weight = 69611.837| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 4.23 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 14334 Z= 0.114 Angle : 0.552 11.079 19628 Z= 0.299 Chirality : 0.040 0.171 2134 Planarity : 0.004 0.048 2288 Dihedral : 18.584 171.169 2370 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.51 % Allowed : 10.76 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.22), residues: 1552 helix: 1.06 (0.20), residues: 710 sheet: -0.61 (0.36), residues: 204 loop : -0.47 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 420 TYR 0.011 0.001 TYR B1122 PHE 0.011 0.001 PHE B 739 TRP 0.008 0.001 TRP B 861 HIS 0.003 0.001 HIS B 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.11 (14334) covalent geometry : angle 0.55155 / 0.30 (19628) hydrogen bonds : bond 0.03382 / 2.24 ( 593) hydrogen bonds : angle 4.59524 / 3.25 ( 1693) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.541 Fit side-chains REVERT: A 635 MET cc_start: 0.8751 (ppp) cc_final: 0.8328 (ppp) REVERT: A 756 MET cc_start: 0.8610 (tpp) cc_final: 0.8307 (tpp) REVERT: A 957 MET cc_start: 0.8969 (mmp) cc_final: 0.8619 (mpt) REVERT: B 756 MET cc_start: 0.8669 (tpp) cc_final: 0.8418 (tpp) REVERT: B 957 MET cc_start: 0.8937 (mmp) cc_final: 0.8656 (mpt) outliers start: 7 outliers final: 4 residues processed: 48 average time/residue: 0.6675 time to fit residues: 35.5483 Evaluate side-chains 46 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 981 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 89 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1099 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.059112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.044606 restraints weight = 70384.536| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 4.15 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 14334 Z= 0.259 Angle : 0.675 10.955 19628 Z= 0.362 Chirality : 0.043 0.225 2134 Planarity : 0.004 0.041 2288 Dihedral : 18.736 175.184 2368 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.02 % Allowed : 12.45 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.22), residues: 1552 helix: 1.19 (0.20), residues: 712 sheet: -0.72 (0.36), residues: 206 loop : -0.60 (0.26), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 929 TYR 0.017 0.002 TYR A1122 PHE 0.022 0.002 PHE A1107 TRP 0.008 0.001 TRP A 560 HIS 0.005 0.001 HIS A 887 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.26 (14334) covalent geometry : angle 0.67495 / 0.36 (19628) hydrogen bonds : bond 0.03812 / 2.53 ( 593) hydrogen bonds : angle 4.51360 / 3.17 ( 1693) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.547 Fit side-chains REVERT: A 635 MET cc_start: 0.8709 (ppp) cc_final: 0.8121 (ppp) REVERT: A 756 MET cc_start: 0.8648 (tpp) cc_final: 0.8369 (tpp) REVERT: A 957 MET cc_start: 0.9089 (mmp) cc_final: 0.8650 (mpt) REVERT: A 1148 MET cc_start: 0.9606 (mtm) cc_final: 0.9207 (ptp) REVERT: B 474 ILE cc_start: 0.9163 (OUTLIER) cc_final: 0.8943 (pp) REVERT: B 635 MET cc_start: 0.8843 (ppp) cc_final: 0.8432 (ppp) REVERT: B 756 MET cc_start: 0.8726 (tpp) cc_final: 0.8453 (tpp) REVERT: B 957 MET cc_start: 0.9064 (mmp) cc_final: 0.8690 (mpt) outliers start: 14 outliers final: 4 residues processed: 52 average time/residue: 0.6059 time to fit residues: 35.2021 Evaluate side-chains 47 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 840 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 57 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 147 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 132 optimal weight: 0.1980 chunk 61 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 ASN ** 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 = 0.3635 r_free = 0.3635 target = 0.060770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.046243 restraints weight = 69669.466| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 4.35 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14334 Z= 0.126 Angle : 0.567 11.479 19628 Z= 0.307 Chirality : 0.040 0.164 2134 Planarity : 0.003 0.039 2288 Dihedral : 18.667 176.388 2366 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.95 % Allowed : 13.40 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.22), residues: 1552 helix: 1.22 (0.20), residues: 714 sheet: -0.70 (0.36), residues: 206 loop : -0.47 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 929 TYR 0.014 0.001 TYR B1122 PHE 0.016 0.001 PHE B1107 TRP 0.008 0.001 TRP B 861 HIS 0.003 0.001 HIS B 887 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.13 (14334) covalent geometry : angle 0.56703 / 0.31 (19628) hydrogen bonds : bond 0.03332 / 2.22 ( 593) hydrogen bonds : angle 4.38086 / 3.10 ( 1693) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.539 Fit side-chains REVERT: A 635 MET cc_start: 0.8663 (ppp) cc_final: 0.8200 (ppp) REVERT: A 756 MET cc_start: 0.8641 (tpp) cc_final: 0.8332 (tpp) REVERT: A 957 MET cc_start: 0.9089 (mmp) cc_final: 0.8646 (mpt) REVERT: A 1148 MET cc_start: 0.9563 (mtm) cc_final: 0.9090 (mtm) REVERT: B 635 MET cc_start: 0.8758 (ppp) cc_final: 0.8163 (ppp) REVERT: B 756 MET cc_start: 0.8731 (tpp) cc_final: 0.8413 (tpp) REVERT: B 957 MET cc_start: 0.9034 (mmp) cc_final: 0.8652 (mpt) REVERT: B 966 TYR cc_start: 0.8901 (m-80) cc_final: 0.8600 (m-80) outliers start: 13 outliers final: 4 residues processed: 52 average time/residue: 0.6210 time to fit residues: 36.0777 Evaluate side-chains 47 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 840 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 27 optimal weight: 4.9990 chunk 17 optimal weight: 0.0060 chunk 2 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 141 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 31 optimal weight: 0.0970 chunk 57 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 476 ASN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.058989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.044392 restraints weight = 69911.682| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 4.27 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14334 Z= 0.198 Angle : 0.608 11.720 19628 Z= 0.328 Chirality : 0.042 0.203 2134 Planarity : 0.004 0.041 2288 Dihedral : 18.763 177.727 2366 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.32 % Allowed : 14.06 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.22), residues: 1552 helix: 1.23 (0.20), residues: 718 sheet: -0.56 (0.39), residues: 182 loop : -0.46 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 929 TYR 0.015 0.002 TYR B 848 PHE 0.019 0.001 PHE B1107 TRP 0.006 0.001 TRP A 560 HIS 0.005 0.001 HIS A 887 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.20 (14334) covalent geometry : angle 0.60776 / 0.33 (19628) hydrogen bonds : bond 0.03532 / 2.35 ( 593) hydrogen bonds : angle 4.38412 / 3.10 ( 1693) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 44 time to evaluate : 0.530 Fit side-chains REVERT: A 635 MET cc_start: 0.8674 (ppp) cc_final: 0.8183 (ppp) REVERT: A 756 MET cc_start: 0.8639 (tpp) cc_final: 0.8414 (tpp) REVERT: A 957 MET cc_start: 0.9117 (mmp) cc_final: 0.8657 (mpt) REVERT: A 1148 MET cc_start: 0.9578 (mtm) cc_final: 0.9138 (mtm) REVERT: B 474 ILE cc_start: 0.9129 (OUTLIER) cc_final: 0.8905 (pp) REVERT: B 635 MET cc_start: 0.8747 (ppp) cc_final: 0.8498 (ppp) REVERT: B 756 MET cc_start: 0.8715 (tpp) cc_final: 0.8484 (tpp) REVERT: B 957 MET cc_start: 0.9050 (mmp) cc_final: 0.8654 (mpt) REVERT: B 966 TYR cc_start: 0.9029 (m-80) cc_final: 0.8796 (m-80) outliers start: 18 outliers final: 4 residues processed: 57 average time/residue: 0.5888 time to fit residues: 37.5082 Evaluate side-chains 48 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 840 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 131 optimal weight: 9.9990 chunk 133 optimal weight: 0.9990 chunk 120 optimal weight: 0.6980 chunk 141 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 ASN ** 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 = 0.3613 r_free = 0.3613 target = 0.059687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.045141 restraints weight = 68457.253| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 4.26 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14334 Z= 0.129 Angle : 0.595 11.979 19628 Z= 0.319 Chirality : 0.041 0.200 2134 Planarity : 0.004 0.040 2288 Dihedral : 18.733 178.157 2366 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.66 % Allowed : 15.15 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.22), residues: 1552 helix: 1.21 (0.20), residues: 714 sheet: -0.47 (0.39), residues: 182 loop : -0.44 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 447 TYR 0.014 0.001 TYR A 848 PHE 0.016 0.001 PHE B1107 TRP 0.008 0.001 TRP A 560 HIS 0.003 0.001 HIS A 887 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (14334) covalent geometry : angle 0.59464 / 0.32 (19628) hydrogen bonds : bond 0.03318 / 2.22 ( 593) hydrogen bonds : angle 4.35617 / 3.09 ( 1693) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.575 Fit side-chains REVERT: A 467 MET cc_start: 0.8472 (mmm) cc_final: 0.8089 (mmt) REVERT: A 635 MET cc_start: 0.8663 (ppp) cc_final: 0.8169 (ppp) REVERT: A 756 MET cc_start: 0.8644 (tpp) cc_final: 0.8342 (tpp) REVERT: A 957 MET cc_start: 0.9097 (mmp) cc_final: 0.8638 (mpt) REVERT: B 467 MET cc_start: 0.8159 (mmm) cc_final: 0.7863 (mmt) REVERT: B 474 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8925 (pp) REVERT: B 635 MET cc_start: 0.8747 (ppp) cc_final: 0.8238 (ppp) REVERT: B 756 MET cc_start: 0.8694 (tpp) cc_final: 0.8379 (tpp) REVERT: B 835 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7382 (mp0) REVERT: B 957 MET cc_start: 0.9047 (mmp) cc_final: 0.8656 (mpt) REVERT: B 966 TYR cc_start: 0.9001 (m-80) cc_final: 0.8770 (m-80) outliers start: 9 outliers final: 5 residues processed: 49 average time/residue: 0.7112 time to fit residues: 38.5078 Evaluate side-chains 50 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 835 GLU Chi-restraints excluded: chain B residue 840 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 18 optimal weight: 9.9990 chunk 152 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 142 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 78 optimal weight: 9.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** 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 = 0.3609 r_free = 0.3609 target = 0.059121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.044469 restraints weight = 68327.846| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 4.29 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14334 Z= 0.169 Angle : 0.605 12.288 19628 Z= 0.325 Chirality : 0.041 0.230 2134 Planarity : 0.004 0.041 2288 Dihedral : 18.782 178.586 2366 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.66 % Allowed : 15.59 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.22), residues: 1552 helix: 1.24 (0.20), residues: 714 sheet: -0.40 (0.39), residues: 182 loop : -0.43 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 929 TYR 0.014 0.001 TYR A 848 PHE 0.017 0.001 PHE B1107 TRP 0.006 0.001 TRP A 560 HIS 0.004 0.001 HIS B 887 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 (14334) covalent geometry : angle 0.60495 / 0.32 (19628) hydrogen bonds : bond 0.03384 / 2.27 ( 593) hydrogen bonds : angle 4.36792 / 3.10 ( 1693) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.490 Fit side-chains REVERT: A 635 MET cc_start: 0.8644 (ppp) cc_final: 0.8095 (ppp) REVERT: A 756 MET cc_start: 0.8643 (tpp) cc_final: 0.8341 (tpp) REVERT: A 957 MET cc_start: 0.9109 (mmp) cc_final: 0.8646 (mpt) REVERT: A 1148 MET cc_start: 0.9639 (mtm) cc_final: 0.9028 (mtm) REVERT: B 474 ILE cc_start: 0.9130 (OUTLIER) cc_final: 0.8912 (pp) REVERT: B 635 MET cc_start: 0.8751 (ppp) cc_final: 0.8248 (ppp) REVERT: B 756 MET cc_start: 0.8698 (tpp) cc_final: 0.8459 (tpp) REVERT: B 835 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7358 (mp0) REVERT: B 957 MET cc_start: 0.9052 (mmp) cc_final: 0.8647 (mpt) REVERT: B 966 TYR cc_start: 0.8989 (m-80) cc_final: 0.8749 (m-80) outliers start: 9 outliers final: 4 residues processed: 48 average time/residue: 0.6604 time to fit residues: 35.1166 Evaluate side-chains 49 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 835 GLU Chi-restraints excluded: chain B residue 840 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 143 optimal weight: 9.9990 chunk 125 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 130 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 96 optimal weight: 9.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.061344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.046378 restraints weight = 74425.311| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 4.47 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14334 Z= 0.151 Angle : 0.612 13.887 19628 Z= 0.324 Chirality : 0.041 0.258 2134 Planarity : 0.004 0.040 2288 Dihedral : 18.825 179.192 2366 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.88 % Allowed : 15.59 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.22), residues: 1552 helix: 1.21 (0.20), residues: 714 sheet: -0.31 (0.40), residues: 182 loop : -0.40 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 495 TYR 0.014 0.001 TYR B 848 PHE 0.016 0.001 PHE B1107 TRP 0.006 0.001 TRP A 861 HIS 0.006 0.001 HIS B 887 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 (14334) covalent geometry : angle 0.61176 / 0.32 (19628) hydrogen bonds : bond 0.03321 / 2.22 ( 593) hydrogen bonds : angle 4.35497 / 3.10 ( 1693) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 635 MET cc_start: 0.8652 (ppp) cc_final: 0.8092 (ppp) REVERT: A 756 MET cc_start: 0.8674 (tpp) cc_final: 0.8367 (tpp) REVERT: A 835 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7412 (mp0) REVERT: A 957 MET cc_start: 0.9217 (mmp) cc_final: 0.8722 (mpt) REVERT: B 635 MET cc_start: 0.8726 (ppp) cc_final: 0.8202 (ppp) REVERT: B 756 MET cc_start: 0.8694 (tpp) cc_final: 0.8341 (tpp) REVERT: B 835 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7380 (mp0) REVERT: B 957 MET cc_start: 0.9140 (mmp) cc_final: 0.8726 (mpt) REVERT: B 966 TYR cc_start: 0.9040 (m-80) cc_final: 0.8789 (m-80) REVERT: B 1148 MET cc_start: 0.9575 (mtm) cc_final: 0.8726 (pmm) outliers start: 12 outliers final: 6 residues processed: 54 average time/residue: 0.7225 time to fit residues: 42.7925 Evaluate side-chains 53 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 835 GLU Chi-restraints excluded: chain B residue 840 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 67 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 117 optimal weight: 0.0050 chunk 26 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 130 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 ASN ** 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 = 0.3622 r_free = 0.3622 target = 0.061856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.047000 restraints weight = 74013.183| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 4.45 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14334 Z= 0.124 Angle : 0.608 12.857 19628 Z= 0.322 Chirality : 0.041 0.274 2134 Planarity : 0.004 0.041 2288 Dihedral : 18.841 179.174 2366 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.66 % Allowed : 15.81 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.22), residues: 1552 helix: 1.16 (0.20), residues: 714 sheet: -0.29 (0.40), residues: 182 loop : -0.37 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 420 TYR 0.016 0.001 TYR B 888 PHE 0.012 0.001 PHE B1107 TRP 0.007 0.001 TRP B 861 HIS 0.003 0.001 HIS B 887 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (14334) covalent geometry : angle 0.60819 / 0.32 (19628) hydrogen bonds : bond 0.03239 / 2.17 ( 593) hydrogen bonds : angle 4.33163 / 3.09 ( 1693) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 635 MET cc_start: 0.8655 (ppp) cc_final: 0.8089 (ppp) REVERT: A 756 MET cc_start: 0.8643 (tpp) cc_final: 0.8347 (tpp) REVERT: A 835 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7440 (mp0) REVERT: A 957 MET cc_start: 0.9182 (mmp) cc_final: 0.8713 (mpt) REVERT: A 1148 MET cc_start: 0.9616 (mtm) cc_final: 0.9248 (mtm) REVERT: B 635 MET cc_start: 0.8724 (ppp) cc_final: 0.8201 (ppp) REVERT: B 749 MET cc_start: 0.9400 (mmm) cc_final: 0.8943 (mtp) REVERT: B 756 MET cc_start: 0.8675 (tpp) cc_final: 0.8375 (tpp) REVERT: B 835 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7393 (mp0) REVERT: B 957 MET cc_start: 0.9109 (mmp) cc_final: 0.8692 (mpt) REVERT: B 966 TYR cc_start: 0.9039 (m-80) cc_final: 0.8791 (m-80) outliers start: 9 outliers final: 4 residues processed: 51 average time/residue: 0.6984 time to fit residues: 39.1081 Evaluate side-chains 51 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 835 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 84 optimal weight: 20.0000 chunk 142 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 120 optimal weight: 0.9990 chunk 133 optimal weight: 0.0570 chunk 78 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 71 optimal weight: 0.1980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 ASN ** 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 = 0.3625 r_free = 0.3625 target = 0.061996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.047172 restraints weight = 74508.973| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 4.47 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 14334 Z= 0.122 Angle : 0.605 13.375 19628 Z= 0.319 Chirality : 0.041 0.292 2134 Planarity : 0.004 0.041 2288 Dihedral : 18.888 178.810 2366 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.81 % Allowed : 15.67 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.22), residues: 1552 helix: 1.19 (0.20), residues: 714 sheet: -0.27 (0.40), residues: 182 loop : -0.39 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 447 TYR 0.012 0.001 TYR B 848 PHE 0.010 0.001 PHE B1107 TRP 0.007 0.001 TRP B 861 HIS 0.003 0.001 HIS B 887 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (14334) covalent geometry : angle 0.60473 / 0.32 (19628) hydrogen bonds : bond 0.03200 / 2.14 ( 593) hydrogen bonds : angle 4.29171 / 3.05 ( 1693) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2820.25 seconds wall clock time: 49 minutes 36.09 seconds (2976.09 seconds total)