Starting phenix.real_space_refine on Fri May 16 05:08:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j9x_36118/05_2025/8j9x_36118.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j9x_36118/05_2025/8j9x_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_36118/05_2025/8j9x_36118.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j9x_36118/05_2025/8j9x_36118.map" model { file = "/net/cci-nas-00/data/ceres_data/8j9x_36118/05_2025/8j9x_36118.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j9x_36118/05_2025/8j9x_36118.cif" } resolution = 3.0 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= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.73, per 1000 atoms: 0.63 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: 3.36 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 4.88 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: 4.68 Time building geometry restraints manager: 3.91 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=" 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=" O3' DG C 8 " pdb=" P DT C 9 " ideal model delta sigma weight residual 1.607 1.549 0.058 1.50e-02 4.44e+03 1.50e+01 bond pdb=" O3' DG C 11 " pdb=" P DG C 12 " ideal model delta sigma weight residual 1.607 1.552 0.055 1.50e-02 4.44e+03 1.33e+01 bond pdb=" N ILE A 474 " pdb=" CA ILE A 474 " ideal model delta sigma weight residual 1.455 1.494 -0.038 1.18e-02 7.18e+03 1.05e+01 bond pdb=" N ILE A 468 " pdb=" CA ILE A 468 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.14e-02 7.69e+03 1.03e+01 ... (remaining 14329 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 19294 2.09 - 4.18: 300 4.18 - 6.27: 23 6.27 - 8.36: 8 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=" C4' DG C 11 " pdb=" C3' DG C 11 " pdb=" O3' DG C 11 " ideal model delta sigma weight residual 110.00 103.00 7.00 1.50e+00 4.44e-01 2.18e+01 angle pdb=" CA SER B 954 " pdb=" C SER B 954 " pdb=" N ASN B 955 " ideal model delta sigma weight residual 119.98 116.28 3.70 8.50e-01 1.38e+00 1.89e+01 angle pdb=" CA SER A 954 " pdb=" C SER A 954 " pdb=" N ASN A 955 " ideal model delta sigma weight residual 119.98 116.28 3.70 8.50e-01 1.38e+00 1.89e+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 - 0.044: 1620 0.044 - 0.088: 400 0.088 - 0.132: 99 0.132 - 0.176: 13 0.176 - 0.220: 2 Chirality restraints: 2134 Sorted by residual: chirality pdb=" C3' DG C 11 " pdb=" C4' DG C 11 " pdb=" O3' DG C 11 " pdb=" C2' DG C 11 " both_signs ideal model delta sigma weight residual False -2.66 -2.88 0.22 2.00e-01 2.50e+01 1.21e+00 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: 0.07 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 35.780 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 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:11.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 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 : 0.003 0.058 14334 Z= 0.187 Angle : 0.593 10.448 19628 Z= 0.335 Chirality : 0.042 0.220 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 (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: 0.43 (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 TRP 0.011 0.001 TRP B 560 HIS 0.002 0.000 HIS A 566 PHE 0.013 0.001 PHE A 739 TYR 0.010 0.001 TYR B 837 ARG 0.003 0.000 ARG A 863 Details of bonding type rmsd hydrogen bonds : bond 0.16200 ( 593) hydrogen bonds : angle 6.08936 ( 1693) covalent geometry : bond 0.00319 (14334) covalent geometry : angle 0.59332 (19628) *********************** 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 : 1.517 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: 0.8529 (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: 1.6237 time to fit residues: 124.0168 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 : 1.526 ------------------------------------------------------------------------------- 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 133 optimal weight: 10.0000 chunk 119 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 143 optimal weight: 0.0270 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN A 709 ASN A1114 ASN B1114 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.065529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.051056 restraints weight = 74238.114| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 4.45 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14334 Z= 0.127 Angle : 0.568 10.363 19628 Z= 0.300 Chirality : 0.039 0.134 2134 Planarity : 0.004 0.043 2288 Dihedral : 18.578 171.083 2370 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.51 % Allowed : 8.13 % Favored : 91.36 % 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: 0.37 (0.22), residues: 1552 helix: 1.19 (0.20), residues: 712 sheet: -0.65 (0.36), residues: 204 loop : -0.44 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 861 HIS 0.003 0.001 HIS B 909 PHE 0.011 0.001 PHE B1107 TYR 0.013 0.001 TYR B1122 ARG 0.004 0.000 ARG B 929 Details of bonding type rmsd hydrogen bonds : bond 0.03382 ( 593) hydrogen bonds : angle 4.54391 ( 1693) covalent geometry : bond 0.00276 (14334) covalent geometry : angle 0.56809 (19628) *********************** 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 60 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 1.432 Fit side-chains REVERT: A 635 MET cc_start: 0.8765 (ppp) cc_final: 0.8387 (ppp) REVERT: A 756 MET cc_start: 0.8625 (tpp) cc_final: 0.8399 (tpp) REVERT: A 957 MET cc_start: 0.9057 (mmp) cc_final: 0.8653 (mpt) REVERT: B 635 MET cc_start: 0.8796 (ppp) cc_final: 0.8340 (ppp) REVERT: B 756 MET cc_start: 0.8709 (tpp) cc_final: 0.8451 (tpp) REVERT: B 957 MET cc_start: 0.9057 (mmp) cc_final: 0.8695 (mpt) outliers start: 7 outliers final: 4 residues processed: 54 average time/residue: 1.3450 time to fit residues: 80.6349 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 : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 981 ASN Chi-restraints excluded: chain B residue 782 ILE 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 136 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 129 optimal weight: 0.0050 chunk 25 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 106 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 overall best weight: 1.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN A1099 HIS ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.059028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.044661 restraints weight = 68625.074| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 4.16 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14334 Z= 0.175 Angle : 0.592 12.516 19628 Z= 0.313 Chirality : 0.041 0.161 2134 Planarity : 0.004 0.038 2288 Dihedral : 18.652 177.523 2370 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.59 % Allowed : 11.35 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.22), residues: 1552 helix: 1.25 (0.20), residues: 718 sheet: -0.71 (0.39), residues: 182 loop : -0.60 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 560 HIS 0.003 0.001 HIS B 650 PHE 0.021 0.001 PHE B1107 TYR 0.016 0.001 TYR B1122 ARG 0.005 0.000 ARG B 863 Details of bonding type rmsd hydrogen bonds : bond 0.03622 ( 593) hydrogen bonds : angle 4.31794 ( 1693) covalent geometry : bond 0.00385 (14334) covalent geometry : angle 0.59249 (19628) *********************** 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 53 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 1.493 Fit side-chains REVERT: A 635 MET cc_start: 0.8685 (ppp) cc_final: 0.8115 (ppp) REVERT: A 756 MET cc_start: 0.8666 (tpp) cc_final: 0.8434 (tpp) REVERT: A 957 MET cc_start: 0.9137 (mmp) cc_final: 0.8712 (mpt) REVERT: B 635 MET cc_start: 0.8803 (ppp) cc_final: 0.8296 (ppp) REVERT: B 756 MET cc_start: 0.8706 (tpp) cc_final: 0.8472 (tpp) REVERT: B 957 MET cc_start: 0.9086 (mmp) cc_final: 0.8682 (mpt) outliers start: 8 outliers final: 5 residues processed: 49 average time/residue: 1.3261 time to fit residues: 72.6663 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 : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 838 VAL 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 21 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 52 optimal weight: 0.0670 chunk 43 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 133 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3576 r_free = 0.3576 target = 0.059223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.044902 restraints weight = 68402.124| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 4.11 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14334 Z= 0.133 Angle : 0.552 12.252 19628 Z= 0.291 Chirality : 0.039 0.163 2134 Planarity : 0.003 0.040 2288 Dihedral : 18.676 177.433 2368 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.32 % Allowed : 12.59 % Favored : 86.09 % 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: 0.42 (0.22), residues: 1552 helix: 1.29 (0.20), residues: 714 sheet: -0.64 (0.39), residues: 182 loop : -0.50 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 861 HIS 0.010 0.001 HIS A1099 PHE 0.012 0.001 PHE B1107 TYR 0.012 0.001 TYR A 848 ARG 0.002 0.000 ARG A 578 Details of bonding type rmsd hydrogen bonds : bond 0.03185 ( 593) hydrogen bonds : angle 4.21379 ( 1693) covalent geometry : bond 0.00293 (14334) covalent geometry : angle 0.55244 (19628) *********************** 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 63 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 45 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 MET cc_start: 0.8710 (ppp) cc_final: 0.8270 (ppp) REVERT: A 756 MET cc_start: 0.8605 (tpp) cc_final: 0.8326 (tpp) REVERT: A 835 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7372 (mp0) REVERT: A 957 MET cc_start: 0.9080 (mmp) cc_final: 0.8660 (mpt) REVERT: B 474 ILE cc_start: 0.9130 (OUTLIER) cc_final: 0.8899 (pp) REVERT: B 635 MET cc_start: 0.8818 (ppp) cc_final: 0.8290 (ppp) REVERT: B 756 MET cc_start: 0.8614 (tpp) cc_final: 0.8332 (tpp) REVERT: B 835 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7381 (mp0) REVERT: B 860 THR cc_start: 0.9222 (OUTLIER) cc_final: 0.8855 (p) REVERT: B 957 MET cc_start: 0.9021 (mmp) cc_final: 0.8593 (mpt) outliers start: 18 outliers final: 3 residues processed: 59 average time/residue: 1.4727 time to fit residues: 95.6370 Evaluate side-chains 51 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 740 GLN Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 835 GLU 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 860 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 62 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 102 optimal weight: 8.9990 chunk 129 optimal weight: 0.0980 chunk 79 optimal weight: 7.9990 chunk 145 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 557 HIS ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.056416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.041903 restraints weight = 68310.022| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 4.08 r_work: 0.2846 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14334 Z= 0.199 Angle : 0.614 12.584 19628 Z= 0.326 Chirality : 0.042 0.181 2134 Planarity : 0.004 0.035 2288 Dihedral : 18.943 179.669 2366 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.34 % Allowed : 13.47 % 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 (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: 0.38 (0.22), residues: 1552 helix: 1.23 (0.20), residues: 716 sheet: -0.83 (0.35), residues: 210 loop : -0.39 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 560 HIS 0.007 0.001 HIS A1099 PHE 0.026 0.002 PHE B1107 TYR 0.018 0.002 TYR A 848 ARG 0.004 0.000 ARG B 736 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 593) hydrogen bonds : angle 4.32476 ( 1693) covalent geometry : bond 0.00443 (14334) covalent geometry : angle 0.61426 (19628) *********************** 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 81 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 49 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 MET cc_start: 0.8671 (ppp) cc_final: 0.8121 (ppp) REVERT: A 756 MET cc_start: 0.9060 (tpp) cc_final: 0.8787 (tpp) REVERT: A 835 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7938 (mp0) REVERT: A 957 MET cc_start: 0.9207 (mmp) cc_final: 0.8765 (mpt) REVERT: A 1148 MET cc_start: 0.9710 (mtm) cc_final: 0.9134 (mtm) REVERT: B 474 ILE cc_start: 0.9246 (OUTLIER) cc_final: 0.9019 (pp) REVERT: B 635 MET cc_start: 0.8788 (ppp) cc_final: 0.8174 (ppp) REVERT: B 756 MET cc_start: 0.9064 (tpp) cc_final: 0.8790 (tpp) REVERT: B 835 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7904 (mp0) REVERT: B 957 MET cc_start: 0.9166 (mmp) cc_final: 0.8703 (mpt) outliers start: 32 outliers final: 7 residues processed: 70 average time/residue: 1.4537 time to fit residues: 112.6797 Evaluate side-chains 55 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 1.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 740 GLN Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 838 VAL 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 838 VAL 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 0 optimal weight: 10.0000 chunk 154 optimal weight: 3.9990 chunk 119 optimal weight: 0.6980 chunk 50 optimal weight: 7.9990 chunk 76 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 47 optimal weight: 0.0020 chunk 150 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3548 r_free = 0.3548 target = 0.057925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.043609 restraints weight = 69123.385| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 4.10 r_work: 0.2902 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.2922 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 : 0.569 12.927 19628 Z= 0.299 Chirality : 0.040 0.161 2134 Planarity : 0.003 0.037 2288 Dihedral : 18.951 178.299 2366 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.81 % Allowed : 16.03 % Favored : 83.16 % 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: 0.45 (0.22), residues: 1552 helix: 1.22 (0.20), residues: 720 sheet: -0.58 (0.38), residues: 182 loop : -0.39 (0.26), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 861 HIS 0.007 0.001 HIS A1099 PHE 0.011 0.001 PHE B1107 TYR 0.012 0.001 TYR A 698 ARG 0.002 0.000 ARG B 863 Details of bonding type rmsd hydrogen bonds : bond 0.03210 ( 593) hydrogen bonds : angle 4.21395 ( 1693) covalent geometry : bond 0.00277 (14334) covalent geometry : angle 0.56879 (19628) *********************** 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 59 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 1.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 MET cc_start: 0.8647 (ppp) cc_final: 0.8054 (ppp) REVERT: A 756 MET cc_start: 0.9001 (tpp) cc_final: 0.8725 (tpp) REVERT: A 835 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7939 (mp0) REVERT: A 957 MET cc_start: 0.9188 (mmp) cc_final: 0.8750 (mpt) REVERT: B 467 MET cc_start: 0.8341 (mmm) cc_final: 0.8141 (mmt) REVERT: B 474 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.9033 (pp) REVERT: B 635 MET cc_start: 0.8773 (ppp) cc_final: 0.8154 (ppp) REVERT: B 756 MET cc_start: 0.9019 (tpp) cc_final: 0.8733 (tpp) REVERT: B 835 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7950 (mp0) REVERT: B 957 MET cc_start: 0.9138 (mmp) cc_final: 0.8688 (mpt) outliers start: 11 outliers final: 1 residues processed: 53 average time/residue: 1.5236 time to fit residues: 89.1497 Evaluate side-chains 49 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 740 GLN Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 835 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 101 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 153 optimal weight: 0.8980 chunk 128 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 chunk 139 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 ASN B 748 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.055481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.040919 restraints weight = 67792.862| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 4.09 r_work: 0.2829 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14334 Z= 0.195 Angle : 0.612 13.333 19628 Z= 0.322 Chirality : 0.041 0.162 2134 Planarity : 0.004 0.035 2288 Dihedral : 19.291 178.454 2366 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.73 % Allowed : 16.47 % Favored : 82.80 % 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: 0.37 (0.22), residues: 1552 helix: 1.21 (0.20), residues: 718 sheet: -0.64 (0.39), residues: 182 loop : -0.50 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 560 HIS 0.006 0.001 HIS A1099 PHE 0.026 0.002 PHE B1107 TYR 0.017 0.002 TYR A 848 ARG 0.003 0.000 ARG A 831 Details of bonding type rmsd hydrogen bonds : bond 0.03507 ( 593) hydrogen bonds : angle 4.27104 ( 1693) covalent geometry : bond 0.00433 (14334) covalent geometry : angle 0.61158 (19628) *********************** 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 55 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 MET cc_start: 0.8647 (ppp) cc_final: 0.8038 (ppp) REVERT: A 756 MET cc_start: 0.9059 (tpp) cc_final: 0.8787 (tpp) REVERT: A 835 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7921 (mp0) REVERT: A 957 MET cc_start: 0.9218 (mmp) cc_final: 0.8759 (mpt) REVERT: A 1148 MET cc_start: 0.9737 (mtm) cc_final: 0.9147 (mtm) REVERT: B 467 MET cc_start: 0.8490 (mmm) cc_final: 0.8245 (mmm) REVERT: B 474 ILE cc_start: 0.9273 (OUTLIER) cc_final: 0.9072 (pp) REVERT: B 635 MET cc_start: 0.8766 (ppp) cc_final: 0.8082 (ppp) REVERT: B 756 MET cc_start: 0.9043 (tpp) cc_final: 0.8772 (tpp) REVERT: B 835 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7913 (mp0) REVERT: B 957 MET cc_start: 0.9229 (mmp) cc_final: 0.8789 (mpt) REVERT: B 1148 MET cc_start: 0.9663 (mtm) cc_final: 0.9366 (mtm) outliers start: 10 outliers final: 3 residues processed: 52 average time/residue: 1.5352 time to fit residues: 88.0122 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 : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 740 GLN Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 835 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 131 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 chunk 125 optimal weight: 0.0970 chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 130 optimal weight: 0.9990 chunk 36 optimal weight: 0.0980 chunk 59 optimal weight: 4.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3542 r_free = 0.3542 target = 0.057263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.042731 restraints weight = 67253.751| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 4.19 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14334 Z= 0.115 Angle : 0.578 13.137 19628 Z= 0.297 Chirality : 0.040 0.162 2134 Planarity : 0.003 0.039 2288 Dihedral : 19.132 172.555 2366 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.02 % Allowed : 16.76 % Favored : 82.21 % 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: 0.46 (0.22), residues: 1552 helix: 1.22 (0.20), residues: 718 sheet: -0.53 (0.39), residues: 182 loop : -0.38 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 861 HIS 0.007 0.001 HIS A1099 PHE 0.010 0.001 PHE A 739 TYR 0.011 0.001 TYR B 888 ARG 0.004 0.000 ARG B 495 Details of bonding type rmsd hydrogen bonds : bond 0.03125 ( 593) hydrogen bonds : angle 4.15727 ( 1693) covalent geometry : bond 0.00257 (14334) covalent geometry : angle 0.57791 (19628) *********************** 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 61 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 MET cc_start: 0.9029 (mmm) cc_final: 0.8497 (mmt) REVERT: A 635 MET cc_start: 0.8699 (ppp) cc_final: 0.8099 (ppp) REVERT: A 756 MET cc_start: 0.8599 (tpp) cc_final: 0.8332 (tpp) REVERT: A 835 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7392 (mp0) REVERT: A 957 MET cc_start: 0.9069 (mmp) cc_final: 0.8674 (mpt) REVERT: A 1060 MET cc_start: 0.9065 (tmm) cc_final: 0.8265 (pp-130) REVERT: B 635 MET cc_start: 0.8771 (ppp) cc_final: 0.8461 (ppp) REVERT: B 756 MET cc_start: 0.8572 (tpp) cc_final: 0.8337 (tpp) REVERT: B 835 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7387 (mp0) REVERT: B 957 MET cc_start: 0.9068 (mmp) cc_final: 0.8668 (mpt) REVERT: B 1060 MET cc_start: 0.9065 (tmm) cc_final: 0.8287 (pp-130) REVERT: B 1148 MET cc_start: 0.9597 (mtm) cc_final: 0.9235 (mtm) outliers start: 14 outliers final: 1 residues processed: 56 average time/residue: 1.4681 time to fit residues: 90.6796 Evaluate side-chains 47 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 740 GLN Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain B residue 835 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 97 optimal weight: 9.9990 chunk 75 optimal weight: 0.0980 chunk 109 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 20 optimal weight: 10.0000 chunk 154 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 3 optimal weight: 0.4980 chunk 70 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3541 r_free = 0.3541 target = 0.057354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.042931 restraints weight = 67490.295| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 4.14 r_work: 0.2903 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14334 Z= 0.120 Angle : 0.566 13.257 19628 Z= 0.295 Chirality : 0.039 0.158 2134 Planarity : 0.003 0.037 2288 Dihedral : 19.185 173.416 2366 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.51 % Allowed : 17.72 % Favored : 81.77 % 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: 0.52 (0.22), residues: 1552 helix: 1.26 (0.20), residues: 720 sheet: -0.32 (0.42), residues: 158 loop : -0.40 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 861 HIS 0.006 0.001 HIS A1099 PHE 0.011 0.001 PHE B1107 TYR 0.016 0.001 TYR A 966 ARG 0.002 0.000 ARG B 447 Details of bonding type rmsd hydrogen bonds : bond 0.03014 ( 593) hydrogen bonds : angle 4.10284 ( 1693) covalent geometry : bond 0.00268 (14334) covalent geometry : angle 0.56585 (19628) *********************** 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: 7 poor density : 51 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 635 MET cc_start: 0.8653 (ppp) cc_final: 0.8020 (ppp) REVERT: A 756 MET cc_start: 0.9009 (tpp) cc_final: 0.8734 (tpp) REVERT: A 957 MET cc_start: 0.9126 (mmp) cc_final: 0.8702 (mpt) REVERT: A 1148 MET cc_start: 0.9733 (mtm) cc_final: 0.9482 (ptp) REVERT: B 635 MET cc_start: 0.8762 (ppp) cc_final: 0.8448 (ppp) REVERT: B 756 MET cc_start: 0.9017 (tpp) cc_final: 0.8733 (tpp) REVERT: B 835 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7895 (mp0) REVERT: B 957 MET cc_start: 0.9112 (mmp) cc_final: 0.8695 (mpt) REVERT: B 1148 MET cc_start: 0.9665 (mtm) cc_final: 0.9210 (mtm) outliers start: 7 outliers final: 3 residues processed: 56 average time/residue: 1.3925 time to fit residues: 86.7003 Evaluate side-chains 49 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 740 GLN Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain B residue 835 GLU Chi-restraints excluded: chain B residue 909 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 56 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 126 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 125 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 456 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.055082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.040623 restraints weight = 68205.949| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 4.10 r_work: 0.2819 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14334 Z= 0.208 Angle : 0.634 13.305 19628 Z= 0.328 Chirality : 0.042 0.183 2134 Planarity : 0.004 0.036 2288 Dihedral : 19.171 177.839 2366 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.44 % Allowed : 18.16 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.22), residues: 1552 helix: 1.23 (0.20), residues: 720 sheet: -0.42 (0.42), residues: 158 loop : -0.49 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 861 HIS 0.005 0.001 HIS A1099 PHE 0.025 0.001 PHE A1107 TYR 0.016 0.002 TYR A 848 ARG 0.005 0.000 ARG A1046 Details of bonding type rmsd hydrogen bonds : bond 0.03458 ( 593) hydrogen bonds : angle 4.23474 ( 1693) covalent geometry : bond 0.00464 (14334) covalent geometry : angle 0.63380 (19628) ********************** 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 51 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 MET cc_start: 0.8639 (ppp) cc_final: 0.7993 (ppp) REVERT: A 756 MET cc_start: 0.9048 (tpp) cc_final: 0.8719 (tpp) REVERT: A 957 MET cc_start: 0.9245 (mmp) cc_final: 0.8777 (mpt) REVERT: A 1148 MET cc_start: 0.9758 (mtm) cc_final: 0.9543 (mtm) REVERT: B 467 MET cc_start: 0.8516 (mmm) cc_final: 0.8096 (mmm) REVERT: B 635 MET cc_start: 0.8705 (ppp) cc_final: 0.8380 (ppp) REVERT: B 756 MET cc_start: 0.9037 (tpp) cc_final: 0.8709 (tpp) REVERT: B 835 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7910 (mp0) REVERT: B 957 MET cc_start: 0.9090 (mmp) cc_final: 0.8634 (mpt) REVERT: B 1148 MET cc_start: 0.9676 (mtm) cc_final: 0.9204 (mtm) outliers start: 6 outliers final: 4 residues processed: 51 average time/residue: 1.5181 time to fit residues: 85.3687 Evaluate side-chains 46 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 740 GLN Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 1050 GLU Chi-restraints excluded: chain B residue 835 GLU Chi-restraints excluded: chain B residue 909 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 86 optimal weight: 0.7980 chunk 113 optimal weight: 0.7980 chunk 7 optimal weight: 20.0000 chunk 154 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3515 r_free = 0.3515 target = 0.056183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.041798 restraints weight = 68185.454| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 4.11 r_work: 0.2867 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.3536 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= 0.130 Angle : 0.586 13.268 19628 Z= 0.302 Chirality : 0.040 0.187 2134 Planarity : 0.003 0.038 2288 Dihedral : 19.051 178.878 2366 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.66 % Allowed : 17.79 % Favored : 81.55 % 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: 0.50 (0.22), residues: 1552 helix: 1.23 (0.20), residues: 716 sheet: -0.22 (0.39), residues: 178 loop : -0.42 (0.26), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 861 HIS 0.006 0.001 HIS A1099 PHE 0.011 0.001 PHE A1107 TYR 0.014 0.001 TYR B 966 ARG 0.002 0.000 ARG A 863 Details of bonding type rmsd hydrogen bonds : bond 0.03226 ( 593) hydrogen bonds : angle 4.16215 ( 1693) covalent geometry : bond 0.00293 (14334) covalent geometry : angle 0.58586 (19628) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6898.22 seconds wall clock time: 120 minutes 38.48 seconds (7238.48 seconds total)