Starting phenix.real_space_refine on Thu Jun 12 15:01:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j9x_36118/06_2025/8j9x_36118.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j9x_36118/06_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_36118/06_2025/8j9x_36118.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j9x_36118/06_2025/8j9x_36118.map" model { file = "/net/cci-nas-00/data/ceres_data/8j9x_36118/06_2025/8j9x_36118.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j9x_36118/06_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 9.19, per 1000 atoms: 0.66 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: 3.39 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: 4.44 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: 4.59 Time building geometry restraints manager: 4.02 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: 0.06 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: 3.670 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: 0.100 Set scattering table: 0.110 Process input model: 36.040 Find NCS groups from input model: 0.480 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: 0.000 Load rotamer database and sin/cos tables:11.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.840 ------------------------------------------------------------------------------- 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 : 1.402 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: 1.6002 time to fit residues: 122.3316 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 : 1.620 ------------------------------------------------------------------------------- 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 = 49)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.051055 restraints weight = 74238.114| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 4.45 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 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 : 1.463 Fit side-chains REVERT: A 635 MET cc_start: 0.8763 (ppp) cc_final: 0.8385 (ppp) REVERT: A 756 MET cc_start: 0.8626 (tpp) cc_final: 0.8399 (tpp) REVERT: A 957 MET cc_start: 0.9059 (mmp) cc_final: 0.8654 (mpt) REVERT: B 635 MET cc_start: 0.8794 (ppp) cc_final: 0.8339 (ppp) REVERT: B 756 MET cc_start: 0.8712 (tpp) cc_final: 0.8452 (tpp) REVERT: B 957 MET cc_start: 0.9059 (mmp) cc_final: 0.8697 (mpt) outliers start: 7 outliers final: 4 residues processed: 54 average time/residue: 1.3289 time to fit residues: 80.0858 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 : 1.624 ------------------------------------------------------------------------------- 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: 0.0970 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 overall best weight: 0.7194 ------------------------------------------------------------------------------- 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 502 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 = 0.3678 r_free = 0.3678 target = 0.064469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.049933 restraints weight = 73900.808| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 4.46 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1669 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= 0.121 Angle : 0.544 12.896 19628 Z= 0.286 Chirality : 0.039 0.168 2134 Planarity : 0.003 0.038 2288 Dihedral : 18.507 171.761 2370 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.29 % Allowed : 10.98 % 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 (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: 1.24 (0.20), residues: 716 sheet: -0.69 (0.36), residues: 206 loop : -0.47 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 861 HIS 0.002 0.001 HIS A 887 PHE 0.011 0.001 PHE B1107 TYR 0.012 0.001 TYR B1122 ARG 0.003 0.000 ARG A 863 Details of bonding type rmsd hydrogen bonds : bond 0.03229 ( 593) hydrogen bonds : angle 4.24477 ( 1693) covalent geometry : bond 0.00267 (14334) covalent geometry : angle 0.54357 (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 49 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 1.569 Fit side-chains revert: symmetry clash REVERT: A 635 MET cc_start: 0.8682 (ppp) cc_final: 0.8361 (ppp) REVERT: A 756 MET cc_start: 0.8624 (tpp) cc_final: 0.8317 (tpp) REVERT: A 957 MET cc_start: 0.9092 (mmp) cc_final: 0.8672 (mpt) REVERT: B 635 MET cc_start: 0.8768 (ppp) cc_final: 0.8338 (ppp) REVERT: B 756 MET cc_start: 0.8706 (tpp) cc_final: 0.8443 (tpp) REVERT: B 957 MET cc_start: 0.9049 (mmp) cc_final: 0.8678 (mpt) outliers start: 4 outliers final: 3 residues processed: 46 average time/residue: 1.4440 time to fit residues: 74.0935 Evaluate side-chains 46 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 1.544 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 21 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 82 optimal weight: 8.9990 chunk 139 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 69 optimal weight: 0.4980 chunk 133 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.059538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.045222 restraints weight = 68883.995| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 4.25 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14334 Z= 0.159 Angle : 0.568 12.607 19628 Z= 0.299 Chirality : 0.040 0.161 2134 Planarity : 0.004 0.039 2288 Dihedral : 18.593 172.960 2366 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.02 % Allowed : 12.01 % Favored : 86.97 % 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: 1.32 (0.20), residues: 718 sheet: -0.66 (0.38), residues: 182 loop : -0.54 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 560 HIS 0.003 0.001 HIS B 887 PHE 0.017 0.001 PHE B1107 TYR 0.014 0.001 TYR A 837 ARG 0.004 0.000 ARG B 929 Details of bonding type rmsd hydrogen bonds : bond 0.03231 ( 593) hydrogen bonds : angle 4.16941 ( 1693) covalent geometry : bond 0.00352 (14334) covalent geometry : angle 0.56756 (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 59 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 1.698 Fit side-chains REVERT: A 635 MET cc_start: 0.8671 (ppp) cc_final: 0.8042 (ppp) REVERT: A 756 MET cc_start: 0.8644 (tpp) cc_final: 0.8332 (tpp) REVERT: A 957 MET cc_start: 0.9108 (mmp) cc_final: 0.8670 (mpt) REVERT: A 1148 MET cc_start: 0.9615 (mtm) cc_final: 0.8983 (mtm) REVERT: B 474 ILE cc_start: 0.9123 (OUTLIER) cc_final: 0.8896 (pp) REVERT: B 635 MET cc_start: 0.8788 (ppp) cc_final: 0.8283 (ppp) REVERT: B 756 MET cc_start: 0.8702 (tpp) cc_final: 0.8391 (tpp) REVERT: B 957 MET cc_start: 0.9051 (mmp) cc_final: 0.8664 (mpt) outliers start: 14 outliers final: 4 residues processed: 54 average time/residue: 1.4821 time to fit residues: 89.8785 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 : 1.524 ------------------------------------------------------------------------------- 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 474 ILE Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 838 VAL 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: 0.9990 chunk 115 optimal weight: 8.9990 chunk 42 optimal weight: 0.3980 chunk 13 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 145 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3558 r_free = 0.3558 target = 0.058404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.043956 restraints weight = 68981.573| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 4.13 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14334 Z= 0.156 Angle : 0.580 12.948 19628 Z= 0.303 Chirality : 0.040 0.217 2134 Planarity : 0.004 0.041 2288 Dihedral : 18.724 175.851 2366 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.76 % Allowed : 13.10 % Favored : 85.14 % 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: 1.30 (0.20), residues: 718 sheet: -0.61 (0.38), residues: 182 loop : -0.49 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 560 HIS 0.003 0.001 HIS A 887 PHE 0.016 0.001 PHE B1107 TYR 0.014 0.001 TYR A 848 ARG 0.003 0.000 ARG B 447 Details of bonding type rmsd hydrogen bonds : bond 0.03248 ( 593) hydrogen bonds : angle 4.18624 ( 1693) covalent geometry : bond 0.00345 (14334) covalent geometry : angle 0.57958 (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 70 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 46 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 MET cc_start: 0.8562 (mmm) cc_final: 0.8236 (mmt) REVERT: A 635 MET cc_start: 0.8699 (ppp) cc_final: 0.8220 (ppp) REVERT: A 756 MET cc_start: 0.8622 (tpp) cc_final: 0.8389 (tpp) REVERT: A 835 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7377 (mp0) REVERT: A 957 MET cc_start: 0.9093 (mmp) cc_final: 0.8683 (mpt) REVERT: B 474 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8904 (pp) REVERT: B 635 MET cc_start: 0.8812 (ppp) cc_final: 0.8251 (ppp) REVERT: B 756 MET cc_start: 0.8629 (tpp) cc_final: 0.8299 (tpp) REVERT: B 835 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7335 (mp0) REVERT: B 957 MET cc_start: 0.9047 (mmp) cc_final: 0.8632 (mpt) outliers start: 24 outliers final: 7 residues processed: 63 average time/residue: 1.6208 time to fit residues: 111.9848 Evaluate side-chains 53 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 1.753 ------------------------------------------------------------------------------- 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 740 GLN 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=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: 0.9980 chunk 50 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 150 optimal weight: 0.6980 chunk 8 optimal weight: 0.4980 chunk 11 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.056368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.041896 restraints weight = 68684.009| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 4.05 r_work: 0.2851 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14334 Z= 0.187 Angle : 0.608 13.119 19628 Z= 0.319 Chirality : 0.041 0.160 2134 Planarity : 0.004 0.035 2288 Dihedral : 19.005 177.066 2366 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.61 % Allowed : 14.49 % Favored : 83.89 % 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: 0.40 (0.22), residues: 1552 helix: 1.26 (0.20), residues: 718 sheet: -0.64 (0.38), residues: 182 loop : -0.50 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 560 HIS 0.012 0.001 HIS A1099 PHE 0.022 0.001 PHE B1107 TYR 0.017 0.002 TYR A 848 ARG 0.004 0.000 ARG B 420 Details of bonding type rmsd hydrogen bonds : bond 0.03462 ( 593) hydrogen bonds : angle 4.21337 ( 1693) covalent geometry : bond 0.00416 (14334) covalent geometry : angle 0.60765 (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 70 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 48 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 MET cc_start: 0.8645 (ppp) cc_final: 0.8047 (ppp) REVERT: A 756 MET cc_start: 0.9023 (tpp) cc_final: 0.8756 (tpp) REVERT: A 835 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7959 (mp0) REVERT: A 957 MET cc_start: 0.9209 (mmp) cc_final: 0.8774 (mpt) REVERT: A 1148 MET cc_start: 0.9733 (mtm) cc_final: 0.9204 (mtm) REVERT: B 467 MET cc_start: 0.8485 (mmm) cc_final: 0.8146 (mmm) REVERT: B 474 ILE cc_start: 0.9264 (OUTLIER) cc_final: 0.9044 (pp) REVERT: B 635 MET cc_start: 0.8768 (ppp) cc_final: 0.8166 (ppp) REVERT: B 756 MET cc_start: 0.9047 (tpp) cc_final: 0.8773 (tpp) REVERT: B 835 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7933 (mp0) REVERT: B 957 MET cc_start: 0.9187 (mmp) cc_final: 0.8766 (mpt) outliers start: 22 outliers final: 8 residues processed: 63 average time/residue: 1.4290 time to fit residues: 99.6224 Evaluate side-chains 52 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 1.485 ------------------------------------------------------------------------------- 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 740 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 101 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 chunk 139 optimal weight: 0.4980 chunk 63 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3537 r_free = 0.3537 target = 0.057332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.042961 restraints weight = 68065.112| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 4.08 r_work: 0.2887 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.3042 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 : 0.566 12.855 19628 Z= 0.297 Chirality : 0.040 0.160 2134 Planarity : 0.003 0.037 2288 Dihedral : 19.073 179.403 2366 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.02 % Allowed : 16.18 % 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: 0.46 (0.22), residues: 1552 helix: 1.25 (0.20), residues: 718 sheet: -0.57 (0.38), residues: 182 loop : -0.40 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 861 HIS 0.009 0.001 HIS A1099 PHE 0.011 0.001 PHE B1107 TYR 0.013 0.001 TYR A 848 ARG 0.004 0.000 ARG A 985 Details of bonding type rmsd hydrogen bonds : bond 0.03176 ( 593) hydrogen bonds : angle 4.14160 ( 1693) covalent geometry : bond 0.00290 (14334) covalent geometry : angle 0.56572 (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 59 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 1.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 MET cc_start: 0.8811 (mmm) cc_final: 0.8542 (mmt) REVERT: A 635 MET cc_start: 0.8667 (ppp) cc_final: 0.8057 (ppp) REVERT: A 756 MET cc_start: 0.8998 (tpp) cc_final: 0.8679 (tpp) REVERT: A 835 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7929 (mp0) REVERT: A 957 MET cc_start: 0.9136 (mmp) cc_final: 0.8714 (mpt) REVERT: A 1060 MET cc_start: 0.9259 (tmm) cc_final: 0.8514 (pp-130) REVERT: B 467 MET cc_start: 0.8425 (mmm) cc_final: 0.8021 (mmm) REVERT: B 635 MET cc_start: 0.8757 (ppp) cc_final: 0.8485 (ppp) REVERT: B 756 MET cc_start: 0.9012 (tpp) cc_final: 0.8734 (tpp) REVERT: B 835 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7938 (mp0) REVERT: B 957 MET cc_start: 0.9092 (mmp) cc_final: 0.8664 (mpt) outliers start: 14 outliers final: 3 residues processed: 51 average time/residue: 1.8067 time to fit residues: 101.6254 Evaluate side-chains 49 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 2.827 ------------------------------------------------------------------------------- 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 B residue 740 GLN 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: 0.5980 chunk 125 optimal weight: 0.4980 chunk 5 optimal weight: 6.9990 chunk 10 optimal weight: 0.0040 chunk 129 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 36 optimal weight: 0.2980 chunk 59 optimal weight: 5.9990 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3536 r_free = 0.3536 target = 0.057132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.042730 restraints weight = 67801.753| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 4.10 r_work: 0.2894 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14334 Z= 0.130 Angle : 0.580 13.061 19628 Z= 0.299 Chirality : 0.039 0.156 2134 Planarity : 0.003 0.037 2288 Dihedral : 19.117 179.601 2366 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.81 % Allowed : 16.40 % 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: 0.50 (0.22), residues: 1552 helix: 1.26 (0.20), residues: 720 sheet: -0.53 (0.39), residues: 182 loop : -0.37 (0.26), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 861 HIS 0.009 0.001 HIS A1099 PHE 0.013 0.001 PHE A1107 TYR 0.012 0.001 TYR A 698 ARG 0.002 0.000 ARG B 831 Details of bonding type rmsd hydrogen bonds : bond 0.03081 ( 593) hydrogen bonds : angle 4.08235 ( 1693) covalent geometry : bond 0.00292 (14334) covalent geometry : angle 0.57993 (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 56 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 1.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 MET cc_start: 0.8783 (mmm) cc_final: 0.8432 (mmt) REVERT: A 635 MET cc_start: 0.8659 (ppp) cc_final: 0.8040 (ppp) REVERT: A 756 MET cc_start: 0.9005 (tpp) cc_final: 0.8679 (tpp) REVERT: A 957 MET cc_start: 0.9133 (mmp) cc_final: 0.8706 (mpt) REVERT: A 1148 MET cc_start: 0.9737 (mtm) cc_final: 0.9151 (mtm) REVERT: B 467 MET cc_start: 0.8368 (mmm) cc_final: 0.8159 (mmm) REVERT: B 635 MET cc_start: 0.8761 (ppp) cc_final: 0.8155 (ppp) REVERT: B 756 MET cc_start: 0.9000 (tpp) cc_final: 0.8722 (tpp) REVERT: B 835 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7932 (mp0) REVERT: B 957 MET cc_start: 0.9101 (mmp) cc_final: 0.8678 (mpt) outliers start: 11 outliers final: 4 residues processed: 53 average time/residue: 1.5687 time to fit residues: 91.7989 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 : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain B residue 740 GLN 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 97 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 154 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 3 optimal weight: 0.0370 chunk 70 optimal weight: 0.9980 chunk 55 optimal weight: 0.0980 chunk 21 optimal weight: 3.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 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 = 0.3539 r_free = 0.3539 target = 0.057245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.042949 restraints weight = 68132.995| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 4.10 r_work: 0.2904 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.3160 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= 0.125 Angle : 0.572 13.161 19628 Z= 0.297 Chirality : 0.040 0.154 2134 Planarity : 0.003 0.038 2288 Dihedral : 19.139 177.920 2366 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.88 % Allowed : 16.62 % Favored : 82.50 % 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: 0.53 (0.22), residues: 1552 helix: 1.31 (0.20), residues: 716 sheet: -0.51 (0.39), residues: 182 loop : -0.37 (0.26), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 861 HIS 0.008 0.001 HIS A1099 PHE 0.011 0.001 PHE A 741 TYR 0.012 0.001 TYR A 698 ARG 0.002 0.000 ARG B 863 Details of bonding type rmsd hydrogen bonds : bond 0.03066 ( 593) hydrogen bonds : angle 4.09793 ( 1693) covalent geometry : bond 0.00279 (14334) covalent geometry : angle 0.57234 (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 55 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 MET cc_start: 0.8827 (mmm) cc_final: 0.8475 (mmt) REVERT: A 635 MET cc_start: 0.8655 (ppp) cc_final: 0.8019 (ppp) REVERT: A 756 MET cc_start: 0.9001 (tpp) cc_final: 0.8685 (tpp) REVERT: A 835 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7932 (mp0) REVERT: A 957 MET cc_start: 0.9109 (mmp) cc_final: 0.8692 (mpt) REVERT: B 635 MET cc_start: 0.8761 (ppp) cc_final: 0.8152 (ppp) REVERT: B 756 MET cc_start: 0.9016 (tpp) cc_final: 0.8771 (tpp) REVERT: B 835 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7929 (mp0) REVERT: B 957 MET cc_start: 0.9067 (mmp) cc_final: 0.8648 (mpt) outliers start: 12 outliers final: 3 residues processed: 53 average time/residue: 1.9164 time to fit residues: 112.0922 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 : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain B residue 740 GLN 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 56 optimal weight: 0.0570 chunk 107 optimal weight: 0.8980 chunk 147 optimal weight: 0.5980 chunk 116 optimal weight: 0.6980 chunk 126 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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 = 0.057507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.043196 restraints weight = 68451.704| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 4.16 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.3216 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= 0.119 Angle : 0.588 13.379 19628 Z= 0.301 Chirality : 0.039 0.158 2134 Planarity : 0.003 0.038 2288 Dihedral : 19.161 175.909 2366 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.66 % Allowed : 16.98 % Favored : 82.36 % 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: 0.55 (0.22), residues: 1552 helix: 1.30 (0.20), residues: 716 sheet: -0.36 (0.40), residues: 178 loop : -0.39 (0.26), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 861 HIS 0.008 0.001 HIS A1099 PHE 0.010 0.001 PHE B 739 TYR 0.020 0.001 TYR B 966 ARG 0.004 0.000 ARG B 447 Details of bonding type rmsd hydrogen bonds : bond 0.02991 ( 593) hydrogen bonds : angle 4.06815 ( 1693) covalent geometry : bond 0.00267 (14334) covalent geometry : angle 0.58811 (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 54 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 MET cc_start: 0.8811 (mmm) cc_final: 0.8507 (mmt) REVERT: A 635 MET cc_start: 0.8690 (ppp) cc_final: 0.8475 (ppp) REVERT: A 756 MET cc_start: 0.8584 (tpp) cc_final: 0.8310 (tpp) REVERT: A 835 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7408 (mp0) REVERT: A 957 MET cc_start: 0.9043 (mmp) cc_final: 0.8655 (mpt) REVERT: A 1148 MET cc_start: 0.9622 (mtm) cc_final: 0.9207 (mtm) REVERT: B 635 MET cc_start: 0.8782 (ppp) cc_final: 0.8180 (ppp) REVERT: B 835 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7361 (mp0) REVERT: B 957 MET cc_start: 0.9026 (mmp) cc_final: 0.8626 (mpt) REVERT: B 1148 MET cc_start: 0.9604 (mtm) cc_final: 0.8814 (pmm) outliers start: 9 outliers final: 5 residues processed: 54 average time/residue: 1.8671 time to fit residues: 111.2592 Evaluate side-chains 49 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain B residue 740 GLN Chi-restraints excluded: chain B residue 835 GLU Chi-restraints excluded: chain B residue 840 VAL 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: 3.9990 chunk 113 optimal weight: 1.9990 chunk 7 optimal weight: 20.0000 chunk 154 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 58 optimal weight: 0.8980 chunk 77 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 HIS B 456 ASN 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 = 0.055603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.040946 restraints weight = 68670.314| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 4.21 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.3488 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= 0.184 Angle : 0.626 13.231 19628 Z= 0.323 Chirality : 0.041 0.157 2134 Planarity : 0.004 0.035 2288 Dihedral : 19.129 178.963 2366 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.51 % Allowed : 17.28 % 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: 0.53 (0.22), residues: 1552 helix: 1.29 (0.20), residues: 716 sheet: -0.27 (0.40), residues: 178 loop : -0.44 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 861 HIS 0.007 0.001 HIS A1099 PHE 0.024 0.001 PHE B1107 TYR 0.017 0.001 TYR A 966 ARG 0.003 0.000 ARG B 831 Details of bonding type rmsd hydrogen bonds : bond 0.03333 ( 593) hydrogen bonds : angle 4.15523 ( 1693) covalent geometry : bond 0.00412 (14334) covalent geometry : angle 0.62602 (19628) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7321.08 seconds wall clock time: 132 minutes 4.66 seconds (7924.66 seconds total)