Starting phenix.real_space_refine on Sun Nov 17 15:33:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9x_36118/11_2024/8j9x_36118.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9x_36118/11_2024/8j9x_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9x_36118/11_2024/8j9x_36118.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9x_36118/11_2024/8j9x_36118.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9x_36118/11_2024/8j9x_36118.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9x_36118/11_2024/8j9x_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 9.88, per 1000 atoms: 0.71 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: 3.72 Conformation dependent library (CDL) restraints added in 1.8 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: 4.93 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: 5.18 Time building geometry restraints manager: 4.25 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: 0.00 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: 4.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 39.270 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.090 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:15.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.770 ------------------------------------------------------------------------------- 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= 0.201 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 *********************** 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 : 1.595 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: 1.6192 time to fit residues: 123.6057 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 : 1.256 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 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= 0.173 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 *********************** 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 : 1.636 Fit side-chains REVERT: A 635 MET cc_start: 0.8762 (ppp) cc_final: 0.8382 (ppp) REVERT: A 957 MET cc_start: 0.8893 (mmp) cc_final: 0.8514 (mpt) REVERT: B 635 MET cc_start: 0.8777 (ppp) cc_final: 0.8342 (ppp) REVERT: B 957 MET cc_start: 0.8883 (mmp) cc_final: 0.8550 (mpt) outliers start: 7 outliers final: 4 residues processed: 54 average time/residue: 1.4430 time to fit residues: 86.7468 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 : 2.035 ------------------------------------------------------------------------------- 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 79 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 115 optimal weight: 0.0770 overall best weight: 2.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN A 557 HIS A1099 HIS ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14334 Z= 0.334 Angle : 0.658 12.682 19628 Z= 0.347 Chirality : 0.043 0.148 2134 Planarity : 0.004 0.046 2288 Dihedral : 18.819 177.395 2370 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.81 % Allowed : 11.71 % Favored : 87.48 % 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: 0.22 (0.22), residues: 1552 helix: 1.14 (0.20), residues: 718 sheet: -0.89 (0.36), residues: 210 loop : -0.55 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 560 HIS 0.005 0.001 HIS B 650 PHE 0.031 0.002 PHE B1107 TYR 0.021 0.002 TYR A 848 ARG 0.004 0.001 ARG A 716 *********************** 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 57 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 1.798 Fit side-chains REVERT: A 635 MET cc_start: 0.8669 (ppp) cc_final: 0.8069 (ppp) REVERT: A 957 MET cc_start: 0.9099 (mmp) cc_final: 0.8645 (mpt) REVERT: B 635 MET cc_start: 0.8811 (ppp) cc_final: 0.8256 (ppp) REVERT: B 957 MET cc_start: 0.9099 (mmp) cc_final: 0.8639 (mpt) outliers start: 11 outliers final: 7 residues processed: 51 average time/residue: 1.5803 time to fit residues: 89.5161 Evaluate side-chains 48 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 981 ASN 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 142 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2729 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= 0.212 Angle : 0.577 12.239 19628 Z= 0.305 Chirality : 0.040 0.165 2134 Planarity : 0.004 0.040 2288 Dihedral : 18.854 176.884 2370 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.12 % Allowed : 12.30 % Favored : 85.58 % 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: 0.31 (0.22), residues: 1552 helix: 1.19 (0.20), residues: 716 sheet: -0.92 (0.35), residues: 214 loop : -0.42 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 560 HIS 0.011 0.001 HIS A1099 PHE 0.017 0.001 PHE B1107 TYR 0.016 0.001 TYR A 848 ARG 0.003 0.000 ARG A1040 *********************** 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 74 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 45 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 MET cc_start: 0.8673 (ppp) cc_final: 0.8201 (ppp) REVERT: A 957 MET cc_start: 0.9098 (mmp) cc_final: 0.8632 (mpt) REVERT: A 1148 MET cc_start: 0.9491 (mtm) cc_final: 0.9041 (mtm) REVERT: B 635 MET cc_start: 0.8765 (ppp) cc_final: 0.8196 (ppp) REVERT: B 957 MET cc_start: 0.9066 (mmp) cc_final: 0.8599 (mpt) outliers start: 29 outliers final: 4 residues processed: 67 average time/residue: 1.5401 time to fit residues: 113.1428 Evaluate side-chains 47 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain A residue 740 GLN Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain B residue 782 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 8.9990 chunk 86 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 113 optimal weight: 0.0670 chunk 63 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2980 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= 0.254 Angle : 0.591 12.063 19628 Z= 0.311 Chirality : 0.041 0.161 2134 Planarity : 0.004 0.039 2288 Dihedral : 18.981 175.780 2366 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.24 % Allowed : 14.57 % 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: 0.30 (0.22), residues: 1552 helix: 1.17 (0.20), residues: 718 sheet: -0.91 (0.35), residues: 214 loop : -0.42 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 560 HIS 0.008 0.001 HIS A1099 PHE 0.020 0.001 PHE B1107 TYR 0.016 0.001 TYR A 848 ARG 0.003 0.000 ARG A1040 *********************** 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 65 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 MET cc_start: 0.8684 (ppp) cc_final: 0.8122 (ppp) REVERT: A 957 MET cc_start: 0.9106 (mmp) cc_final: 0.8679 (mpt) REVERT: B 467 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.8085 (mmm) REVERT: B 635 MET cc_start: 0.8802 (ppp) cc_final: 0.8185 (ppp) REVERT: B 957 MET cc_start: 0.9090 (mmp) cc_final: 0.8670 (mpt) outliers start: 17 outliers final: 7 residues processed: 61 average time/residue: 1.3489 time to fit residues: 91.9053 Evaluate side-chains 51 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 1.954 ------------------------------------------------------------------------------- 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 838 VAL Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain B residue 467 MET Chi-restraints excluded: chain B residue 782 ILE 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 51 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 50 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.3354 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= 0.270 Angle : 0.617 12.804 19628 Z= 0.325 Chirality : 0.041 0.165 2134 Planarity : 0.004 0.036 2288 Dihedral : 19.299 176.654 2366 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.24 % Allowed : 15.59 % 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: 0.27 (0.22), residues: 1552 helix: 1.20 (0.20), residues: 716 sheet: -0.80 (0.37), residues: 186 loop : -0.59 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1170 HIS 0.006 0.001 HIS A1099 PHE 0.022 0.001 PHE B1107 TYR 0.017 0.001 TYR A 848 ARG 0.003 0.000 ARG A1040 *********************** 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 65 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 MET cc_start: 0.8650 (ppp) cc_final: 0.8075 (ppp) REVERT: A 957 MET cc_start: 0.9144 (mmp) cc_final: 0.8718 (mpt) REVERT: A 1148 MET cc_start: 0.9538 (mtm) cc_final: 0.9002 (mtm) REVERT: B 635 MET cc_start: 0.8746 (ppp) cc_final: 0.8065 (ppp) REVERT: B 957 MET cc_start: 0.9148 (mmp) cc_final: 0.8719 (mpt) outliers start: 17 outliers final: 7 residues processed: 58 average time/residue: 0.9963 time to fit residues: 64.5576 Evaluate side-chains 52 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 838 VAL Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain B residue 462 PHE 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 147 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 87 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 85 optimal weight: 0.1980 chunk 152 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.3316 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= 0.189 Angle : 0.580 13.136 19628 Z= 0.304 Chirality : 0.040 0.161 2134 Planarity : 0.004 0.037 2288 Dihedral : 19.261 176.637 2366 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.73 % Allowed : 17.20 % Favored : 82.06 % 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: 0.39 (0.22), residues: 1552 helix: 1.23 (0.20), residues: 716 sheet: -0.60 (0.39), residues: 182 loop : -0.49 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 861 HIS 0.007 0.001 HIS A1099 PHE 0.012 0.001 PHE B1107 TYR 0.013 0.001 TYR A 848 ARG 0.002 0.000 ARG B1040 *********************** 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 57 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 MET cc_start: 0.8670 (ppp) cc_final: 0.8071 (ppp) REVERT: A 957 MET cc_start: 0.9084 (mmp) cc_final: 0.8672 (mpt) REVERT: A 966 TYR cc_start: 0.8773 (m-80) cc_final: 0.8563 (m-80) REVERT: B 467 MET cc_start: 0.8496 (mmm) cc_final: 0.8218 (mmm) REVERT: B 635 MET cc_start: 0.8708 (ppp) cc_final: 0.8408 (ppp) REVERT: B 957 MET cc_start: 0.9088 (mmp) cc_final: 0.8673 (mpt) outliers start: 10 outliers final: 2 residues processed: 55 average time/residue: 1.4866 time to fit residues: 90.9437 Evaluate side-chains 47 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 740 GLN Chi-restraints excluded: chain A residue 840 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 96 optimal weight: 0.1980 chunk 103 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14334 Z= 0.172 Angle : 0.599 13.183 19628 Z= 0.306 Chirality : 0.040 0.162 2134 Planarity : 0.003 0.039 2288 Dihedral : 19.200 175.228 2366 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.44 % Allowed : 17.79 % 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: 0.47 (0.22), residues: 1552 helix: 1.27 (0.20), residues: 716 sheet: -0.38 (0.42), residues: 158 loop : -0.49 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 861 HIS 0.007 0.001 HIS A1099 PHE 0.010 0.001 PHE B1107 TYR 0.017 0.001 TYR B 966 ARG 0.003 0.000 ARG B 495 *********************** 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 54 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 MET cc_start: 0.9025 (mmm) cc_final: 0.8523 (mmt) REVERT: A 635 MET cc_start: 0.8668 (ppp) cc_final: 0.8048 (ppp) REVERT: A 957 MET cc_start: 0.9066 (mmp) cc_final: 0.8680 (mpt) REVERT: A 1060 MET cc_start: 0.8982 (tmm) cc_final: 0.8225 (pp-130) REVERT: A 1148 MET cc_start: 0.9511 (mtm) cc_final: 0.9240 (mtm) REVERT: B 467 MET cc_start: 0.8416 (mmm) cc_final: 0.8208 (mmm) REVERT: B 635 MET cc_start: 0.8721 (ppp) cc_final: 0.8391 (ppp) REVERT: B 957 MET cc_start: 0.9065 (mmp) cc_final: 0.8665 (mpt) outliers start: 6 outliers final: 4 residues processed: 53 average time/residue: 1.4431 time to fit residues: 84.9238 Evaluate side-chains 48 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 740 GLN Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain B residue 909 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 85 optimal weight: 0.4980 chunk 61 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 128 optimal weight: 2.9990 chunk 134 optimal weight: 8.9990 chunk 93 optimal weight: 10.0000 chunk 150 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3445 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= 0.198 Angle : 0.589 13.285 19628 Z= 0.304 Chirality : 0.040 0.158 2134 Planarity : 0.004 0.038 2288 Dihedral : 19.094 179.550 2366 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.59 % Allowed : 17.86 % 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: 0.47 (0.22), residues: 1552 helix: 1.28 (0.20), residues: 718 sheet: -0.36 (0.42), residues: 158 loop : -0.52 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 861 HIS 0.006 0.001 HIS A1099 PHE 0.016 0.001 PHE B1107 TYR 0.013 0.001 TYR A 966 ARG 0.003 0.000 ARG B1039 *********************** 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 54 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 635 MET cc_start: 0.8641 (ppp) cc_final: 0.8009 (ppp) REVERT: A 957 MET cc_start: 0.9092 (mmp) cc_final: 0.8675 (mpt) REVERT: B 635 MET cc_start: 0.8736 (ppp) cc_final: 0.8396 (ppp) REVERT: B 957 MET cc_start: 0.9086 (mmp) cc_final: 0.8678 (mpt) REVERT: B 1148 MET cc_start: 0.9406 (mtm) cc_final: 0.9077 (mtm) outliers start: 8 outliers final: 4 residues processed: 53 average time/residue: 1.4657 time to fit residues: 86.5382 Evaluate side-chains 48 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 975 LEU 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 91 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 104 optimal weight: 0.5980 chunk 157 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.3606 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= 0.249 Angle : 0.629 13.309 19628 Z= 0.321 Chirality : 0.041 0.153 2134 Planarity : 0.004 0.038 2288 Dihedral : 19.093 176.106 2366 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.37 % Allowed : 18.16 % Favored : 81.48 % 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: 1.27 (0.20), residues: 716 sheet: -0.40 (0.42), residues: 158 loop : -0.56 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 861 HIS 0.006 0.001 HIS A1099 PHE 0.020 0.001 PHE B1107 TYR 0.014 0.001 TYR B 848 ARG 0.003 0.000 ARG B 447 ********************** 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 50 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 635 MET cc_start: 0.8658 (ppp) cc_final: 0.8004 (ppp) REVERT: A 957 MET cc_start: 0.9153 (mmp) cc_final: 0.8753 (mpt) REVERT: A 1148 MET cc_start: 0.9514 (mtm) cc_final: 0.9130 (mtm) REVERT: B 635 MET cc_start: 0.8719 (ppp) cc_final: 0.8393 (ppp) REVERT: B 957 MET cc_start: 0.9139 (mmp) cc_final: 0.8712 (mpt) outliers start: 5 outliers final: 4 residues processed: 50 average time/residue: 1.5624 time to fit residues: 86.7203 Evaluate side-chains 47 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 975 LEU 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 38 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 52 optimal weight: 0.0870 chunk 128 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- 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 = 0.3466 r_free = 0.3466 target = 0.054559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.040110 restraints weight = 68408.970| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 4.13 r_work: 0.2804 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.3773 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= 0.279 Angle : 0.644 13.132 19628 Z= 0.329 Chirality : 0.041 0.152 2134 Planarity : 0.004 0.039 2288 Dihedral : 19.122 173.696 2366 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.59 % Allowed : 18.01 % 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: 0.41 (0.22), residues: 1552 helix: 1.25 (0.20), residues: 714 sheet: -0.51 (0.39), residues: 182 loop : -0.51 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 820 HIS 0.005 0.001 HIS A1099 PHE 0.023 0.001 PHE B1107 TYR 0.016 0.001 TYR A 848 ARG 0.003 0.000 ARG B1040 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3148.78 seconds wall clock time: 71 minutes 43.21 seconds (4303.21 seconds total)