Starting phenix.real_space_refine on Mon Apr 8 16:20:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9x_36118/04_2024/8j9x_36118_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9x_36118/04_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_36118/04_2024/8j9x_36118.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9x_36118/04_2024/8j9x_36118.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9x_36118/04_2024/8j9x_36118_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9x_36118/04_2024/8j9x_36118_updated.pdb" } 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 Residue "A ASP 643": "OD1" <-> "OD2" Residue "A PHE 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 966": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 643": "OD1" <-> "OD2" Residue "B PHE 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 966": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 7.69, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.11 Conformation dependent library (CDL) restraints added in 2.5 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... running ksdssp... Secondary structure from input PDB file: 66 helices and 14 sheets defined 44.3% alpha, 8.0% beta 5 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 6.30 Creating SS restraints... Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 440 through 452 Processing helix chain 'A' and resid 497 through 500 No H-bonds generated for 'chain 'A' and resid 497 through 500' Processing helix chain 'A' and resid 503 through 512 Processing helix chain 'A' and resid 523 through 527 Processing helix chain 'A' and resid 548 through 559 Processing helix chain 'A' and resid 561 through 565 Processing helix chain 'A' and resid 593 through 602 Processing helix chain 'A' and resid 617 through 619 No H-bonds generated for 'chain 'A' and resid 617 through 619' Processing helix chain 'A' and resid 622 through 630 Processing helix chain 'A' and resid 643 through 652 removed outlier: 3.899A pdb=" N LYS A 646 " --> pdb=" O ASP A 643 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU A 647 " --> pdb=" O SER A 644 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR A 652 " --> pdb=" O PHE A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 664 removed outlier: 3.750A pdb=" N GLU A 663 " --> pdb=" O LEU A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 681 Processing helix chain 'A' and resid 687 through 706 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 716 through 731 removed outlier: 4.541A pdb=" N SER A 731 " --> pdb=" O LYS A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 749 Processing helix chain 'A' and resid 756 through 766 Processing helix chain 'A' and resid 807 through 813 Processing helix chain 'A' and resid 816 through 821 Processing helix chain 'A' and resid 843 through 846 No H-bonds generated for 'chain 'A' and resid 843 through 846' Processing helix chain 'A' and resid 867 through 876 Processing helix chain 'A' and resid 882 through 892 Processing helix chain 'A' and resid 945 through 952 Processing helix chain 'A' and resid 954 through 959 Processing helix chain 'A' and resid 980 through 990 removed outlier: 4.405A pdb=" N LEU A 983 " --> pdb=" O PRO A 980 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASN A 984 " --> pdb=" O ASN A 981 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE A 990 " --> pdb=" O VAL A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1002 Processing helix chain 'A' and resid 1028 through 1074 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) Processing helix chain 'A' and resid 1082 through 1091 Processing helix chain 'A' and resid 1099 through 1102 No H-bonds generated for 'chain 'A' and resid 1099 through 1102' Processing helix chain 'A' and resid 1110 through 1117 Processing helix chain 'A' and resid 1123 through 1127 Processing helix chain 'A' and resid 1135 through 1158 Processing helix chain 'A' and resid 1167 through 1186 Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 440 through 452 Processing helix chain 'B' and resid 497 through 500 No H-bonds generated for 'chain 'B' and resid 497 through 500' Processing helix chain 'B' and resid 503 through 512 Processing helix chain 'B' and resid 523 through 527 Processing helix chain 'B' and resid 548 through 559 Processing helix chain 'B' and resid 561 through 565 Processing helix chain 'B' and resid 593 through 602 Processing helix chain 'B' and resid 617 through 619 No H-bonds generated for 'chain 'B' and resid 617 through 619' Processing helix chain 'B' and resid 622 through 630 Processing helix chain 'B' and resid 643 through 652 removed outlier: 3.898A pdb=" N LYS B 646 " --> pdb=" O ASP B 643 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU B 647 " --> pdb=" O SER B 644 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR B 652 " --> pdb=" O PHE B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 664 removed outlier: 3.750A pdb=" N GLU B 663 " --> pdb=" O LEU B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 681 Processing helix chain 'B' and resid 687 through 706 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 716 through 731 removed outlier: 4.542A pdb=" N SER B 731 " --> pdb=" O LYS B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 749 Processing helix chain 'B' and resid 756 through 766 Processing helix chain 'B' and resid 807 through 813 Processing helix chain 'B' and resid 816 through 821 Processing helix chain 'B' and resid 843 through 846 No H-bonds generated for 'chain 'B' and resid 843 through 846' Processing helix chain 'B' and resid 867 through 876 Processing helix chain 'B' and resid 882 through 892 Processing helix chain 'B' and resid 945 through 952 Processing helix chain 'B' and resid 954 through 959 Processing helix chain 'B' and resid 980 through 990 removed outlier: 4.406A pdb=" N LEU B 983 " --> pdb=" O PRO B 980 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ASN B 984 " --> pdb=" O ASN B 981 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE B 990 " --> pdb=" O VAL B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1002 Processing helix chain 'B' and resid 1028 through 1074 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) Processing helix chain 'B' and resid 1082 through 1091 Processing helix chain 'B' and resid 1099 through 1102 No H-bonds generated for 'chain 'B' and resid 1099 through 1102' Processing helix chain 'B' and resid 1110 through 1117 Processing helix chain 'B' and resid 1123 through 1127 Processing helix chain 'B' and resid 1135 through 1158 Processing helix chain 'B' and resid 1167 through 1186 Processing sheet with id= A, first strand: chain 'A' and resid 433 through 437 removed outlier: 6.662A pdb=" N CYS A 533 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ALA A 436 " --> pdb=" O CYS A 533 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL A 535 " --> pdb=" O ALA A 436 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N VAL A 569 " --> pdb=" O PHE A 639 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 577 through 581 Processing sheet with id= C, first strand: chain 'A' and resid 779 through 782 Processing sheet with id= D, first strand: chain 'A' and resid 850 through 853 Processing sheet with id= E, first strand: chain 'A' and resid 909 through 913 Processing sheet with id= F, 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) Processing sheet with id= G, 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= H, first strand: chain 'B' and resid 433 through 437 removed outlier: 6.663A pdb=" N CYS B 533 " --> pdb=" O LEU B 434 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ALA B 436 " --> pdb=" O CYS B 533 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL B 535 " --> pdb=" O ALA B 436 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL B 569 " --> pdb=" O PHE B 639 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 577 through 581 Processing sheet with id= J, first strand: chain 'B' and resid 779 through 782 Processing sheet with id= K, first strand: chain 'B' and resid 850 through 853 Processing sheet with id= L, first strand: chain 'B' and resid 909 through 913 Processing sheet with id= M, 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) Processing sheet with id= N, first strand: chain 'B' and resid 1013 through 1016 removed outlier: 4.405A pdb=" N LEU B1013 " --> pdb=" O PHE B1025 " (cutoff:3.500A) 482 hydrogen bonds defined for protein. 1338 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: 4.58 Time building geometry restraints manager: 6.46 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: 99.92 - 106.73: 690 106.73 - 113.54: 7724 113.54 - 120.35: 5375 120.35 - 127.16: 5596 127.16 - 133.98: 243 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: 2206 2.76 - 3.29: 13848 3.29 - 3.83: 24434 3.83 - 4.36: 28332 4.36 - 4.90: 46220 Nonbonded interactions: 115040 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 2.520 nonbonded pdb=" O PHE B1094 " pdb=" OH TYR B1122 " model vdw 2.231 2.440 nonbonded pdb=" O PHE A1094 " pdb=" OH TYR A1122 " model vdw 2.231 2.440 nonbonded pdb=" N7 DG C 8 " pdb=" O4 DT C 9 " model vdw 2.269 3.120 ... (remaining 115035 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain '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: 3.340 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: 13.500 Check model and map are aligned: 0.210 Set scattering table: 0.150 Process input model: 43.680 Find NCS groups from input model: 0.700 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: 0.000 Load rotamer database and sin/cos tables:12.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.140 ------------------------------------------------------------------------------- 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= 0.199 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 fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 1.584 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: 1.6339 time to fit residues: 124.6655 Evaluate side-chains 51 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 1.677 ------------------------------------------------------------------------------- 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: 9.9990 chunk 119 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 63 optimal weight: 0.7980 chunk 123 optimal weight: 0.1980 chunk 47 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 92 optimal weight: 0.2980 chunk 143 optimal weight: 1.9990 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 A 709 ASN A1114 ASN B1114 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14334 Z= 0.178 Angle : 0.548 10.417 19628 Z= 0.289 Chirality : 0.039 0.137 2134 Planarity : 0.004 0.043 2288 Dihedral : 18.579 176.237 2370 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.73 % Allowed : 7.83 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.22), residues: 1552 helix: 1.21 (0.20), residues: 732 sheet: -0.68 (0.37), residues: 206 loop : -0.51 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 560 HIS 0.003 0.001 HIS B 883 PHE 0.012 0.001 PHE A1107 TYR 0.011 0.001 TYR A 837 ARG 0.004 0.000 ARG A 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 61 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 51 time to evaluate : 1.566 Fit side-chains revert: symmetry clash REVERT: A 635 MET cc_start: 0.8787 (ppp) cc_final: 0.8378 (ppp) REVERT: A 756 MET cc_start: 0.8427 (tpp) cc_final: 0.8192 (tpp) REVERT: A 957 MET cc_start: 0.8877 (mmp) cc_final: 0.8531 (mpt) REVERT: B 635 MET cc_start: 0.8828 (ppp) cc_final: 0.8324 (ppp) REVERT: B 756 MET cc_start: 0.8489 (tpp) cc_final: 0.8241 (tpp) REVERT: B 957 MET cc_start: 0.8859 (mmp) cc_final: 0.8549 (mpt) outliers start: 10 outliers final: 6 residues processed: 54 average time/residue: 1.3668 time to fit residues: 82.5535 Evaluate side-chains 49 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 1.580 ------------------------------------------------------------------------------- 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 143 optimal weight: 8.9990 chunk 155 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 142 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 115 optimal weight: 0.0070 overall best weight: 2.3604 ------------------------------------------------------------------------------- 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 ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14334 Z= 0.337 Angle : 0.631 9.119 19628 Z= 0.337 Chirality : 0.043 0.218 2134 Planarity : 0.004 0.046 2288 Dihedral : 18.841 167.529 2370 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.24 % Allowed : 11.93 % Favored : 86.82 % 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: 0.29 (0.22), residues: 1552 helix: 1.27 (0.21), residues: 714 sheet: -0.87 (0.37), residues: 214 loop : -0.58 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 560 HIS 0.004 0.001 HIS A 887 PHE 0.031 0.002 PHE B1107 TYR 0.023 0.002 TYR A 848 ARG 0.009 0.001 ARG B 929 *********************** 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 67 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 50 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 635 MET cc_start: 0.8612 (ppp) cc_final: 0.8024 (ppp) REVERT: A 756 MET cc_start: 0.8540 (tpp) cc_final: 0.8337 (tpp) REVERT: A 835 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7251 (mp0) REVERT: A 957 MET cc_start: 0.9124 (mmp) cc_final: 0.8723 (mpt) REVERT: B 474 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8926 (pp) REVERT: B 635 MET cc_start: 0.8785 (ppp) cc_final: 0.8110 (ppp) REVERT: B 835 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7240 (mp0) REVERT: B 957 MET cc_start: 0.9063 (mmp) cc_final: 0.8650 (mpt) outliers start: 17 outliers final: 7 residues processed: 58 average time/residue: 1.5756 time to fit residues: 100.5014 Evaluate side-chains 52 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 42 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 981 ASN Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 835 GLU Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain B residue 981 ASN Chi-restraints excluded: chain B residue 1148 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 0.3980 chunk 108 optimal weight: 0.6980 chunk 74 optimal weight: 0.0470 chunk 15 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 96 optimal weight: 8.9990 chunk 144 optimal weight: 0.5980 chunk 152 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 136 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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: 0.8509 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14334 Z= 0.150 Angle : 0.533 8.576 19628 Z= 0.279 Chirality : 0.039 0.168 2134 Planarity : 0.003 0.041 2288 Dihedral : 18.728 165.945 2370 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.61 % Allowed : 12.88 % Favored : 85.51 % 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 (0.23), residues: 1552 helix: 1.29 (0.21), residues: 716 sheet: -0.55 (0.38), residues: 202 loop : -0.43 (0.26), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 560 HIS 0.002 0.000 HIS B 887 PHE 0.010 0.001 PHE B 739 TYR 0.012 0.001 TYR A 848 ARG 0.004 0.000 ARG A 929 *********************** 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 67 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 45 time to evaluate : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 MET cc_start: 0.8616 (ppp) cc_final: 0.8165 (ppp) REVERT: A 957 MET cc_start: 0.9018 (mmp) cc_final: 0.8653 (mpt) REVERT: A 1148 MET cc_start: 0.9485 (mtm) cc_final: 0.9027 (mtm) REVERT: B 635 MET cc_start: 0.8739 (ppp) cc_final: 0.8223 (ppp) REVERT: B 957 MET cc_start: 0.8952 (mmp) cc_final: 0.8619 (mpt) outliers start: 22 outliers final: 7 residues processed: 62 average time/residue: 1.3186 time to fit residues: 91.2075 Evaluate side-chains 52 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 1.634 ------------------------------------------------------------------------------- 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 840 VAL Chi-restraints excluded: chain A residue 981 ASN Chi-restraints excluded: chain B residue 740 GLN Chi-restraints excluded: chain B residue 840 VAL Chi-restraints excluded: chain B residue 981 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 ASN A 476 ASN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 14334 Z= 0.491 Angle : 0.732 10.762 19628 Z= 0.384 Chirality : 0.045 0.166 2134 Planarity : 0.005 0.052 2288 Dihedral : 19.421 167.868 2370 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.34 % Allowed : 14.71 % Favored : 82.94 % 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: 0.16 (0.22), residues: 1552 helix: 1.10 (0.20), residues: 720 sheet: -1.00 (0.36), residues: 204 loop : -0.57 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 560 HIS 0.006 0.001 HIS A 887 PHE 0.038 0.002 PHE A1107 TYR 0.022 0.002 TYR A 848 ARG 0.005 0.001 ARG B1040 *********************** 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 77 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 45 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 835 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7248 (mp0) REVERT: A 1098 ASN cc_start: 0.7867 (OUTLIER) cc_final: 0.7505 (p0) REVERT: B 474 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8936 (pp) REVERT: B 835 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7212 (mp0) REVERT: B 957 MET cc_start: 0.9179 (mmp) cc_final: 0.8963 (mpm) REVERT: B 1098 ASN cc_start: 0.7807 (OUTLIER) cc_final: 0.7508 (p0) outliers start: 32 outliers final: 9 residues processed: 68 average time/residue: 1.0473 time to fit residues: 79.3732 Evaluate side-chains 56 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 42 time to evaluate : 1.460 ------------------------------------------------------------------------------- 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 A residue 981 ASN Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 835 GLU Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain B residue 840 VAL Chi-restraints excluded: chain B residue 981 ASN Chi-restraints excluded: chain B residue 1098 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 9.9990 chunk 137 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 152 optimal weight: 0.7980 chunk 126 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14334 Z= 0.203 Angle : 0.592 9.310 19628 Z= 0.307 Chirality : 0.040 0.162 2134 Planarity : 0.003 0.036 2288 Dihedral : 19.215 178.948 2370 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.02 % Allowed : 16.47 % 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: 0.47 (0.23), residues: 1552 helix: 1.37 (0.21), residues: 698 sheet: -0.78 (0.37), residues: 206 loop : -0.40 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 820 HIS 0.003 0.001 HIS A 887 PHE 0.016 0.001 PHE A1107 TYR 0.014 0.001 TYR A 848 ARG 0.003 0.000 ARG B1039 *********************** 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 61 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 47 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 MET cc_start: 0.8728 (mmm) cc_final: 0.8392 (mmm) REVERT: A 635 MET cc_start: 0.8624 (ppp) cc_final: 0.8411 (ppp) REVERT: A 835 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: A 966 TYR cc_start: 0.8997 (m-80) cc_final: 0.8736 (m-80) REVERT: B 467 MET cc_start: 0.8968 (mmm) cc_final: 0.8535 (mmt) REVERT: B 835 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7168 (mp0) REVERT: B 846 MET cc_start: 0.9323 (mpt) cc_final: 0.9100 (mpt) REVERT: B 966 TYR cc_start: 0.8954 (m-80) cc_final: 0.8716 (m-80) outliers start: 14 outliers final: 7 residues processed: 56 average time/residue: 1.5415 time to fit residues: 95.0455 Evaluate side-chains 52 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 43 time to evaluate : 1.598 ------------------------------------------------------------------------------- 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 782 ILE Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 981 ASN Chi-restraints excluded: chain B residue 835 GLU Chi-restraints excluded: chain B residue 840 VAL Chi-restraints excluded: chain B residue 981 ASN 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: 0.8980 chunk 87 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 128 optimal weight: 0.1980 chunk 85 optimal weight: 0.0770 chunk 152 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14334 Z= 0.174 Angle : 0.572 11.149 19628 Z= 0.297 Chirality : 0.039 0.160 2134 Planarity : 0.003 0.040 2288 Dihedral : 19.139 175.228 2370 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.46 % Allowed : 16.54 % Favored : 81.99 % 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 (0.23), residues: 1552 helix: 1.39 (0.21), residues: 706 sheet: -0.66 (0.37), residues: 210 loop : -0.34 (0.27), 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 887 PHE 0.013 0.001 PHE A1107 TYR 0.011 0.001 TYR B1043 ARG 0.007 0.000 ARG B 956 *********************** 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 66 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 46 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 MET cc_start: 0.8648 (ppp) cc_final: 0.8112 (ppp) REVERT: A 966 TYR cc_start: 0.8925 (m-80) cc_final: 0.8640 (m-80) REVERT: A 1148 MET cc_start: 0.9528 (mtm) cc_final: 0.8914 (mtm) REVERT: B 467 MET cc_start: 0.8758 (mmm) cc_final: 0.8469 (mmt) REVERT: B 835 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7264 (mp0) REVERT: B 966 TYR cc_start: 0.8903 (m-80) cc_final: 0.8652 (m-80) REVERT: B 1148 MET cc_start: 0.9442 (mtm) cc_final: 0.8875 (mtm) outliers start: 20 outliers final: 5 residues processed: 62 average time/residue: 1.4342 time to fit residues: 98.7823 Evaluate side-chains 50 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 1.742 ------------------------------------------------------------------------------- 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 840 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 96 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 119 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.3507 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= 0.179 Angle : 0.577 10.828 19628 Z= 0.296 Chirality : 0.039 0.160 2134 Planarity : 0.003 0.055 2288 Dihedral : 19.133 177.945 2366 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.17 % Allowed : 17.28 % 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: 0.57 (0.23), residues: 1552 helix: 1.32 (0.21), residues: 712 sheet: -0.45 (0.37), residues: 206 loop : -0.32 (0.27), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 861 HIS 0.003 0.001 HIS A 887 PHE 0.015 0.001 PHE A1107 TYR 0.015 0.001 TYR A1043 ARG 0.016 0.000 ARG A 929 *********************** 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 59 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 43 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 MET cc_start: 0.8648 (ppp) cc_final: 0.8104 (ppp) REVERT: A 835 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7316 (mp0) REVERT: A 966 TYR cc_start: 0.8944 (m-80) cc_final: 0.8659 (m-80) REVERT: B 467 MET cc_start: 0.8789 (mmm) cc_final: 0.8452 (mmt) REVERT: B 474 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8964 (pp) REVERT: B 635 MET cc_start: 0.8669 (ppp) cc_final: 0.8156 (ppp) REVERT: B 835 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7285 (mp0) REVERT: B 966 TYR cc_start: 0.8926 (m-80) cc_final: 0.8659 (m-80) REVERT: B 1148 MET cc_start: 0.9512 (mtm) cc_final: 0.9122 (mtm) outliers start: 16 outliers final: 7 residues processed: 56 average time/residue: 1.3900 time to fit residues: 86.4780 Evaluate side-chains 52 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 42 time to evaluate : 1.677 ------------------------------------------------------------------------------- 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 A residue 909 HIS Chi-restraints excluded: chain B residue 474 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 4.9990 chunk 133 optimal weight: 8.9990 chunk 141 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 134 optimal weight: 10.0000 chunk 93 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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: 0.8615 moved from start: 0.3690 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= 0.221 Angle : 0.594 11.169 19628 Z= 0.304 Chirality : 0.039 0.156 2134 Planarity : 0.004 0.046 2288 Dihedral : 18.937 177.418 2366 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.10 % Allowed : 17.57 % Favored : 81.33 % 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: 0.48 (0.23), residues: 1552 helix: 1.28 (0.21), residues: 722 sheet: -0.56 (0.37), residues: 210 loop : -0.41 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 861 HIS 0.003 0.001 HIS A 887 PHE 0.020 0.001 PHE A1107 TYR 0.014 0.001 TYR A 848 ARG 0.012 0.000 ARG A 929 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 43 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 MET cc_start: 0.8764 (mmm) cc_final: 0.8511 (mmt) REVERT: A 635 MET cc_start: 0.8655 (ppp) cc_final: 0.8098 (ppp) REVERT: A 835 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7293 (mp0) REVERT: A 966 TYR cc_start: 0.8928 (m-80) cc_final: 0.8645 (m-80) REVERT: A 1148 MET cc_start: 0.9527 (mtm) cc_final: 0.9312 (mtm) REVERT: B 467 MET cc_start: 0.8708 (mmm) cc_final: 0.8439 (mmm) REVERT: B 474 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8982 (pp) REVERT: B 635 MET cc_start: 0.8661 (ppp) cc_final: 0.8136 (ppp) REVERT: B 966 TYR cc_start: 0.8919 (m-80) cc_final: 0.8649 (m-80) outliers start: 15 outliers final: 9 residues processed: 56 average time/residue: 1.3820 time to fit residues: 85.9886 Evaluate side-chains 53 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 42 time to evaluate : 1.544 ------------------------------------------------------------------------------- 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 A residue 909 HIS Chi-restraints excluded: chain A residue 1107 PHE Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 840 VAL Chi-restraints excluded: chain B residue 909 HIS Chi-restraints excluded: chain B residue 1107 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 144 optimal weight: 0.8980 chunk 125 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14334 Z= 0.244 Angle : 0.617 11.245 19628 Z= 0.315 Chirality : 0.040 0.156 2134 Planarity : 0.004 0.046 2288 Dihedral : 18.811 175.369 2366 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.88 % Allowed : 17.72 % 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: 0.48 (0.23), residues: 1552 helix: 1.28 (0.21), residues: 720 sheet: -0.54 (0.38), residues: 210 loop : -0.41 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 560 HIS 0.003 0.001 HIS A 887 PHE 0.016 0.001 PHE A1107 TYR 0.017 0.001 TYR A 848 ARG 0.011 0.000 ARG A 929 ********************** 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 53 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 41 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 MET cc_start: 0.8633 (ppp) cc_final: 0.8066 (ppp) REVERT: A 835 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7273 (mp0) REVERT: A 1148 MET cc_start: 0.9510 (mtm) cc_final: 0.9097 (mtm) REVERT: B 635 MET cc_start: 0.8646 (ppp) cc_final: 0.8082 (ppp) REVERT: B 966 TYR cc_start: 0.8908 (m-80) cc_final: 0.8630 (m-80) outliers start: 12 outliers final: 7 residues processed: 49 average time/residue: 1.4553 time to fit residues: 79.3030 Evaluate side-chains 48 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 40 time to evaluate : 1.553 ------------------------------------------------------------------------------- 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 A residue 909 HIS 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 38 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 52 optimal weight: 0.5980 chunk 128 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 7 optimal weight: 0.0170 overall best weight: 1.1222 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.054869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.040494 restraints weight = 68576.662| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 4.18 r_work: 0.2812 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14334 Z= 0.201 Angle : 0.572 11.101 19628 Z= 0.296 Chirality : 0.039 0.157 2134 Planarity : 0.004 0.057 2288 Dihedral : 18.766 176.321 2366 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.81 % Allowed : 18.08 % Favored : 81.11 % 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: 0.49 (0.23), residues: 1552 helix: 1.28 (0.21), residues: 720 sheet: -0.50 (0.38), residues: 210 loop : -0.41 (0.27), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 861 HIS 0.003 0.001 HIS A 887 PHE 0.014 0.001 PHE A1107 TYR 0.016 0.001 TYR B 888 ARG 0.015 0.000 ARG B 929 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3220.68 seconds wall clock time: 61 minutes 44.06 seconds (3704.06 seconds total)