Starting phenix.real_space_refine on Thu Sep 26 00:44:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6se6_10152/09_2024/6se6_10152.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6se6_10152/09_2024/6se6_10152.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6se6_10152/09_2024/6se6_10152.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6se6_10152/09_2024/6se6_10152.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6se6_10152/09_2024/6se6_10152.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6se6_10152/09_2024/6se6_10152.cif" } resolution = 3.5 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= 0.004 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: 5 Type Number sf(0) Gaussians P 288 5.49 5 S 10 5.16 5 C 6706 2.51 5 N 2263 2.21 5 O 2801 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12068 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 812 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "B" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 652 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 776 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 812 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 672 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "G" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 827 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "V" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 160 Classifications: {'peptide': 18} Link IDs: {'PTRANS': 1, 'TRANS': 16} Time building chain proxies: 7.87, per 1000 atoms: 0.65 Number of scatterers: 12068 At special positions: 0 Unit cell: (78, 120.25, 114.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 288 15.00 O 2801 8.00 N 2263 7.00 C 6706 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: 2.92 Conformation dependent library (CDL) restraints added in 995.8 milliseconds 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1430 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 8 sheets defined 69.4% alpha, 2.3% beta 144 base pairs and 250 stacking pairs defined. Time for finding SS restraints: 6.10 Creating SS restraints... Processing helix chain 'A' and resid 45 through 57 removed outlier: 4.271A pdb=" N LYS A 49 " --> pdb=" O GLN A 45 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.526A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 116 removed outlier: 3.808A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 134 removed outlier: 3.547A pdb=" N VAL A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 removed outlier: 3.705A pdb=" N ARG B 40 " --> pdb=" O ARG B 36 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.234A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.668A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.673A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.458A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.599A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.836A pdb=" N ASN D 67 " --> pdb=" O ASN D 63 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU D 71 " --> pdb=" O ASN D 67 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 122 removed outlier: 3.594A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR D 115 " --> pdb=" O VAL D 111 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS D 120 " --> pdb=" O LYS D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 removed outlier: 4.192A pdb=" N LYS E 49 " --> pdb=" O GLN E 45 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.565A pdb=" N VAL E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 116 removed outlier: 3.785A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU E 111 " --> pdb=" O GLU E 107 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU E 112 " --> pdb=" O ASP E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 134 removed outlier: 4.276A pdb=" N GLY E 134 " --> pdb=" O ARG E 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.745A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE F 61 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.631A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 72 removed outlier: 4.070A pdb=" N ASP G 72 " --> pdb=" O ASN G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.654A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.990A pdb=" N LEU G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.771A pdb=" N ASN H 67 " --> pdb=" O ASN H 63 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU H 71 " --> pdb=" O ASN H 67 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.511A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.594A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA H 110 " --> pdb=" O LEU H 106 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR H 119 " --> pdb=" O THR H 115 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS H 120 " --> pdb=" O LYS H 116 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 7.073A pdb=" N ASN A 85 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 121 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.658A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA6, first strand: chain 'E' and resid 120 through 121 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.678A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 351 hydrogen bonds defined for protein. 1044 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 359 hydrogen bonds 686 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 250 stacking parallelities Total time for adding SS restraints: 4.82 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.32: 1874 1.32 - 1.44: 4461 1.44 - 1.56: 5947 1.56 - 1.68: 580 1.68 - 1.79: 18 Bond restraints: 12880 Sorted by residual: bond pdb=" CB VAL C 27 " pdb=" CG2 VAL C 27 " ideal model delta sigma weight residual 1.521 1.426 0.095 3.30e-02 9.18e+02 8.27e+00 bond pdb=" C3' DA J -38 " pdb=" O3' DA J -38 " ideal model delta sigma weight residual 1.422 1.482 -0.060 3.00e-02 1.11e+03 3.99e+00 bond pdb=" CB THR F 73 " pdb=" CG2 THR F 73 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.77e+00 bond pdb=" CB VAL G 27 " pdb=" CG2 VAL G 27 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.76e+00 bond pdb=" C3' DC I 4 " pdb=" O3' DC I 4 " ideal model delta sigma weight residual 1.422 1.480 -0.058 3.00e-02 1.11e+03 3.74e+00 ... (remaining 12875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 18038 2.43 - 4.87: 535 4.87 - 7.30: 54 7.30 - 9.74: 8 9.74 - 12.17: 2 Bond angle restraints: 18637 Sorted by residual: angle pdb=" C THR A 79 " pdb=" N ARG A 80 " pdb=" CA ARG A 80 " ideal model delta sigma weight residual 121.54 128.72 -7.18 1.91e+00 2.74e-01 1.41e+01 angle pdb=" C ARG A 44 " pdb=" N GLN A 45 " pdb=" CA GLN A 45 " ideal model delta sigma weight residual 122.46 127.70 -5.24 1.41e+00 5.03e-01 1.38e+01 angle pdb=" CA TRP V 530 " pdb=" CB TRP V 530 " pdb=" CG TRP V 530 " ideal model delta sigma weight residual 113.60 120.65 -7.05 1.90e+00 2.77e-01 1.38e+01 angle pdb=" C3' DA J -38 " pdb=" O3' DA J -38 " pdb=" P DG J -37 " ideal model delta sigma weight residual 120.20 125.57 -5.37 1.50e+00 4.44e-01 1.28e+01 angle pdb=" C3' DC I -29 " pdb=" O3' DC I -29 " pdb=" P DT I -28 " ideal model delta sigma weight residual 120.20 125.55 -5.35 1.50e+00 4.44e-01 1.27e+01 ... (remaining 18632 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 5551 35.73 - 71.45: 1381 71.45 - 107.18: 18 107.18 - 142.90: 6 142.90 - 178.63: 2 Dihedral angle restraints: 6958 sinusoidal: 4740 harmonic: 2218 Sorted by residual: dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual -140.00 38.63 -178.63 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 75.72 144.28 1 3.50e+01 8.16e-04 1.42e+01 dihedral pdb=" C4' DT J 54 " pdb=" C3' DT J 54 " pdb=" O3' DT J 54 " pdb=" P DC J 55 " ideal model delta sinusoidal sigma weight residual 220.00 94.35 125.65 1 3.50e+01 8.16e-04 1.24e+01 ... (remaining 6955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1290 0.047 - 0.093: 600 0.093 - 0.140: 167 0.140 - 0.187: 51 0.187 - 0.233: 6 Chirality restraints: 2114 Sorted by residual: chirality pdb=" CG LEU G 97 " pdb=" CB LEU G 97 " pdb=" CD1 LEU G 97 " pdb=" CD2 LEU G 97 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA VAL B 21 " pdb=" N VAL B 21 " pdb=" C VAL B 21 " pdb=" CB VAL B 21 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA VAL F 21 " pdb=" N VAL F 21 " pdb=" C VAL F 21 " pdb=" CB VAL F 21 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 2111 not shown) Planarity restraints: 1347 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 26 " -0.054 2.00e-02 2.50e+03 2.34e-02 1.64e+01 pdb=" N9 DG I 26 " 0.056 2.00e-02 2.50e+03 pdb=" C8 DG I 26 " 0.006 2.00e-02 2.50e+03 pdb=" N7 DG I 26 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DG I 26 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DG I 26 " 0.001 2.00e-02 2.50e+03 pdb=" O6 DG I 26 " -0.019 2.00e-02 2.50e+03 pdb=" N1 DG I 26 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DG I 26 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 26 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 26 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DG I 26 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 28 " -0.043 2.00e-02 2.50e+03 1.98e-02 1.18e+01 pdb=" N9 DG I 28 " 0.049 2.00e-02 2.50e+03 pdb=" C8 DG I 28 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DG I 28 " 0.009 2.00e-02 2.50e+03 pdb=" C5 DG I 28 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 28 " -0.016 2.00e-02 2.50e+03 pdb=" O6 DG I 28 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 28 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 28 " 0.004 2.00e-02 2.50e+03 pdb=" N2 DG I 28 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 28 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DG I 28 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I -26 " 0.044 2.00e-02 2.50e+03 2.06e-02 1.07e+01 pdb=" N1 DT I -26 " -0.043 2.00e-02 2.50e+03 pdb=" C2 DT I -26 " -0.007 2.00e-02 2.50e+03 pdb=" O2 DT I -26 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DT I -26 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DT I -26 " 0.002 2.00e-02 2.50e+03 pdb=" O4 DT I -26 " 0.019 2.00e-02 2.50e+03 pdb=" C5 DT I -26 " -0.000 2.00e-02 2.50e+03 pdb=" C7 DT I -26 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DT I -26 " -0.008 2.00e-02 2.50e+03 ... (remaining 1344 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2460 2.78 - 3.31: 10073 3.31 - 3.84: 24303 3.84 - 4.37: 27108 4.37 - 4.90: 38480 Nonbonded interactions: 102424 Sorted by model distance: nonbonded pdb=" O2 DC I -4 " pdb=" N2 DG J 4 " model vdw 2.247 2.496 nonbonded pdb=" O2 DC I -62 " pdb=" N2 DG J 62 " model vdw 2.249 2.496 nonbonded pdb=" O2 DC I -56 " pdb=" N2 DG J 56 " model vdw 2.264 2.496 nonbonded pdb=" N2 DG I -60 " pdb=" O2 DC J 60 " model vdw 2.268 2.496 nonbonded pdb=" O2 DC I 5 " pdb=" N2 DG J -5 " model vdw 2.275 2.496 ... (remaining 102419 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 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 21 through 102) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 116) } ncs_group { reference = (chain 'D' and resid 35 through 124) selection = chain 'H' } 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 group one per residue 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: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 34.490 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 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 : 0.010 0.095 12880 Z= 0.593 Angle : 0.998 12.172 18637 Z= 0.571 Chirality : 0.059 0.233 2114 Planarity : 0.008 0.074 1347 Dihedral : 27.962 178.630 5528 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % 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: -3.83 (0.22), residues: 753 helix: -2.55 (0.16), residues: 508 sheet: None (None), residues: 0 loop : -2.06 (0.30), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP V 530 HIS 0.015 0.002 HIS F 75 PHE 0.016 0.003 PHE A 84 TYR 0.022 0.003 TYR G 50 ARG 0.008 0.001 ARG E 133 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.7960 (pp30) cc_final: 0.7738 (pm20) REVERT: A 96 GLU cc_start: 0.8131 (tp30) cc_final: 0.7898 (mm-30) REVERT: B 53 GLU cc_start: 0.8926 (tm-30) cc_final: 0.8414 (tm-30) REVERT: B 88 TYR cc_start: 0.8395 (m-10) cc_final: 0.8023 (m-10) REVERT: C 56 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8308 (tm-30) REVERT: C 75 LYS cc_start: 0.8976 (mmtp) cc_final: 0.8644 (mmtm) REVERT: D 59 MET cc_start: 0.8838 (tpp) cc_final: 0.8635 (tpp) REVERT: D 63 ASN cc_start: 0.8898 (t0) cc_final: 0.8215 (t0) REVERT: D 67 ASN cc_start: 0.8841 (m-40) cc_final: 0.8383 (t0) REVERT: D 68 ASP cc_start: 0.8095 (t70) cc_final: 0.7869 (t0) REVERT: D 71 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7930 (tm-30) REVERT: D 76 GLU cc_start: 0.8063 (tp30) cc_final: 0.7842 (tp30) REVERT: E 73 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7548 (tm-30) REVERT: F 64 ASN cc_start: 0.8302 (t0) cc_final: 0.7761 (t0) REVERT: F 88 TYR cc_start: 0.8906 (m-10) cc_final: 0.7888 (m-10) REVERT: F 91 LYS cc_start: 0.9185 (ttmt) cc_final: 0.8898 (ttpp) REVERT: F 93 GLN cc_start: 0.7584 (mt0) cc_final: 0.6771 (mt0) REVERT: G 64 GLU cc_start: 0.8568 (tp30) cc_final: 0.8344 (tp30) REVERT: H 42 TYR cc_start: 0.7781 (t80) cc_final: 0.7298 (t80) REVERT: H 68 ASP cc_start: 0.8689 (t0) cc_final: 0.8459 (t0) REVERT: H 83 TYR cc_start: 0.8742 (m-10) cc_final: 0.8298 (m-80) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.3713 time to fit residues: 112.0889 Evaluate side-chains 180 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 79 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN B 27 GLN B 93 GLN C 31 HIS C 73 ASN H 67 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12880 Z= 0.221 Angle : 0.615 6.486 18637 Z= 0.365 Chirality : 0.034 0.175 2114 Planarity : 0.004 0.045 1347 Dihedral : 30.776 175.387 4019 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.57 % Allowed : 17.55 % Favored : 80.88 % 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: -0.83 (0.27), residues: 753 helix: 0.03 (0.21), residues: 515 sheet: None (None), residues: 0 loop : -1.69 (0.32), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP V 530 HIS 0.007 0.001 HIS F 75 PHE 0.009 0.001 PHE A 84 TYR 0.016 0.002 TYR D 40 ARG 0.006 0.001 ARG D 79 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 218 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.7952 (pp30) cc_final: 0.7732 (pm20) REVERT: A 127 GLN cc_start: 0.8066 (tp40) cc_final: 0.7858 (tp40) REVERT: B 53 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8251 (tm-30) REVERT: B 88 TYR cc_start: 0.8371 (m-10) cc_final: 0.8011 (m-10) REVERT: B 91 LYS cc_start: 0.8816 (tttt) cc_final: 0.8450 (tptp) REVERT: C 56 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8318 (tm-30) REVERT: C 57 TYR cc_start: 0.9097 (t80) cc_final: 0.8828 (t80) REVERT: C 61 GLU cc_start: 0.8307 (tm-30) cc_final: 0.8038 (tm-30) REVERT: C 71 ARG cc_start: 0.8650 (ttm110) cc_final: 0.8367 (ttp80) REVERT: D 34 LYS cc_start: 0.9148 (mmmm) cc_final: 0.8506 (mptt) REVERT: D 63 ASN cc_start: 0.8573 (t0) cc_final: 0.7972 (t0) REVERT: D 67 ASN cc_start: 0.8726 (m-40) cc_final: 0.8367 (t0) REVERT: D 71 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7987 (tm-30) REVERT: F 64 ASN cc_start: 0.8340 (t0) cc_final: 0.7803 (t0) REVERT: F 91 LYS cc_start: 0.9149 (ttmt) cc_final: 0.8885 (ttpp) REVERT: F 93 GLN cc_start: 0.7706 (mt0) cc_final: 0.6649 (mt0) REVERT: G 64 GLU cc_start: 0.8543 (tp30) cc_final: 0.8112 (tp30) REVERT: G 92 GLU cc_start: 0.7036 (tt0) cc_final: 0.6572 (tt0) REVERT: H 42 TYR cc_start: 0.7914 (t80) cc_final: 0.7456 (t80) REVERT: H 68 ASP cc_start: 0.8594 (t0) cc_final: 0.8374 (t0) REVERT: H 83 TYR cc_start: 0.8574 (m-10) cc_final: 0.8150 (m-80) outliers start: 10 outliers final: 6 residues processed: 220 average time/residue: 0.2993 time to fit residues: 87.9457 Evaluate side-chains 192 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 186 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain F residue 70 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 12880 Z= 0.390 Angle : 0.671 7.985 18637 Z= 0.389 Chirality : 0.038 0.167 2114 Planarity : 0.005 0.048 1347 Dihedral : 30.778 173.011 4019 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 4.39 % Allowed : 19.75 % Favored : 75.86 % 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: 0.15 (0.29), residues: 753 helix: 0.91 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -1.66 (0.33), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP V 530 HIS 0.010 0.002 HIS C 31 PHE 0.011 0.002 PHE E 101 TYR 0.024 0.002 TYR D 83 ARG 0.008 0.001 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 186 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8033 (pp30) cc_final: 0.7780 (pm20) REVERT: A 127 GLN cc_start: 0.8359 (tp40) cc_final: 0.8128 (tp40) REVERT: B 53 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8267 (tm-30) REVERT: B 79 LYS cc_start: 0.8470 (ttpp) cc_final: 0.8221 (ttpp) REVERT: B 91 LYS cc_start: 0.8821 (tttt) cc_final: 0.8519 (tptp) REVERT: C 56 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8576 (tm-30) REVERT: C 104 GLN cc_start: 0.8460 (mp10) cc_final: 0.7965 (mp10) REVERT: D 63 ASN cc_start: 0.8794 (t0) cc_final: 0.8299 (t0) REVERT: D 67 ASN cc_start: 0.8788 (m-40) cc_final: 0.8442 (t0) REVERT: E 53 LYS cc_start: 0.9318 (tppp) cc_final: 0.9096 (tppt) REVERT: F 64 ASN cc_start: 0.8481 (t0) cc_final: 0.7827 (t0) REVERT: F 91 LYS cc_start: 0.9250 (ttmt) cc_final: 0.8934 (ttpp) REVERT: F 93 GLN cc_start: 0.7856 (mt0) cc_final: 0.6679 (mt0) REVERT: G 24 GLN cc_start: 0.8659 (mm-40) cc_final: 0.8200 (mp10) REVERT: G 92 GLU cc_start: 0.6824 (tt0) cc_final: 0.6047 (tt0) REVERT: H 42 TYR cc_start: 0.7976 (t80) cc_final: 0.7693 (t80) REVERT: H 68 ASP cc_start: 0.8708 (t0) cc_final: 0.8482 (t0) REVERT: H 83 TYR cc_start: 0.8665 (m-10) cc_final: 0.8237 (m-80) outliers start: 28 outliers final: 23 residues processed: 196 average time/residue: 0.2768 time to fit residues: 73.9935 Evaluate side-chains 200 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 177 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain V residue 532 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12880 Z= 0.215 Angle : 0.582 5.630 18637 Z= 0.346 Chirality : 0.034 0.163 2114 Planarity : 0.004 0.042 1347 Dihedral : 30.648 172.995 4019 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.66 % Allowed : 23.82 % Favored : 73.51 % 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: 0.80 (0.30), residues: 753 helix: 1.41 (0.23), residues: 515 sheet: None (None), residues: 0 loop : -1.44 (0.35), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP V 530 HIS 0.008 0.001 HIS F 75 PHE 0.009 0.001 PHE E 67 TYR 0.023 0.002 TYR B 88 ARG 0.005 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 198 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 GLN cc_start: 0.8259 (tp40) cc_final: 0.7968 (tp40) REVERT: B 91 LYS cc_start: 0.8771 (tttt) cc_final: 0.8499 (tptp) REVERT: C 56 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8244 (tm-30) REVERT: C 57 TYR cc_start: 0.9050 (t80) cc_final: 0.8810 (t80) REVERT: C 104 GLN cc_start: 0.8397 (mp10) cc_final: 0.8107 (mp10) REVERT: D 34 LYS cc_start: 0.9164 (mmmm) cc_final: 0.8588 (mptt) REVERT: D 63 ASN cc_start: 0.8523 (t0) cc_final: 0.8073 (t0) REVERT: D 67 ASN cc_start: 0.8694 (m-40) cc_final: 0.8450 (t0) REVERT: D 71 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7842 (tt0) REVERT: E 53 LYS cc_start: 0.9272 (tppp) cc_final: 0.9068 (tppt) REVERT: F 27 GLN cc_start: 0.8285 (tm-30) cc_final: 0.8083 (tm-30) REVERT: F 64 ASN cc_start: 0.8465 (t0) cc_final: 0.8149 (t0) REVERT: F 88 TYR cc_start: 0.8833 (m-10) cc_final: 0.7670 (m-10) REVERT: F 91 LYS cc_start: 0.9186 (ttmt) cc_final: 0.8884 (ttpp) REVERT: G 24 GLN cc_start: 0.8560 (mm-40) cc_final: 0.8304 (mp10) REVERT: G 92 GLU cc_start: 0.6764 (tt0) cc_final: 0.6291 (tt0) REVERT: G 111 ILE cc_start: 0.7242 (OUTLIER) cc_final: 0.6919 (pt) REVERT: H 68 ASP cc_start: 0.8573 (t0) cc_final: 0.8353 (t0) REVERT: H 76 GLU cc_start: 0.7884 (tp30) cc_final: 0.7635 (tp30) REVERT: H 83 TYR cc_start: 0.8490 (m-10) cc_final: 0.8261 (m-80) outliers start: 17 outliers final: 11 residues processed: 207 average time/residue: 0.2710 time to fit residues: 77.5619 Evaluate side-chains 197 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 185 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain V residue 532 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 72 optimal weight: 20.0000 chunk 40 optimal weight: 8.9990 chunk 83 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 87 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12880 Z= 0.311 Angle : 0.620 6.178 18637 Z= 0.363 Chirality : 0.036 0.160 2114 Planarity : 0.004 0.040 1347 Dihedral : 30.708 169.998 4019 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.92 % Allowed : 24.76 % Favored : 71.32 % 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: 0.96 (0.30), residues: 753 helix: 1.51 (0.23), residues: 514 sheet: None (None), residues: 0 loop : -1.30 (0.36), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP V 530 HIS 0.013 0.001 HIS D 82 PHE 0.008 0.001 PHE D 70 TYR 0.049 0.002 TYR B 88 ARG 0.005 0.000 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 183 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 GLN cc_start: 0.8336 (tp40) cc_final: 0.8046 (tp40) REVERT: B 91 LYS cc_start: 0.8824 (tttt) cc_final: 0.8535 (tptp) REVERT: C 56 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8520 (tm-30) REVERT: C 104 GLN cc_start: 0.8466 (mp10) cc_final: 0.8110 (mp10) REVERT: D 34 LYS cc_start: 0.9177 (mmmm) cc_final: 0.8592 (mptt) REVERT: D 63 ASN cc_start: 0.8663 (t0) cc_final: 0.8218 (t0) REVERT: D 67 ASN cc_start: 0.8751 (m-40) cc_final: 0.8432 (t0) REVERT: F 64 ASN cc_start: 0.8502 (t0) cc_final: 0.7761 (t0) REVERT: F 91 LYS cc_start: 0.9213 (ttmt) cc_final: 0.8904 (ttpp) REVERT: F 93 GLN cc_start: 0.7939 (mt0) cc_final: 0.6774 (mt0) REVERT: G 24 GLN cc_start: 0.8570 (mm-40) cc_final: 0.8282 (mp10) REVERT: H 83 TYR cc_start: 0.8618 (m-10) cc_final: 0.8254 (m-80) outliers start: 25 outliers final: 21 residues processed: 195 average time/residue: 0.2636 time to fit residues: 71.0709 Evaluate side-chains 199 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 178 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 82 HIS Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain V residue 532 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 94 optimal weight: 8.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN D 82 HIS ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12880 Z= 0.211 Angle : 0.583 6.624 18637 Z= 0.345 Chirality : 0.033 0.159 2114 Planarity : 0.003 0.041 1347 Dihedral : 30.597 168.743 4019 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.04 % Allowed : 28.53 % Favored : 69.44 % 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: 1.20 (0.30), residues: 753 helix: 1.65 (0.23), residues: 517 sheet: None (None), residues: 0 loop : -1.12 (0.37), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 47 HIS 0.019 0.001 HIS D 82 PHE 0.010 0.001 PHE A 67 TYR 0.039 0.002 TYR B 88 ARG 0.003 0.000 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 188 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7873 (pt0) cc_final: 0.7571 (pt0) REVERT: A 127 GLN cc_start: 0.8278 (tp40) cc_final: 0.7956 (tp40) REVERT: B 91 LYS cc_start: 0.8795 (tttt) cc_final: 0.8533 (tptp) REVERT: C 56 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8465 (tm-30) REVERT: C 57 TYR cc_start: 0.9038 (t80) cc_final: 0.8815 (t80) REVERT: C 104 GLN cc_start: 0.8334 (mp10) cc_final: 0.7922 (mp10) REVERT: D 34 LYS cc_start: 0.9175 (mmmm) cc_final: 0.8605 (mptt) REVERT: D 63 ASN cc_start: 0.8475 (t0) cc_final: 0.8068 (t0) REVERT: D 67 ASN cc_start: 0.8691 (m-40) cc_final: 0.8456 (t0) REVERT: D 71 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7796 (tt0) REVERT: F 64 ASN cc_start: 0.8490 (t0) cc_final: 0.7739 (t0) REVERT: F 88 TYR cc_start: 0.8829 (m-10) cc_final: 0.7739 (m-10) REVERT: F 91 LYS cc_start: 0.9182 (ttmt) cc_final: 0.8928 (ttpp) REVERT: F 93 GLN cc_start: 0.7931 (mt0) cc_final: 0.6817 (mt0) REVERT: G 111 ILE cc_start: 0.7354 (OUTLIER) cc_final: 0.6945 (pt) REVERT: H 76 GLU cc_start: 0.7920 (tp30) cc_final: 0.7659 (tp30) outliers start: 13 outliers final: 12 residues processed: 196 average time/residue: 0.2643 time to fit residues: 71.8024 Evaluate side-chains 193 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 180 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain V residue 532 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 97 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 chunk 59 optimal weight: 0.0070 chunk 44 optimal weight: 0.6980 chunk 38 optimal weight: 0.2980 chunk 58 optimal weight: 1.9990 overall best weight: 0.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12880 Z= 0.186 Angle : 0.572 7.311 18637 Z= 0.338 Chirality : 0.033 0.156 2114 Planarity : 0.003 0.043 1347 Dihedral : 30.418 165.080 4019 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.35 % Allowed : 28.68 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.30), residues: 753 helix: 1.84 (0.23), residues: 517 sheet: None (None), residues: 0 loop : -1.12 (0.37), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 47 HIS 0.007 0.001 HIS F 75 PHE 0.009 0.001 PHE A 78 TYR 0.056 0.002 TYR D 83 ARG 0.004 0.000 ARG V 522 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 194 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 GLN cc_start: 0.8197 (tp40) cc_final: 0.7837 (tp40) REVERT: B 91 LYS cc_start: 0.8780 (tttt) cc_final: 0.8557 (tptp) REVERT: C 56 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8217 (tm-30) REVERT: C 57 TYR cc_start: 0.8941 (t80) cc_final: 0.8477 (t80) REVERT: C 61 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7906 (tm-30) REVERT: C 81 ARG cc_start: 0.8406 (tpt170) cc_final: 0.8171 (tpt170) REVERT: C 104 GLN cc_start: 0.8278 (mp10) cc_final: 0.7822 (mp10) REVERT: D 34 LYS cc_start: 0.9185 (mmmm) cc_final: 0.8645 (mptt) REVERT: D 71 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7811 (tt0) REVERT: E 43 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7915 (ptt-90) REVERT: E 45 GLN cc_start: 0.8364 (pt0) cc_final: 0.8027 (pp30) REVERT: E 128 LEU cc_start: 0.8831 (tt) cc_final: 0.8575 (tp) REVERT: E 132 ILE cc_start: 0.9057 (tt) cc_final: 0.8856 (tt) REVERT: F 64 ASN cc_start: 0.8488 (t0) cc_final: 0.7719 (t0) REVERT: F 91 LYS cc_start: 0.9151 (ttmt) cc_final: 0.8895 (ttpp) REVERT: F 93 GLN cc_start: 0.7891 (mt0) cc_final: 0.6821 (mt0) REVERT: G 111 ILE cc_start: 0.7254 (OUTLIER) cc_final: 0.6908 (pt) REVERT: H 76 GLU cc_start: 0.7901 (tp30) cc_final: 0.7633 (tp30) outliers start: 15 outliers final: 12 residues processed: 202 average time/residue: 0.2690 time to fit residues: 75.4970 Evaluate side-chains 193 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 179 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain V residue 532 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12880 Z= 0.214 Angle : 0.587 7.712 18637 Z= 0.347 Chirality : 0.033 0.180 2114 Planarity : 0.004 0.042 1347 Dihedral : 30.414 160.726 4019 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.66 % Allowed : 29.62 % Favored : 67.71 % 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: 1.46 (0.30), residues: 753 helix: 1.87 (0.23), residues: 517 sheet: None (None), residues: 0 loop : -1.11 (0.36), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 47 HIS 0.016 0.001 HIS D 82 PHE 0.025 0.001 PHE A 84 TYR 0.078 0.003 TYR D 83 ARG 0.004 0.000 ARG V 522 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 180 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 GLN cc_start: 0.8243 (tp40) cc_final: 0.7892 (tp40) REVERT: B 91 LYS cc_start: 0.8824 (tttt) cc_final: 0.8400 (tptp) REVERT: C 56 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8265 (tm-30) REVERT: C 57 TYR cc_start: 0.9010 (t80) cc_final: 0.8573 (t80) REVERT: C 61 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7910 (tm-30) REVERT: C 81 ARG cc_start: 0.8435 (tpt170) cc_final: 0.8111 (tpt170) REVERT: C 104 GLN cc_start: 0.8347 (mp10) cc_final: 0.7903 (mp10) REVERT: D 34 LYS cc_start: 0.9217 (mmmm) cc_final: 0.8656 (mptt) REVERT: D 62 MET cc_start: 0.8218 (mmm) cc_final: 0.7833 (mmm) REVERT: D 63 ASN cc_start: 0.8440 (t0) cc_final: 0.8040 (t0) REVERT: D 71 GLU cc_start: 0.8363 (tm-30) cc_final: 0.7907 (tt0) REVERT: E 45 GLN cc_start: 0.8365 (pt0) cc_final: 0.8038 (pp30) REVERT: F 64 ASN cc_start: 0.8487 (t0) cc_final: 0.7710 (t0) REVERT: F 88 TYR cc_start: 0.8439 (m-10) cc_final: 0.8123 (m-10) REVERT: F 91 LYS cc_start: 0.9191 (ttmt) cc_final: 0.8930 (ttpp) REVERT: F 93 GLN cc_start: 0.7924 (mt0) cc_final: 0.6861 (mt0) REVERT: G 111 ILE cc_start: 0.7284 (OUTLIER) cc_final: 0.6926 (pt) REVERT: H 76 GLU cc_start: 0.8005 (tp30) cc_final: 0.7774 (tp30) REVERT: H 83 TYR cc_start: 0.7876 (m-80) cc_final: 0.7394 (m-80) outliers start: 17 outliers final: 14 residues processed: 189 average time/residue: 0.2544 time to fit residues: 68.3412 Evaluate side-chains 193 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 178 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain V residue 532 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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: 0.8312 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12880 Z= 0.278 Angle : 0.626 10.229 18637 Z= 0.364 Chirality : 0.035 0.174 2114 Planarity : 0.004 0.041 1347 Dihedral : 30.480 159.720 4019 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.82 % Allowed : 29.78 % Favored : 67.40 % 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: 1.32 (0.30), residues: 753 helix: 1.74 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -1.09 (0.36), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP V 530 HIS 0.006 0.001 HIS F 75 PHE 0.019 0.001 PHE A 84 TYR 0.089 0.003 TYR D 83 ARG 0.005 0.000 ARG V 522 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 182 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 GLN cc_start: 0.8320 (tp40) cc_final: 0.7994 (tp40) REVERT: B 91 LYS cc_start: 0.8877 (tttt) cc_final: 0.8394 (tptp) REVERT: C 56 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8535 (tm-30) REVERT: C 61 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7922 (tm-30) REVERT: C 63 LEU cc_start: 0.9653 (mt) cc_final: 0.9442 (mm) REVERT: C 104 GLN cc_start: 0.8405 (mp10) cc_final: 0.8016 (mp10) REVERT: D 34 LYS cc_start: 0.9205 (mmmm) cc_final: 0.8626 (mptt) REVERT: D 62 MET cc_start: 0.8307 (mmm) cc_final: 0.7544 (mmm) REVERT: D 63 ASN cc_start: 0.8594 (t0) cc_final: 0.8200 (t0) REVERT: E 43 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7909 (ptt-90) REVERT: F 64 ASN cc_start: 0.8532 (t0) cc_final: 0.7693 (t0) REVERT: F 91 LYS cc_start: 0.9194 (ttmt) cc_final: 0.8902 (ttpp) REVERT: F 93 GLN cc_start: 0.7907 (mt0) cc_final: 0.7074 (mt0) REVERT: G 111 ILE cc_start: 0.7377 (OUTLIER) cc_final: 0.6992 (pt) REVERT: H 76 GLU cc_start: 0.8087 (tp30) cc_final: 0.7852 (tp30) outliers start: 18 outliers final: 15 residues processed: 192 average time/residue: 0.2678 time to fit residues: 71.3193 Evaluate side-chains 192 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 175 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain V residue 523 ILE Chi-restraints excluded: chain V residue 532 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 8 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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: 0.8266 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12880 Z= 0.221 Angle : 0.612 9.307 18637 Z= 0.357 Chirality : 0.033 0.169 2114 Planarity : 0.004 0.042 1347 Dihedral : 30.415 162.199 4019 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.51 % Allowed : 31.03 % Favored : 66.46 % 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: 1.34 (0.30), residues: 753 helix: 1.75 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -1.07 (0.36), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 47 HIS 0.007 0.001 HIS F 75 PHE 0.012 0.001 PHE A 84 TYR 0.088 0.003 TYR D 83 ARG 0.004 0.000 ARG V 522 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 185 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 GLN cc_start: 0.8260 (tp40) cc_final: 0.7923 (tp40) REVERT: B 91 LYS cc_start: 0.8788 (tttt) cc_final: 0.8572 (tptp) REVERT: C 56 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8291 (tm-30) REVERT: C 57 TYR cc_start: 0.9027 (t80) cc_final: 0.8737 (t80) REVERT: C 81 ARG cc_start: 0.8438 (tpt170) cc_final: 0.8141 (tpt170) REVERT: C 104 GLN cc_start: 0.8366 (mp10) cc_final: 0.7929 (mp10) REVERT: D 34 LYS cc_start: 0.9185 (mmmm) cc_final: 0.8631 (mptt) REVERT: D 62 MET cc_start: 0.8244 (mmm) cc_final: 0.7897 (mmm) REVERT: D 63 ASN cc_start: 0.8484 (t0) cc_final: 0.8109 (t0) REVERT: D 71 GLU cc_start: 0.8382 (tm-30) cc_final: 0.7853 (tt0) REVERT: E 43 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7950 (ptt-90) REVERT: E 45 GLN cc_start: 0.8363 (pt0) cc_final: 0.8038 (pp30) REVERT: F 64 ASN cc_start: 0.8520 (t0) cc_final: 0.7737 (t0) REVERT: F 91 LYS cc_start: 0.9160 (ttmt) cc_final: 0.8894 (ttpp) REVERT: F 93 GLN cc_start: 0.7864 (mt0) cc_final: 0.6830 (mt0) REVERT: G 111 ILE cc_start: 0.7361 (OUTLIER) cc_final: 0.6986 (pt) REVERT: H 76 GLU cc_start: 0.8009 (tp30) cc_final: 0.7753 (tp30) outliers start: 16 outliers final: 14 residues processed: 195 average time/residue: 0.2630 time to fit residues: 71.2826 Evaluate side-chains 196 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 180 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain V residue 523 ILE Chi-restraints excluded: chain V residue 532 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.086885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.060453 restraints weight = 40501.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.062402 restraints weight = 20146.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.063641 restraints weight = 13511.008| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12880 Z= 0.215 Angle : 0.605 8.130 18637 Z= 0.354 Chirality : 0.033 0.167 2114 Planarity : 0.004 0.042 1347 Dihedral : 30.367 165.690 4019 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.51 % Allowed : 30.56 % Favored : 66.93 % 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: 1.41 (0.30), residues: 753 helix: 1.83 (0.23), residues: 515 sheet: None (None), residues: 0 loop : -1.08 (0.36), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 47 HIS 0.006 0.001 HIS F 75 PHE 0.012 0.001 PHE A 84 TYR 0.073 0.003 TYR B 88 ARG 0.003 0.000 ARG V 522 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2206.07 seconds wall clock time: 42 minutes 8.56 seconds (2528.56 seconds total)