Starting phenix.real_space_refine on Fri Aug 7 16:04:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r5k_53590/08_2026/9r5k_53590.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r5k_53590/08_2026/9r5k_53590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9r5k_53590/08_2026/9r5k_53590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r5k_53590/08_2026/9r5k_53590.map" model { file = "/net/cci-nas-00/data/ceres_data/9r5k_53590/08_2026/9r5k_53590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r5k_53590/08_2026/9r5k_53590.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 sd= 0.030 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 323 5.49 5 S 10 5.16 5 C 6836 2.51 5 N 2339 2.21 5 O 2984 1.98 5 H 9764 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22256 Number of models: 1 Model: "" Number of chains: 10 Chain: "I" Number of atoms: 5129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 5129 Classifications: {'DNA': 162} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 161} Chain: "J" Number of atoms: 5148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 5148 Classifications: {'DNA': 162} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 161} Chain: "A" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1622 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 1314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1314 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 1642 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1492 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1620 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1298 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1537 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "H" Number of atoms: 1454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1454 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.71, per 1000 atoms: 0.17 Number of scatterers: 22256 At special positions: 0 Unit cell: (78.65, 155.65, 124.3, 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 10 16.00 P 323 15.00 O 2984 8.00 N 2339 7.00 C 6836 6.00 H 9764 1.00 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: 2.12 Conformation dependent library (CDL) restraints added in 387.6 milliseconds 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1378 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 9 sheets defined 73.0% alpha, 2.7% beta 159 base pairs and 263 stacking pairs defined. Time for finding SS restraints: 4.08 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 4.139A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.664A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.864A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.880A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.867A pdb=" N ARG B 40 " --> pdb=" O ARG B 36 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY B 42 " --> pdb=" O ALA B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.580A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.572A pdb=" N ARG B 92 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.970A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG C 35 " --> pdb=" O HIS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 74 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.984A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.606A pdb=" N ASN C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.707A pdb=" N VAL D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR D 39 " --> pdb=" O ALA D 35 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS D 40 " --> pdb=" O ILE D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 98 Processing helix chain 'D' and resid 102 through 120 removed outlier: 3.639A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 57 removed outlier: 3.605A pdb=" N GLU E 50 " --> pdb=" O VAL E 46 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.528A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.797A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.857A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN E 125 " --> pdb=" O PRO E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.569A pdb=" N ARG F 40 " --> pdb=" O ARG F 36 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY F 42 " --> pdb=" O ALA F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.009A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N HIS F 75 " --> pdb=" O THR F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.507A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.591A 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 removed outlier: 3.636A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.630A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.883A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.619A pdb=" N ASN G 94 " --> pdb=" O ASP G 90 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.534A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 120 removed outlier: 4.037A pdb=" N ALA H 104 " --> pdb=" O PRO H 100 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.440A pdb=" N ARG A 83 " --> 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 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.390A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.086A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 7.057A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.953A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.516A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.817A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 358 hydrogen bonds defined for protein. 1068 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 407 hydrogen bonds 814 hydrogen bond angles 0 basepair planarities 159 basepair parallelities 263 stacking parallelities Total time for adding SS restraints: 4.67 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9764 1.03 - 1.22: 78 1.22 - 1.42: 5610 1.42 - 1.61: 7667 1.61 - 1.80: 23 Bond restraints: 23142 Sorted by residual: bond pdb=" C1' DC I 7 " pdb=" N1 DC I 7 " ideal model delta sigma weight residual 1.468 1.535 -0.067 1.40e-02 5.10e+03 2.28e+01 bond pdb=" N3 DC I 18 " pdb=" C4 DC I 18 " ideal model delta sigma weight residual 1.335 1.302 0.033 7.00e-03 2.04e+04 2.20e+01 bond pdb=" C6 DG J -18 " pdb=" N1 DG J -18 " ideal model delta sigma weight residual 1.391 1.421 -0.030 7.00e-03 2.04e+04 1.80e+01 bond pdb=" C1' DC J 34 " pdb=" N1 DC J 34 " ideal model delta sigma weight residual 1.468 1.520 -0.052 1.40e-02 5.10e+03 1.38e+01 bond pdb=" C3' DC I 6 " pdb=" C2' DC I 6 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.28e+01 ... (remaining 23137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 40330 2.07 - 4.13: 1582 4.13 - 6.20: 20 6.20 - 8.26: 3 8.26 - 10.33: 3 Bond angle restraints: 41938 Sorted by residual: angle pdb=" O4' DG I 70 " pdb=" C1' DG I 70 " pdb=" N9 DG I 70 " ideal model delta sigma weight residual 108.00 112.64 -4.64 7.00e-01 2.04e+00 4.40e+01 angle pdb=" O4' DG I 25 " pdb=" C1' DG I 25 " pdb=" N9 DG I 25 " ideal model delta sigma weight residual 108.00 112.42 -4.42 7.00e-01 2.04e+00 3.99e+01 angle pdb=" O4' DG I -19 " pdb=" C1' DG I -19 " pdb=" N9 DG I -19 " ideal model delta sigma weight residual 108.00 112.27 -4.27 7.00e-01 2.04e+00 3.71e+01 angle pdb=" O4' DG J 20 " pdb=" C1' DG J 20 " pdb=" N9 DG J 20 " ideal model delta sigma weight residual 108.00 112.08 -4.08 7.00e-01 2.04e+00 3.40e+01 angle pdb=" O4' DT I 68 " pdb=" C1' DT I 68 " pdb=" N1 DT I 68 " ideal model delta sigma weight residual 108.00 111.83 -3.83 7.00e-01 2.04e+00 2.99e+01 ... (remaining 41933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 6644 17.41 - 34.82: 1270 34.82 - 52.24: 1098 52.24 - 69.65: 496 69.65 - 87.06: 16 Dihedral angle restraints: 9524 sinusoidal: 7124 harmonic: 2400 Sorted by residual: dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N GLY H 101 " pdb=" CA GLY H 101 " ideal model delta harmonic sigma weight residual 180.00 161.03 18.97 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA ARG E 63 " pdb=" C ARG E 63 " pdb=" N LYS E 64 " pdb=" CA LYS E 64 " ideal model delta harmonic sigma weight residual -180.00 -162.00 -18.00 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA PRO H 47 " pdb=" C PRO H 47 " pdb=" N ASP H 48 " pdb=" CA ASP H 48 " ideal model delta harmonic sigma weight residual -180.00 -162.42 -17.58 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 9521 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1838 0.080 - 0.159: 364 0.159 - 0.239: 8 0.239 - 0.318: 0 0.318 - 0.398: 2 Chirality restraints: 2212 Sorted by residual: chirality pdb=" P DT I -72 " pdb=" OP1 DT I -72 " pdb=" OP2 DT I -72 " pdb=" O5' DT I -72 " both_signs ideal model delta sigma weight residual True 2.34 -2.73 -0.40 2.00e-01 2.50e+01 3.95e+00 chirality pdb=" P DC I -73 " pdb=" OP1 DC I -73 " pdb=" OP2 DC I -73 " pdb=" O5' DC I -73 " both_signs ideal model delta sigma weight residual True 2.34 -2.72 -0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" C3' DG I 11 " pdb=" C4' DG I 11 " pdb=" O3' DG I 11 " pdb=" C2' DG I 11 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.17 2.00e-01 2.50e+01 6.81e-01 ... (remaining 2209 not shown) Planarity restraints: 2309 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU H 103 " -0.013 2.00e-02 2.50e+03 2.51e-02 6.28e+00 pdb=" C LEU H 103 " 0.043 2.00e-02 2.50e+03 pdb=" O LEU H 103 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA H 104 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I -26 " -0.031 2.00e-02 2.50e+03 1.34e-02 5.42e+00 pdb=" N1 DT I -26 " 0.031 2.00e-02 2.50e+03 pdb=" C2 DT I -26 " 0.005 2.00e-02 2.50e+03 pdb=" O2 DT I -26 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DT I -26 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DT I -26 " -0.003 2.00e-02 2.50e+03 pdb=" O4 DT I -26 " -0.011 2.00e-02 2.50e+03 pdb=" C5 DT I -26 " -0.003 2.00e-02 2.50e+03 pdb=" C7 DT I -26 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DT I -26 " 0.002 2.00e-02 2.50e+03 pdb=" H3 DT I -26 " -0.002 2.00e-02 2.50e+03 pdb=" H6 DT I -26 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 15 " 0.031 2.00e-02 2.50e+03 1.33e-02 5.32e+00 pdb=" N1 DT I 15 " -0.030 2.00e-02 2.50e+03 pdb=" C2 DT I 15 " -0.004 2.00e-02 2.50e+03 pdb=" O2 DT I 15 " -0.006 2.00e-02 2.50e+03 pdb=" N3 DT I 15 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DT I 15 " -0.000 2.00e-02 2.50e+03 pdb=" O4 DT I 15 " 0.013 2.00e-02 2.50e+03 pdb=" C5 DT I 15 " 0.002 2.00e-02 2.50e+03 pdb=" C7 DT I 15 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DT I 15 " -0.002 2.00e-02 2.50e+03 pdb=" H3 DT I 15 " 0.001 2.00e-02 2.50e+03 pdb=" H6 DT I 15 " -0.003 2.00e-02 2.50e+03 ... (remaining 2306 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 1155 2.21 - 2.81: 38438 2.81 - 3.41: 53006 3.41 - 4.00: 75238 4.00 - 4.60: 113497 Nonbonded interactions: 281334 Sorted by model distance: nonbonded pdb=" OP2 DA J -43 " pdb="HH21 ARG G 17 " model vdw 1.619 2.450 nonbonded pdb=" OD1 ASN G 68 " pdb="HH21 ARG G 71 " model vdw 1.639 2.450 nonbonded pdb=" OP1 DC I 18 " pdb=" HZ3 LYS E 64 " model vdw 1.650 2.450 nonbonded pdb=" OP1 DG I -24 " pdb="HE21 GLN A 85 " model vdw 1.666 2.450 nonbonded pdb=" O ILE D 36 " pdb=" HZ3 LYS D 40 " model vdw 1.689 2.450 ... (remaining 281329 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' and ((resid 39 and (name N or name CA or name C or name O or name CB \ or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name HA or name HB \ 2 or name HB3)) or resid 40 through 133 or (resid 134 and (name N or name CA or \ name C or name O or name CB or name H or name HA )))) selection = (chain 'E' and ((resid 39 and (name N or name CA or name C or name O or name CB \ or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name HA or name HB \ 2 or name HB3)) or resid 40 through 134)) } ncs_group { reference = (chain 'B' and ((resid 23 and (name N or name CA or name C or name O or name CB \ or name HA )) or resid 24 through 102)) selection = (chain 'F' and ((resid 23 and (name N or name CA or name C or name O or name CB \ or name HA )) or resid 24 through 102)) } ncs_group { reference = (chain 'C' and resid 14 through 109) selection = (chain 'G' and resid 14 through 109) } ncs_group { reference = (chain 'D' and ((resid 30 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name NE or name CZ or name NH1 or name NH2 or name HA o \ r name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name H \ E or name HH11 or name HH12 or name HH21 or name HH22)) or resid 31 through 120 \ or (resid 121 and (name N or name CA or name C or name O or name H )))) 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: 16.110 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: 0.150 Extract box with map and model: 0.530 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 24.020 Find NCS groups from input model: 0.210 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: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 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 : 0.006 0.067 13378 Z= 0.585 Angle : 0.898 10.328 19465 Z= 0.792 Chirality : 0.057 0.398 2212 Planarity : 0.006 0.050 1343 Dihedral : 27.104 87.062 5801 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.29), residues: 726 helix: 1.68 (0.23), residues: 460 sheet: None (None), residues: 0 loop : -0.39 (0.35), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 129 TYR 0.012 0.001 TYR H 80 PHE 0.012 0.001 PHE B 61 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00639 / 0.59 (13378) covalent geometry : angle 0.89842 / 0.79 (19465) hydrogen bonds : bond 0.13045 / 14.64 ( 765) hydrogen bonds : angle 4.88042 / 6.32 ( 1882) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 328 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.8678 (t80) cc_final: 0.8195 (t80) REVERT: A 76 GLN cc_start: 0.8191 (tp-100) cc_final: 0.7436 (tp-100) REVERT: A 93 GLN cc_start: 0.8343 (tt0) cc_final: 0.7358 (tt0) REVERT: A 94 GLU cc_start: 0.8271 (mt-10) cc_final: 0.8054 (mt-10) REVERT: A 97 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7530 (mt-10) REVERT: A 117 VAL cc_start: 0.7937 (m) cc_final: 0.7599 (t) REVERT: A 131 ARG cc_start: 0.8227 (ttm170) cc_final: 0.7800 (ttm-80) REVERT: B 26 ILE cc_start: 0.8793 (tp) cc_final: 0.8578 (tp) REVERT: B 27 GLN cc_start: 0.8231 (mm110) cc_final: 0.7941 (mm110) REVERT: C 39 TYR cc_start: 0.8207 (m-10) cc_final: 0.7948 (m-80) REVERT: C 61 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7721 (mm-30) REVERT: C 64 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7233 (tm-30) REVERT: C 65 LEU cc_start: 0.8534 (mt) cc_final: 0.8101 (mt) REVERT: C 81 ARG cc_start: 0.8254 (ttt90) cc_final: 0.8005 (ttm-80) REVERT: C 92 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7387 (mt-10) REVERT: D 56 MET cc_start: 0.8575 (tpp) cc_final: 0.8260 (tpp) REVERT: D 65 ASP cc_start: 0.7521 (t0) cc_final: 0.7295 (t0) REVERT: D 73 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7731 (mm-30) REVERT: E 70 LEU cc_start: 0.7920 (tp) cc_final: 0.7678 (tp) REVERT: E 74 ILE cc_start: 0.8938 (mt) cc_final: 0.8698 (mt) REVERT: F 27 GLN cc_start: 0.8546 (mm-40) cc_final: 0.8296 (mm110) REVERT: F 35 ARG cc_start: 0.8327 (ttm-80) cc_final: 0.8079 (ttp80) REVERT: F 52 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7619 (mm-30) REVERT: F 91 LYS cc_start: 0.8674 (ttmt) cc_final: 0.8335 (ttmt) REVERT: G 29 ARG cc_start: 0.8055 (ttm170) cc_final: 0.7683 (mmm-85) REVERT: G 51 LEU cc_start: 0.8881 (tp) cc_final: 0.8427 (tt) REVERT: G 65 LEU cc_start: 0.7815 (mt) cc_final: 0.7506 (mm) REVERT: H 43 LYS cc_start: 0.8564 (mmtp) cc_final: 0.8102 (mmtp) REVERT: H 82 LYS cc_start: 0.8037 (mmtt) cc_final: 0.7791 (mmtt) outliers start: 0 outliers final: 0 residues processed: 328 average time/residue: 0.3369 time to fit residues: 143.2027 Evaluate side-chains 322 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS D 44 GLN E 108 ASN H 79 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.119191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.097696 restraints weight = 60212.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.101572 restraints weight = 19438.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.103808 restraints weight = 8837.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.105219 restraints weight = 5268.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.106065 restraints weight = 3854.214| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13378 Z= 0.230 Angle : 0.762 7.323 19465 Z= 0.485 Chirality : 0.047 0.189 2212 Planarity : 0.005 0.073 1343 Dihedral : 30.308 88.622 4361 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.16 % Allowed : 2.47 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.29), residues: 726 helix: 1.78 (0.22), residues: 485 sheet: None (None), residues: 0 loop : -0.75 (0.36), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 76 TYR 0.021 0.002 TYR H 80 PHE 0.011 0.002 PHE B 61 HIS 0.011 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.23 (13378) covalent geometry : angle 0.76169 / 0.49 (19465) hydrogen bonds : bond 0.07301 / 8.12 ( 765) hydrogen bonds : angle 3.99367 / 5.17 ( 1882) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 338 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8076 (mm) cc_final: 0.7775 (mm) REVERT: A 76 GLN cc_start: 0.8160 (tp-100) cc_final: 0.7525 (tp-100) REVERT: A 93 GLN cc_start: 0.8581 (tt0) cc_final: 0.7630 (tt0) REVERT: A 94 GLU cc_start: 0.8322 (mt-10) cc_final: 0.8084 (mt-10) REVERT: A 97 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7694 (mt-10) REVERT: A 105 GLU cc_start: 0.7490 (mp0) cc_final: 0.7132 (mp0) REVERT: A 131 ARG cc_start: 0.8154 (ttm170) cc_final: 0.7745 (ttm-80) REVERT: B 26 ILE cc_start: 0.8960 (tp) cc_final: 0.8735 (tp) REVERT: B 91 LYS cc_start: 0.8839 (ttmt) cc_final: 0.8501 (ttmt) REVERT: C 39 TYR cc_start: 0.8320 (m-10) cc_final: 0.7900 (m-10) REVERT: C 50 TYR cc_start: 0.8211 (t80) cc_final: 0.8000 (t80) REVERT: C 61 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7675 (mm-30) REVERT: C 64 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7156 (tm-30) REVERT: C 65 LEU cc_start: 0.8500 (mt) cc_final: 0.7876 (mm) REVERT: D 48 ASP cc_start: 0.8718 (p0) cc_final: 0.8484 (p0) REVERT: D 51 ILE cc_start: 0.8129 (tt) cc_final: 0.7914 (tt) REVERT: D 56 MET cc_start: 0.8689 (tpp) cc_final: 0.8431 (tpp) REVERT: D 59 MET cc_start: 0.8243 (mmm) cc_final: 0.7697 (mmm) REVERT: D 65 ASP cc_start: 0.7672 (t0) cc_final: 0.7405 (t0) REVERT: D 73 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7908 (mm-30) REVERT: E 70 LEU cc_start: 0.8151 (tp) cc_final: 0.7794 (tp) REVERT: E 74 ILE cc_start: 0.8920 (mt) cc_final: 0.8589 (mt) REVERT: F 27 GLN cc_start: 0.8572 (mm-40) cc_final: 0.8256 (mm110) REVERT: F 52 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7638 (mm-30) REVERT: F 91 LYS cc_start: 0.8696 (ttmt) cc_final: 0.8378 (ttmt) REVERT: G 20 ARG cc_start: 0.8163 (ptp-170) cc_final: 0.7906 (mtm-85) REVERT: G 51 LEU cc_start: 0.8914 (tp) cc_final: 0.8557 (tt) REVERT: G 59 THR cc_start: 0.8670 (t) cc_final: 0.8465 (p) REVERT: G 65 LEU cc_start: 0.7806 (mt) cc_final: 0.7542 (mm) REVERT: G 81 ARG cc_start: 0.8010 (ttt90) cc_final: 0.7604 (tpt170) REVERT: H 34 TYR cc_start: 0.8377 (m-10) cc_final: 0.8170 (m-10) REVERT: H 43 LYS cc_start: 0.8607 (mmtp) cc_final: 0.8129 (mmtp) REVERT: H 76 ARG cc_start: 0.7987 (ttm110) cc_final: 0.7771 (ttm110) REVERT: H 91 ILE cc_start: 0.8487 (mm) cc_final: 0.8243 (mm) REVERT: H 93 THR cc_start: 0.8627 (m) cc_final: 0.8331 (p) outliers start: 1 outliers final: 0 residues processed: 338 average time/residue: 0.3472 time to fit residues: 151.6119 Evaluate side-chains 332 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 35 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 74 optimal weight: 1.9990 chunk 76 optimal weight: 0.2980 chunk 100 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 46 HIS E 108 ASN H 79 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.117353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.095773 restraints weight = 59495.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.099607 restraints weight = 19148.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.101824 restraints weight = 8758.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.103218 restraints weight = 5239.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.104047 restraints weight = 3846.987| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13378 Z= 0.223 Angle : 0.682 8.667 19465 Z= 0.456 Chirality : 0.044 0.188 2212 Planarity : 0.005 0.070 1343 Dihedral : 30.279 89.188 4361 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.16 % Allowed : 1.64 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.30), residues: 726 helix: 1.99 (0.22), residues: 487 sheet: None (None), residues: 0 loop : -0.97 (0.36), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 96 TYR 0.023 0.002 TYR F 88 PHE 0.012 0.001 PHE H 67 HIS 0.006 0.002 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.22 (13378) covalent geometry : angle 0.68202 / 0.46 (19465) hydrogen bonds : bond 0.07071 / 7.88 ( 765) hydrogen bonds : angle 3.84379 / 4.99 ( 1882) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 357 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8113 (mm) cc_final: 0.7639 (mm) REVERT: A 62 ILE cc_start: 0.8354 (mm) cc_final: 0.8118 (mm) REVERT: A 71 VAL cc_start: 0.8901 (t) cc_final: 0.8691 (t) REVERT: A 72 ARG cc_start: 0.9076 (mmt90) cc_final: 0.8772 (mmt180) REVERT: A 76 GLN cc_start: 0.8145 (tp-100) cc_final: 0.7629 (tp-100) REVERT: A 93 GLN cc_start: 0.8580 (tt0) cc_final: 0.7713 (tt0) REVERT: A 97 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7772 (mt-10) REVERT: A 105 GLU cc_start: 0.7877 (mp0) cc_final: 0.7423 (mp0) REVERT: A 131 ARG cc_start: 0.8134 (ttm170) cc_final: 0.7681 (ttm-80) REVERT: B 26 ILE cc_start: 0.9025 (tp) cc_final: 0.8666 (tp) REVERT: B 54 THR cc_start: 0.8923 (m) cc_final: 0.8685 (m) REVERT: C 39 TYR cc_start: 0.8175 (m-10) cc_final: 0.7797 (m-10) REVERT: C 50 TYR cc_start: 0.8229 (t80) cc_final: 0.7774 (t80) REVERT: C 58 LEU cc_start: 0.8869 (mp) cc_final: 0.8614 (mm) REVERT: C 61 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7677 (mm-30) REVERT: C 64 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7221 (tm-30) REVERT: D 40 LYS cc_start: 0.7968 (mppt) cc_final: 0.7730 (mtmm) REVERT: D 48 ASP cc_start: 0.8681 (p0) cc_final: 0.8254 (p0) REVERT: D 56 MET cc_start: 0.8696 (tpp) cc_final: 0.8314 (tpp) REVERT: D 68 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7946 (mt-10) REVERT: D 73 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7930 (mm-30) REVERT: D 112 THR cc_start: 0.8352 (m) cc_final: 0.8104 (m) REVERT: E 70 LEU cc_start: 0.8137 (tp) cc_final: 0.7809 (tp) REVERT: E 74 ILE cc_start: 0.8870 (mt) cc_final: 0.8561 (mt) REVERT: E 103 LEU cc_start: 0.8297 (tp) cc_final: 0.8079 (tp) REVERT: E 125 GLN cc_start: 0.8023 (mp10) cc_final: 0.7791 (mp10) REVERT: E 128 ARG cc_start: 0.8481 (mtp85) cc_final: 0.8207 (mtm180) REVERT: F 27 GLN cc_start: 0.8529 (mm-40) cc_final: 0.8153 (mm110) REVERT: F 35 ARG cc_start: 0.8214 (ttp-170) cc_final: 0.8001 (ttp80) REVERT: F 52 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7591 (mm-30) REVERT: F 58 LEU cc_start: 0.8815 (tp) cc_final: 0.8611 (tt) REVERT: G 41 GLU cc_start: 0.7068 (tt0) cc_final: 0.6845 (tt0) REVERT: G 51 LEU cc_start: 0.8979 (tp) cc_final: 0.8605 (tt) REVERT: G 65 LEU cc_start: 0.7941 (mt) cc_final: 0.7680 (mm) REVERT: G 81 ARG cc_start: 0.8175 (ttt90) cc_final: 0.7542 (tpt170) REVERT: H 44 GLN cc_start: 0.8488 (tm-30) cc_final: 0.8172 (tm-30) REVERT: H 76 ARG cc_start: 0.7753 (ttm110) cc_final: 0.7473 (ttm110) REVERT: H 82 LYS cc_start: 0.8261 (mptt) cc_final: 0.7745 (mptt) REVERT: H 93 THR cc_start: 0.8655 (m) cc_final: 0.8365 (p) REVERT: H 117 LYS cc_start: 0.8812 (tttm) cc_final: 0.8455 (tttm) outliers start: 1 outliers final: 0 residues processed: 357 average time/residue: 0.3508 time to fit residues: 160.9060 Evaluate side-chains 355 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 15 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS E 108 ASN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN H 46 HIS H 79 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.112955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.091514 restraints weight = 61019.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.095217 restraints weight = 19868.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.097372 restraints weight = 9206.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.098677 restraints weight = 5613.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.099516 restraints weight = 4179.972| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 13378 Z= 0.371 Angle : 0.833 7.642 19465 Z= 0.521 Chirality : 0.048 0.196 2212 Planarity : 0.006 0.055 1343 Dihedral : 30.216 89.760 4361 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.49 % Allowed : 2.63 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.28), residues: 726 helix: 0.99 (0.22), residues: 492 sheet: None (None), residues: 0 loop : -1.71 (0.34), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 92 TYR 0.012 0.002 TYR D 34 PHE 0.018 0.002 PHE D 67 HIS 0.010 0.002 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00634 / 0.37 (13378) covalent geometry : angle 0.83278 / 0.52 (19465) hydrogen bonds : bond 0.08687 / 9.63 ( 765) hydrogen bonds : angle 4.62255 / 5.95 ( 1882) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 385 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8208 (mm) cc_final: 0.7617 (mm) REVERT: A 69 ARG cc_start: 0.8223 (mtp180) cc_final: 0.7656 (ttm-80) REVERT: A 72 ARG cc_start: 0.9090 (mmt90) cc_final: 0.8813 (mmt180) REVERT: A 76 GLN cc_start: 0.8291 (tp-100) cc_final: 0.7770 (tp-100) REVERT: A 93 GLN cc_start: 0.8687 (tt0) cc_final: 0.7756 (tt0) REVERT: A 97 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7907 (mt-10) REVERT: A 105 GLU cc_start: 0.7754 (mp0) cc_final: 0.7210 (mp0) REVERT: A 129 ARG cc_start: 0.7805 (ttt180) cc_final: 0.7489 (ttt-90) REVERT: A 131 ARG cc_start: 0.8120 (ttm170) cc_final: 0.7637 (ttm-80) REVERT: B 57 VAL cc_start: 0.8514 (m) cc_final: 0.8308 (m) REVERT: B 61 PHE cc_start: 0.8677 (t80) cc_final: 0.8465 (t80) REVERT: B 64 ASN cc_start: 0.8769 (m-40) cc_final: 0.8244 (m-40) REVERT: B 91 LYS cc_start: 0.8897 (ttmt) cc_final: 0.8378 (tppp) REVERT: B 98 TYR cc_start: 0.7362 (m-10) cc_final: 0.7148 (m-80) REVERT: C 24 GLN cc_start: 0.8357 (mp10) cc_final: 0.8143 (mp10) REVERT: C 29 ARG cc_start: 0.8740 (ttm170) cc_final: 0.8288 (mtp180) REVERT: C 39 TYR cc_start: 0.8223 (m-10) cc_final: 0.7870 (m-10) REVERT: C 58 LEU cc_start: 0.8873 (mp) cc_final: 0.8628 (mm) REVERT: C 61 GLU cc_start: 0.8324 (mm-30) cc_final: 0.7802 (mm-30) REVERT: C 64 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7313 (tm-30) REVERT: C 81 ARG cc_start: 0.8739 (ttm-80) cc_final: 0.8343 (ttt-90) REVERT: C 110 ASN cc_start: 0.8560 (t0) cc_final: 0.8178 (t0) REVERT: D 40 LYS cc_start: 0.8382 (mppt) cc_final: 0.8106 (mtmm) REVERT: D 48 ASP cc_start: 0.8651 (p0) cc_final: 0.8181 (p0) REVERT: D 51 ILE cc_start: 0.8384 (tt) cc_final: 0.8175 (tt) REVERT: D 56 MET cc_start: 0.8779 (tpp) cc_final: 0.8425 (tpp) REVERT: D 59 MET cc_start: 0.8379 (mmm) cc_final: 0.7974 (mmm) REVERT: D 68 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7906 (mt-10) REVERT: D 102 GLU cc_start: 0.8094 (tp30) cc_final: 0.7847 (tp30) REVERT: E 42 ARG cc_start: 0.8125 (mtp180) cc_final: 0.7890 (mtp180) REVERT: E 48 LEU cc_start: 0.8676 (mt) cc_final: 0.8304 (mt) REVERT: E 74 ILE cc_start: 0.8920 (mt) cc_final: 0.8656 (mt) REVERT: E 92 LEU cc_start: 0.8838 (mp) cc_final: 0.8587 (mm) REVERT: E 94 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8084 (mm-30) REVERT: E 97 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7569 (mt-10) REVERT: E 103 LEU cc_start: 0.8322 (tp) cc_final: 0.8114 (tp) REVERT: E 125 GLN cc_start: 0.7981 (mp10) cc_final: 0.7695 (mp10) REVERT: F 27 GLN cc_start: 0.8509 (mm-40) cc_final: 0.8092 (mm110) REVERT: F 35 ARG cc_start: 0.8216 (ttp-170) cc_final: 0.7986 (ttp80) REVERT: F 40 ARG cc_start: 0.8489 (ttm170) cc_final: 0.8221 (ttm-80) REVERT: F 52 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7898 (mm-30) REVERT: G 20 ARG cc_start: 0.8272 (ptp-170) cc_final: 0.8019 (ptp-110) REVERT: G 41 GLU cc_start: 0.7417 (tt0) cc_final: 0.7097 (tt0) REVERT: G 61 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7915 (mm-30) REVERT: G 65 LEU cc_start: 0.8133 (mt) cc_final: 0.7909 (mm) REVERT: G 78 ILE cc_start: 0.8076 (mt) cc_final: 0.7835 (mm) REVERT: G 81 ARG cc_start: 0.8388 (ttt90) cc_final: 0.7963 (tpt170) REVERT: G 83 LEU cc_start: 0.8946 (mp) cc_final: 0.8689 (mt) REVERT: G 85 LEU cc_start: 0.8840 (mt) cc_final: 0.8590 (mt) REVERT: G 100 VAL cc_start: 0.9026 (t) cc_final: 0.8706 (p) REVERT: H 44 GLN cc_start: 0.8500 (tm-30) cc_final: 0.8249 (tm-30) REVERT: H 54 LYS cc_start: 0.8726 (mmtp) cc_final: 0.8348 (mmtp) REVERT: H 73 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7758 (mm-30) REVERT: H 76 ARG cc_start: 0.8304 (ttm110) cc_final: 0.8004 (ttm-80) REVERT: H 82 LYS cc_start: 0.8315 (mptt) cc_final: 0.7811 (mptt) REVERT: H 117 LYS cc_start: 0.8796 (tttm) cc_final: 0.8489 (tttm) outliers start: 3 outliers final: 2 residues processed: 386 average time/residue: 0.3532 time to fit residues: 174.7956 Evaluate side-chains 375 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 373 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.112355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.090925 restraints weight = 59929.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.094592 restraints weight = 19293.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.096708 restraints weight = 8895.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.098006 restraints weight = 5428.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.098792 restraints weight = 4061.967| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 13378 Z= 0.320 Angle : 0.731 7.409 19465 Z= 0.478 Chirality : 0.045 0.170 2212 Planarity : 0.005 0.045 1343 Dihedral : 30.180 89.227 4361 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.29), residues: 726 helix: 1.11 (0.22), residues: 492 sheet: None (None), residues: 0 loop : -1.56 (0.35), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 96 TYR 0.011 0.002 TYR B 51 PHE 0.013 0.001 PHE D 67 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.32 (13378) covalent geometry : angle 0.73133 / 0.48 (19465) hydrogen bonds : bond 0.07960 / 8.82 ( 765) hydrogen bonds : angle 4.44163 / 5.76 ( 1882) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 379 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8196 (mm) cc_final: 0.7595 (mm) REVERT: A 69 ARG cc_start: 0.8239 (mtp180) cc_final: 0.7666 (ttm-80) REVERT: A 72 ARG cc_start: 0.9076 (mmt90) cc_final: 0.8788 (mtt-85) REVERT: A 76 GLN cc_start: 0.8283 (tp-100) cc_final: 0.7784 (tp-100) REVERT: A 93 GLN cc_start: 0.8688 (tt0) cc_final: 0.7749 (tt0) REVERT: A 97 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7915 (mt-10) REVERT: A 129 ARG cc_start: 0.7757 (ttt180) cc_final: 0.7555 (ttt-90) REVERT: A 131 ARG cc_start: 0.8113 (ttm170) cc_final: 0.7760 (ttm-80) REVERT: B 64 ASN cc_start: 0.8759 (m-40) cc_final: 0.8252 (m-40) REVERT: B 67 ARG cc_start: 0.8205 (ttm110) cc_final: 0.7774 (ttp80) REVERT: B 75 HIS cc_start: 0.8875 (t-90) cc_final: 0.8396 (t-170) REVERT: B 91 LYS cc_start: 0.8820 (ttmt) cc_final: 0.8380 (tppp) REVERT: C 24 GLN cc_start: 0.8377 (mp10) cc_final: 0.8125 (mp10) REVERT: C 29 ARG cc_start: 0.8709 (ttm170) cc_final: 0.8210 (mtp85) REVERT: C 39 TYR cc_start: 0.8139 (m-10) cc_final: 0.7799 (m-10) REVERT: C 58 LEU cc_start: 0.8884 (mp) cc_final: 0.8630 (mm) REVERT: C 61 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7830 (mm-30) REVERT: C 64 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7263 (tm-30) REVERT: C 81 ARG cc_start: 0.8730 (ttm-80) cc_final: 0.8277 (ttt-90) REVERT: C 110 ASN cc_start: 0.8488 (t0) cc_final: 0.8227 (t0) REVERT: D 48 ASP cc_start: 0.8677 (p0) cc_final: 0.8206 (p0) REVERT: D 56 MET cc_start: 0.8748 (tpp) cc_final: 0.8427 (tpp) REVERT: D 59 MET cc_start: 0.8351 (mmm) cc_final: 0.7976 (mmm) REVERT: D 68 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7899 (mt-10) REVERT: D 108 VAL cc_start: 0.7816 (m) cc_final: 0.7598 (m) REVERT: D 110 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7816 (mm-30) REVERT: D 112 THR cc_start: 0.8489 (m) cc_final: 0.8273 (m) REVERT: E 42 ARG cc_start: 0.8085 (mtp180) cc_final: 0.7845 (mtp180) REVERT: E 74 ILE cc_start: 0.8895 (mt) cc_final: 0.8660 (mt) REVERT: E 92 LEU cc_start: 0.8810 (mp) cc_final: 0.8605 (mm) REVERT: E 97 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7522 (mt-10) REVERT: E 103 LEU cc_start: 0.8343 (tp) cc_final: 0.8131 (tp) REVERT: E 125 GLN cc_start: 0.8003 (mp10) cc_final: 0.7541 (mp10) REVERT: F 27 GLN cc_start: 0.8486 (mm-40) cc_final: 0.8079 (mm110) REVERT: F 35 ARG cc_start: 0.8203 (ttp-170) cc_final: 0.7960 (ttp80) REVERT: F 52 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7905 (mm-30) REVERT: F 88 TYR cc_start: 0.8260 (m-80) cc_final: 0.7988 (m-80) REVERT: G 20 ARG cc_start: 0.8281 (ptp-170) cc_final: 0.8035 (ptp-110) REVERT: G 29 ARG cc_start: 0.8360 (ttm170) cc_final: 0.7911 (ttp80) REVERT: G 41 GLU cc_start: 0.7401 (tt0) cc_final: 0.7150 (tt0) REVERT: G 61 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7859 (mm-30) REVERT: G 64 GLU cc_start: 0.7012 (tm-30) cc_final: 0.6341 (tm-30) REVERT: G 65 LEU cc_start: 0.8162 (mt) cc_final: 0.7674 (mm) REVERT: G 79 ILE cc_start: 0.8466 (pt) cc_final: 0.8155 (pt) REVERT: G 81 ARG cc_start: 0.8369 (ttt90) cc_final: 0.7969 (tpt170) REVERT: G 83 LEU cc_start: 0.8896 (mp) cc_final: 0.8690 (mt) REVERT: G 85 LEU cc_start: 0.8871 (mt) cc_final: 0.8624 (mt) REVERT: G 100 VAL cc_start: 0.9016 (t) cc_final: 0.8735 (p) REVERT: H 44 GLN cc_start: 0.8494 (tm-30) cc_final: 0.8260 (tm-30) REVERT: H 73 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7785 (mm-30) REVERT: H 76 ARG cc_start: 0.8164 (ttm110) cc_final: 0.7897 (ttm-80) REVERT: H 82 LYS cc_start: 0.8311 (mptt) cc_final: 0.7853 (mptt) REVERT: H 117 LYS cc_start: 0.8813 (tttm) cc_final: 0.8507 (tttm) outliers start: 0 outliers final: 0 residues processed: 379 average time/residue: 0.3413 time to fit residues: 166.3964 Evaluate side-chains 376 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 48 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 15 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 73 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS E 108 ASN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN H 79 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.115573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.094035 restraints weight = 60363.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.097759 restraints weight = 19525.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.099935 restraints weight = 9059.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.101263 restraints weight = 5569.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.102075 restraints weight = 4173.676| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13378 Z= 0.230 Angle : 0.682 7.445 19465 Z= 0.446 Chirality : 0.043 0.210 2212 Planarity : 0.005 0.056 1343 Dihedral : 30.134 89.632 4361 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.33 % Allowed : 1.32 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.30), residues: 726 helix: 1.55 (0.22), residues: 492 sheet: None (None), residues: 0 loop : -1.48 (0.35), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 92 TYR 0.011 0.001 TYR B 51 PHE 0.010 0.001 PHE H 67 HIS 0.012 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.23 (13378) covalent geometry : angle 0.68232 / 0.45 (19465) hydrogen bonds : bond 0.07114 / 7.94 ( 765) hydrogen bonds : angle 4.00346 / 5.26 ( 1882) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 374 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8220 (mm) cc_final: 0.7614 (mm) REVERT: A 63 ARG cc_start: 0.7626 (mmm160) cc_final: 0.7353 (mmm160) REVERT: A 69 ARG cc_start: 0.8192 (mtp180) cc_final: 0.7502 (ttm110) REVERT: A 72 ARG cc_start: 0.9058 (mmt90) cc_final: 0.8781 (mtt-85) REVERT: A 76 GLN cc_start: 0.8259 (tp-100) cc_final: 0.7748 (tp-100) REVERT: A 93 GLN cc_start: 0.8657 (tt0) cc_final: 0.7741 (tt0) REVERT: A 97 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7873 (mt-10) REVERT: A 129 ARG cc_start: 0.7771 (ttt180) cc_final: 0.7530 (ttt-90) REVERT: A 131 ARG cc_start: 0.8085 (ttm170) cc_final: 0.7615 (ttm-80) REVERT: B 64 ASN cc_start: 0.8719 (m-40) cc_final: 0.8475 (m-40) REVERT: B 67 ARG cc_start: 0.8130 (ttm110) cc_final: 0.7863 (ttp80) REVERT: B 91 LYS cc_start: 0.8737 (ttmt) cc_final: 0.8217 (tppp) REVERT: B 92 ARG cc_start: 0.8745 (mtp-110) cc_final: 0.8522 (mtp85) REVERT: C 24 GLN cc_start: 0.8380 (mp10) cc_final: 0.8056 (mp10) REVERT: C 29 ARG cc_start: 0.8684 (ttm170) cc_final: 0.8153 (mtp85) REVERT: C 39 TYR cc_start: 0.8117 (m-10) cc_final: 0.7747 (m-10) REVERT: C 50 TYR cc_start: 0.8560 (t80) cc_final: 0.8300 (t80) REVERT: C 58 LEU cc_start: 0.8860 (mp) cc_final: 0.8604 (mm) REVERT: C 61 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7728 (mm-30) REVERT: C 64 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7237 (tm-30) REVERT: C 65 LEU cc_start: 0.8490 (mt) cc_final: 0.8159 (mm) REVERT: C 81 ARG cc_start: 0.8714 (ttm-80) cc_final: 0.8395 (tpt-90) REVERT: C 110 ASN cc_start: 0.8508 (t0) cc_final: 0.8065 (t0) REVERT: C 112 GLN cc_start: 0.8782 (mm-40) cc_final: 0.8577 (mm110) REVERT: D 42 LEU cc_start: 0.8320 (tp) cc_final: 0.8114 (tp) REVERT: D 48 ASP cc_start: 0.8676 (p0) cc_final: 0.8209 (p0) REVERT: D 56 MET cc_start: 0.8720 (tpp) cc_final: 0.8388 (tpp) REVERT: D 59 MET cc_start: 0.8350 (mmm) cc_final: 0.8003 (mmm) REVERT: D 68 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7861 (mt-10) REVERT: D 112 THR cc_start: 0.8424 (m) cc_final: 0.8210 (m) REVERT: E 42 ARG cc_start: 0.8051 (mtp180) cc_final: 0.7825 (mtp180) REVERT: E 74 ILE cc_start: 0.8873 (mt) cc_final: 0.8619 (mt) REVERT: E 97 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7417 (mt-10) REVERT: E 115 LYS cc_start: 0.9108 (mtpp) cc_final: 0.8818 (mtpp) REVERT: E 125 GLN cc_start: 0.7923 (mp10) cc_final: 0.7475 (mp10) REVERT: F 27 GLN cc_start: 0.8465 (mm-40) cc_final: 0.8068 (mm110) REVERT: F 35 ARG cc_start: 0.8179 (ttp-170) cc_final: 0.7927 (ttp80) REVERT: F 52 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7838 (mm-30) REVERT: F 84 MET cc_start: 0.7173 (tpt) cc_final: 0.6681 (tpp) REVERT: F 88 TYR cc_start: 0.8305 (m-80) cc_final: 0.7922 (m-80) REVERT: G 20 ARG cc_start: 0.8239 (ptp-170) cc_final: 0.7975 (ptp-110) REVERT: G 61 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7877 (mm-30) REVERT: G 81 ARG cc_start: 0.8107 (ttt90) cc_final: 0.7808 (tpt170) REVERT: G 83 LEU cc_start: 0.8894 (mp) cc_final: 0.8690 (mt) REVERT: G 85 LEU cc_start: 0.8839 (mt) cc_final: 0.8577 (mt) REVERT: G 100 VAL cc_start: 0.9013 (t) cc_final: 0.8754 (p) REVERT: H 43 LYS cc_start: 0.8472 (tppp) cc_final: 0.8091 (tppp) REVERT: H 54 LYS cc_start: 0.8690 (mmtp) cc_final: 0.8317 (mmtp) REVERT: H 73 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7780 (mm-30) REVERT: H 76 ARG cc_start: 0.8106 (ttm110) cc_final: 0.7846 (ttm-80) REVERT: H 82 LYS cc_start: 0.8354 (mptt) cc_final: 0.7858 (mptt) REVERT: H 117 LYS cc_start: 0.8805 (tttm) cc_final: 0.8520 (tttm) outliers start: 2 outliers final: 1 residues processed: 375 average time/residue: 0.3545 time to fit residues: 169.7992 Evaluate side-chains 372 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 371 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 97 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN G 38 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.114660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.093320 restraints weight = 59812.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.096984 restraints weight = 19336.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.099116 restraints weight = 8930.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.100425 restraints weight = 5476.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.101215 restraints weight = 4114.725| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 13378 Z= 0.296 Angle : 0.709 7.542 19465 Z= 0.462 Chirality : 0.044 0.152 2212 Planarity : 0.005 0.042 1343 Dihedral : 30.103 89.761 4361 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.16 % Allowed : 1.64 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.29), residues: 726 helix: 1.30 (0.22), residues: 492 sheet: None (None), residues: 0 loop : -1.52 (0.35), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 29 TYR 0.016 0.001 TYR B 51 PHE 0.010 0.001 PHE H 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.30 (13378) covalent geometry : angle 0.70892 / 0.46 (19465) hydrogen bonds : bond 0.07665 / 8.50 ( 765) hydrogen bonds : angle 4.26363 / 5.54 ( 1882) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 377 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8202 (mm) cc_final: 0.7657 (mm) REVERT: A 63 ARG cc_start: 0.7661 (mmm160) cc_final: 0.7355 (mmm160) REVERT: A 64 LYS cc_start: 0.8428 (mptt) cc_final: 0.8040 (mptt) REVERT: A 69 ARG cc_start: 0.8233 (mtp180) cc_final: 0.7665 (ttm-80) REVERT: A 70 LEU cc_start: 0.8417 (tp) cc_final: 0.8210 (tp) REVERT: A 72 ARG cc_start: 0.9077 (mmt90) cc_final: 0.8822 (mtt-85) REVERT: A 76 GLN cc_start: 0.8306 (tp-100) cc_final: 0.7784 (tp-100) REVERT: A 78 PHE cc_start: 0.8089 (m-80) cc_final: 0.7776 (m-80) REVERT: A 93 GLN cc_start: 0.8673 (tt0) cc_final: 0.7813 (tt0) REVERT: A 97 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7964 (mt-10) REVERT: A 131 ARG cc_start: 0.8098 (ttm170) cc_final: 0.7731 (ttm-80) REVERT: B 52 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8105 (mm-30) REVERT: B 64 ASN cc_start: 0.8738 (m-40) cc_final: 0.8537 (m-40) REVERT: B 91 LYS cc_start: 0.8783 (ttmt) cc_final: 0.8312 (tppp) REVERT: B 92 ARG cc_start: 0.8820 (mtp-110) cc_final: 0.8578 (mtp85) REVERT: C 24 GLN cc_start: 0.8387 (mp10) cc_final: 0.8100 (mp10) REVERT: C 29 ARG cc_start: 0.8670 (ttm170) cc_final: 0.8163 (mtp85) REVERT: C 39 TYR cc_start: 0.8120 (m-10) cc_final: 0.7736 (m-10) REVERT: C 58 LEU cc_start: 0.8885 (mp) cc_final: 0.8621 (mm) REVERT: C 61 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7822 (mm-30) REVERT: C 64 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7254 (tm-30) REVERT: C 81 ARG cc_start: 0.8730 (ttm-80) cc_final: 0.8312 (ttt-90) REVERT: C 110 ASN cc_start: 0.8509 (t0) cc_final: 0.8166 (t0) REVERT: D 40 LYS cc_start: 0.8338 (mtmt) cc_final: 0.8076 (mtmt) REVERT: D 42 LEU cc_start: 0.8336 (tp) cc_final: 0.8131 (tp) REVERT: D 48 ASP cc_start: 0.8696 (p0) cc_final: 0.8227 (p0) REVERT: D 56 MET cc_start: 0.8747 (tpp) cc_final: 0.8437 (tpp) REVERT: D 68 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7894 (mt-10) REVERT: D 110 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7668 (mm-30) REVERT: E 42 ARG cc_start: 0.8096 (mtp180) cc_final: 0.7870 (mtp180) REVERT: E 74 ILE cc_start: 0.8882 (mt) cc_final: 0.8631 (mt) REVERT: E 76 GLN cc_start: 0.8428 (tt0) cc_final: 0.8081 (tp40) REVERT: E 97 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7466 (mt-10) REVERT: E 125 GLN cc_start: 0.7994 (mp10) cc_final: 0.7481 (mp10) REVERT: F 27 GLN cc_start: 0.8442 (mm-40) cc_final: 0.8067 (mm110) REVERT: F 35 ARG cc_start: 0.8191 (ttp-170) cc_final: 0.7963 (ttp80) REVERT: F 52 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7906 (mm-30) REVERT: F 88 TYR cc_start: 0.8322 (m-80) cc_final: 0.8042 (m-80) REVERT: G 61 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7815 (mm-30) REVERT: G 64 GLU cc_start: 0.7079 (tm-30) cc_final: 0.6338 (tm-30) REVERT: G 81 ARG cc_start: 0.8171 (ttt90) cc_final: 0.7945 (tpt170) REVERT: G 85 LEU cc_start: 0.8871 (mt) cc_final: 0.8620 (mt) REVERT: G 100 VAL cc_start: 0.9020 (t) cc_final: 0.8759 (p) REVERT: G 107 VAL cc_start: 0.9041 (m) cc_final: 0.8760 (t) REVERT: H 43 LYS cc_start: 0.8470 (tppp) cc_final: 0.8095 (tppp) REVERT: H 54 LYS cc_start: 0.8703 (mmtp) cc_final: 0.8340 (mmtp) REVERT: H 73 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7789 (mm-30) REVERT: H 82 LYS cc_start: 0.8343 (mptt) cc_final: 0.7871 (mptt) REVERT: H 89 ARG cc_start: 0.8275 (mtp85) cc_final: 0.8072 (mtp85) REVERT: H 117 LYS cc_start: 0.8823 (tttm) cc_final: 0.8514 (tttm) outliers start: 1 outliers final: 0 residues processed: 377 average time/residue: 0.3169 time to fit residues: 153.5165 Evaluate side-chains 376 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 89 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN F 25 ASN H 79 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.114159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.092416 restraints weight = 59105.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.096166 restraints weight = 18991.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.098338 restraints weight = 8763.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.099652 restraints weight = 5377.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.100472 restraints weight = 4033.546| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.4727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13378 Z= 0.258 Angle : 0.685 7.447 19465 Z= 0.449 Chirality : 0.043 0.149 2212 Planarity : 0.005 0.044 1343 Dihedral : 30.111 89.488 4361 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.29), residues: 726 helix: 1.34 (0.22), residues: 493 sheet: None (None), residues: 0 loop : -1.53 (0.36), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 29 TYR 0.022 0.002 TYR F 51 PHE 0.015 0.002 PHE G 25 HIS 0.002 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.26 (13378) covalent geometry : angle 0.68511 / 0.45 (19465) hydrogen bonds : bond 0.07302 / 8.15 ( 765) hydrogen bonds : angle 4.12236 / 5.35 ( 1882) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8202 (mm) cc_final: 0.7686 (mm) REVERT: A 63 ARG cc_start: 0.7648 (mmm160) cc_final: 0.7413 (mmm160) REVERT: A 69 ARG cc_start: 0.8220 (mtp180) cc_final: 0.7646 (ttm-80) REVERT: A 72 ARG cc_start: 0.9043 (mmt90) cc_final: 0.8790 (mtt-85) REVERT: A 76 GLN cc_start: 0.8267 (tp-100) cc_final: 0.7794 (tp-100) REVERT: A 78 PHE cc_start: 0.8093 (m-80) cc_final: 0.7786 (m-80) REVERT: A 93 GLN cc_start: 0.8634 (tt0) cc_final: 0.7783 (tt0) REVERT: A 97 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7919 (mt-10) REVERT: A 122 LYS cc_start: 0.8524 (pttm) cc_final: 0.8320 (pttm) REVERT: A 131 ARG cc_start: 0.8115 (ttm170) cc_final: 0.7737 (ttm-80) REVERT: B 52 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8088 (mm-30) REVERT: B 64 ASN cc_start: 0.8750 (m-40) cc_final: 0.8541 (m-40) REVERT: B 91 LYS cc_start: 0.8764 (ttmt) cc_final: 0.8307 (tppp) REVERT: B 92 ARG cc_start: 0.8799 (mtp-110) cc_final: 0.8559 (mtp85) REVERT: C 24 GLN cc_start: 0.8385 (mp10) cc_final: 0.8092 (mp10) REVERT: C 29 ARG cc_start: 0.8714 (ttm170) cc_final: 0.8116 (mtp85) REVERT: C 39 TYR cc_start: 0.8060 (m-10) cc_final: 0.7686 (m-10) REVERT: C 58 LEU cc_start: 0.8887 (mp) cc_final: 0.8634 (mm) REVERT: C 61 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7773 (mm-30) REVERT: C 64 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7305 (tm-30) REVERT: C 81 ARG cc_start: 0.8739 (ttm-80) cc_final: 0.8443 (tpt-90) REVERT: C 110 ASN cc_start: 0.8492 (t0) cc_final: 0.8114 (t0) REVERT: D 40 LYS cc_start: 0.8343 (mtmt) cc_final: 0.8088 (mtmt) REVERT: D 48 ASP cc_start: 0.8699 (p0) cc_final: 0.8209 (p0) REVERT: D 56 MET cc_start: 0.8743 (tpp) cc_final: 0.8412 (tpp) REVERT: D 68 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7872 (mt-10) REVERT: D 108 VAL cc_start: 0.7665 (m) cc_final: 0.7465 (m) REVERT: D 110 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7608 (mm-30) REVERT: E 42 ARG cc_start: 0.8052 (mtp180) cc_final: 0.7844 (mtp180) REVERT: E 74 ILE cc_start: 0.8864 (mt) cc_final: 0.8617 (mt) REVERT: E 76 GLN cc_start: 0.8395 (tt0) cc_final: 0.8064 (tp40) REVERT: E 115 LYS cc_start: 0.9164 (mtpp) cc_final: 0.8845 (mtpp) REVERT: E 125 GLN cc_start: 0.7971 (mp10) cc_final: 0.7444 (mp10) REVERT: F 27 GLN cc_start: 0.8423 (mm-40) cc_final: 0.8039 (mm110) REVERT: F 35 ARG cc_start: 0.8227 (ttp-170) cc_final: 0.7952 (ttp80) REVERT: F 52 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7821 (mm-30) REVERT: F 88 TYR cc_start: 0.8325 (m-80) cc_final: 0.8087 (m-80) REVERT: G 26 PRO cc_start: 0.8357 (Cg_endo) cc_final: 0.8116 (Cg_exo) REVERT: G 55 LEU cc_start: 0.8770 (mp) cc_final: 0.8513 (mp) REVERT: G 61 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7826 (mm-30) REVERT: G 81 ARG cc_start: 0.8168 (ttt90) cc_final: 0.7966 (tpt170) REVERT: G 85 LEU cc_start: 0.8841 (mt) cc_final: 0.8588 (mt) REVERT: G 100 VAL cc_start: 0.9015 (t) cc_final: 0.8767 (p) REVERT: G 107 VAL cc_start: 0.9061 (m) cc_final: 0.8810 (t) REVERT: H 43 LYS cc_start: 0.8426 (tppp) cc_final: 0.8067 (tppp) REVERT: H 54 LYS cc_start: 0.8689 (mmtp) cc_final: 0.8401 (mmtp) REVERT: H 73 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7775 (mm-30) REVERT: H 76 ARG cc_start: 0.8168 (ttm110) cc_final: 0.7781 (ttm-80) REVERT: H 82 LYS cc_start: 0.8372 (mptt) cc_final: 0.7836 (mptt) REVERT: H 117 LYS cc_start: 0.8792 (tttm) cc_final: 0.8483 (tttm) outliers start: 0 outliers final: 0 residues processed: 375 average time/residue: 0.3417 time to fit residues: 164.9950 Evaluate side-chains 372 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 4 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS C 112 GLN D 46 HIS E 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.114781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.093051 restraints weight = 59627.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.096764 restraints weight = 19089.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.098935 restraints weight = 8819.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.100248 restraints weight = 5421.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.101060 restraints weight = 4084.945| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.4867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13378 Z= 0.241 Angle : 0.669 7.050 19465 Z= 0.439 Chirality : 0.042 0.167 2212 Planarity : 0.005 0.042 1343 Dihedral : 30.093 89.487 4361 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.33 % Allowed : 0.33 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.29), residues: 726 helix: 1.44 (0.22), residues: 494 sheet: None (None), residues: 0 loop : -1.57 (0.36), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 92 TYR 0.016 0.001 TYR B 51 PHE 0.014 0.002 PHE E 104 HIS 0.009 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.24 (13378) covalent geometry : angle 0.66905 / 0.44 (19465) hydrogen bonds : bond 0.06987 / 7.78 ( 765) hydrogen bonds : angle 4.00199 / 5.21 ( 1882) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 378 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8229 (mm) cc_final: 0.7760 (mm) REVERT: A 63 ARG cc_start: 0.7667 (mmm160) cc_final: 0.7399 (mmm160) REVERT: A 69 ARG cc_start: 0.8222 (mtp180) cc_final: 0.7518 (ttm110) REVERT: A 70 LEU cc_start: 0.8378 (tp) cc_final: 0.8139 (tp) REVERT: A 72 ARG cc_start: 0.9045 (mmt90) cc_final: 0.8687 (mtt-85) REVERT: A 76 GLN cc_start: 0.8297 (tp-100) cc_final: 0.7799 (tp-100) REVERT: A 78 PHE cc_start: 0.8081 (m-80) cc_final: 0.7858 (m-80) REVERT: A 93 GLN cc_start: 0.8654 (tt0) cc_final: 0.7830 (tt0) REVERT: A 97 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7916 (mt-10) REVERT: A 122 LYS cc_start: 0.8520 (pttm) cc_final: 0.8313 (pttm) REVERT: A 131 ARG cc_start: 0.8107 (ttm170) cc_final: 0.7721 (ttm-80) REVERT: B 52 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8141 (mm-30) REVERT: B 64 ASN cc_start: 0.8724 (m-40) cc_final: 0.8416 (m-40) REVERT: B 67 ARG cc_start: 0.8158 (ttm110) cc_final: 0.7812 (ttp80) REVERT: B 91 LYS cc_start: 0.8789 (ttmt) cc_final: 0.8309 (tppp) REVERT: B 92 ARG cc_start: 0.8829 (mtp-110) cc_final: 0.8593 (mtp85) REVERT: C 24 GLN cc_start: 0.8368 (mp10) cc_final: 0.8055 (mp10) REVERT: C 29 ARG cc_start: 0.8700 (ttm170) cc_final: 0.8080 (mtp85) REVERT: C 58 LEU cc_start: 0.8882 (mp) cc_final: 0.8630 (mm) REVERT: C 61 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7764 (mm-30) REVERT: C 63 LEU cc_start: 0.8991 (mm) cc_final: 0.8775 (mm) REVERT: C 64 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7357 (tm-30) REVERT: C 65 LEU cc_start: 0.8424 (mt) cc_final: 0.8219 (mt) REVERT: C 81 ARG cc_start: 0.8727 (ttm-80) cc_final: 0.8435 (tpt-90) REVERT: C 110 ASN cc_start: 0.8439 (t0) cc_final: 0.8172 (t0) REVERT: D 40 LYS cc_start: 0.8323 (mtmt) cc_final: 0.8045 (mtmt) REVERT: D 42 LEU cc_start: 0.8327 (tp) cc_final: 0.8102 (tp) REVERT: D 48 ASP cc_start: 0.8729 (p0) cc_final: 0.8228 (p0) REVERT: D 56 MET cc_start: 0.8751 (tpp) cc_final: 0.8439 (tpp) REVERT: D 68 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7900 (mt-10) REVERT: D 108 VAL cc_start: 0.7695 (m) cc_final: 0.7402 (m) REVERT: D 110 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7647 (mm-30) REVERT: E 42 ARG cc_start: 0.8088 (mtp180) cc_final: 0.7857 (mtp180) REVERT: E 74 ILE cc_start: 0.8872 (mt) cc_final: 0.8649 (mt) REVERT: E 76 GLN cc_start: 0.8427 (tt0) cc_final: 0.8107 (tp40) REVERT: E 115 LYS cc_start: 0.9170 (mtpp) cc_final: 0.8849 (mtpp) REVERT: E 125 GLN cc_start: 0.7973 (mp10) cc_final: 0.7450 (mp10) REVERT: E 129 ARG cc_start: 0.8302 (ttt-90) cc_final: 0.8094 (ttt-90) REVERT: F 27 GLN cc_start: 0.8436 (mm-40) cc_final: 0.8054 (mm110) REVERT: F 35 ARG cc_start: 0.8196 (ttp-170) cc_final: 0.7914 (ttp80) REVERT: F 88 TYR cc_start: 0.8367 (m-80) cc_final: 0.8129 (m-80) REVERT: G 20 ARG cc_start: 0.8238 (ptp-170) cc_final: 0.7972 (ptp-110) REVERT: G 55 LEU cc_start: 0.8697 (mp) cc_final: 0.8454 (mp) REVERT: G 61 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7837 (mm-30) REVERT: G 100 VAL cc_start: 0.9006 (t) cc_final: 0.8777 (p) REVERT: G 107 VAL cc_start: 0.9072 (m) cc_final: 0.8798 (t) REVERT: H 43 LYS cc_start: 0.8380 (tppp) cc_final: 0.8033 (tppp) REVERT: H 54 LYS cc_start: 0.8674 (mmtp) cc_final: 0.8372 (mmtp) REVERT: H 73 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7533 (mm-30) REVERT: H 76 ARG cc_start: 0.8145 (ttm110) cc_final: 0.7777 (ttm-80) REVERT: H 82 LYS cc_start: 0.8313 (mptt) cc_final: 0.7867 (mptt) REVERT: H 117 LYS cc_start: 0.8789 (tttm) cc_final: 0.8513 (tttm) outliers start: 2 outliers final: 0 residues processed: 378 average time/residue: 0.3123 time to fit residues: 152.0100 Evaluate side-chains 375 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 15 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 81 ASN E 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.113817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.092099 restraints weight = 59756.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.095841 restraints weight = 19159.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.097999 restraints weight = 8832.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.099312 restraints weight = 5415.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.100106 restraints weight = 4064.938| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13378 Z= 0.264 Angle : 0.675 6.807 19465 Z= 0.443 Chirality : 0.042 0.168 2212 Planarity : 0.005 0.056 1343 Dihedral : 30.091 89.285 4361 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.16 % Allowed : 0.33 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.29), residues: 726 helix: 1.36 (0.22), residues: 494 sheet: None (None), residues: 0 loop : -1.57 (0.36), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 81 TYR 0.015 0.001 TYR B 51 PHE 0.012 0.002 PHE E 104 HIS 0.010 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.26 (13378) covalent geometry : angle 0.67500 / 0.44 (19465) hydrogen bonds : bond 0.07165 / 7.98 ( 765) hydrogen bonds : angle 4.08446 / 5.29 ( 1882) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 376 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8228 (mm) cc_final: 0.7775 (mm) REVERT: A 63 ARG cc_start: 0.7644 (mmm160) cc_final: 0.7404 (mmm160) REVERT: A 69 ARG cc_start: 0.8236 (mtp180) cc_final: 0.7675 (ttm-80) REVERT: A 70 LEU cc_start: 0.8435 (tp) cc_final: 0.8194 (tp) REVERT: A 72 ARG cc_start: 0.9033 (mmt90) cc_final: 0.8697 (mtt-85) REVERT: A 76 GLN cc_start: 0.8276 (tp-100) cc_final: 0.7819 (tp-100) REVERT: A 78 PHE cc_start: 0.8103 (m-80) cc_final: 0.7785 (m-80) REVERT: A 93 GLN cc_start: 0.8650 (tt0) cc_final: 0.7833 (tt0) REVERT: A 97 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7926 (mt-10) REVERT: A 109 LEU cc_start: 0.8535 (mp) cc_final: 0.8303 (mp) REVERT: A 122 LYS cc_start: 0.8542 (pttm) cc_final: 0.8338 (pttm) REVERT: A 128 ARG cc_start: 0.8415 (mmm-85) cc_final: 0.8022 (mmm-85) REVERT: B 64 ASN cc_start: 0.8756 (m-40) cc_final: 0.8512 (m-40) REVERT: B 91 LYS cc_start: 0.8774 (ttmt) cc_final: 0.8358 (tppp) REVERT: C 24 GLN cc_start: 0.8347 (mp10) cc_final: 0.8019 (mp10) REVERT: C 29 ARG cc_start: 0.8672 (ttm170) cc_final: 0.8078 (mtp85) REVERT: C 58 LEU cc_start: 0.8915 (mp) cc_final: 0.8656 (mm) REVERT: C 61 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7779 (mm-30) REVERT: C 64 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7354 (tm-30) REVERT: C 81 ARG cc_start: 0.8747 (ttm-80) cc_final: 0.8467 (tpt-90) REVERT: C 110 ASN cc_start: 0.8498 (t0) cc_final: 0.8231 (t0) REVERT: D 40 LYS cc_start: 0.8377 (mtmt) cc_final: 0.8122 (mtmt) REVERT: D 42 LEU cc_start: 0.8334 (tp) cc_final: 0.8112 (tp) REVERT: D 48 ASP cc_start: 0.8706 (p0) cc_final: 0.8192 (p0) REVERT: D 56 MET cc_start: 0.8747 (tpp) cc_final: 0.8415 (tpp) REVERT: D 68 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7902 (mt-10) REVERT: D 110 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7590 (mm-30) REVERT: E 42 ARG cc_start: 0.8073 (mtp180) cc_final: 0.7857 (mtp180) REVERT: E 74 ILE cc_start: 0.8876 (mt) cc_final: 0.8625 (mt) REVERT: E 76 GLN cc_start: 0.8436 (tt0) cc_final: 0.8141 (tp40) REVERT: E 115 LYS cc_start: 0.9174 (mtpp) cc_final: 0.8852 (mtpp) REVERT: E 125 GLN cc_start: 0.7991 (mp10) cc_final: 0.7436 (mp10) REVERT: E 129 ARG cc_start: 0.8301 (ttt-90) cc_final: 0.7957 (ttt-90) REVERT: F 35 ARG cc_start: 0.8212 (ttp-170) cc_final: 0.7952 (ttp80) REVERT: F 52 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7829 (mm-30) REVERT: F 53 GLU cc_start: 0.7690 (tt0) cc_final: 0.7474 (tt0) REVERT: F 88 TYR cc_start: 0.8361 (m-80) cc_final: 0.8115 (m-80) REVERT: G 50 TYR cc_start: 0.8177 (t80) cc_final: 0.7971 (t80) REVERT: G 55 LEU cc_start: 0.8698 (mp) cc_final: 0.8457 (mp) REVERT: G 61 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7761 (mm-30) REVERT: G 100 VAL cc_start: 0.9021 (t) cc_final: 0.8787 (p) REVERT: G 107 VAL cc_start: 0.9035 (m) cc_final: 0.8738 (t) REVERT: H 43 LYS cc_start: 0.8371 (tppp) cc_final: 0.8021 (tppp) REVERT: H 54 LYS cc_start: 0.8693 (mmtp) cc_final: 0.8399 (mmtp) REVERT: H 73 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7633 (mm-30) REVERT: H 76 ARG cc_start: 0.8186 (ttm110) cc_final: 0.7815 (ttm-80) REVERT: H 82 LYS cc_start: 0.8317 (mptt) cc_final: 0.7885 (mptt) REVERT: H 117 LYS cc_start: 0.8787 (tttm) cc_final: 0.8507 (tttm) outliers start: 1 outliers final: 0 residues processed: 376 average time/residue: 0.3140 time to fit residues: 151.9776 Evaluate side-chains 375 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 30 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 75 optimal weight: 0.5980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS E 108 ASN F 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.116118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.094141 restraints weight = 58949.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.097875 restraints weight = 18904.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.100048 restraints weight = 8762.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.101386 restraints weight = 5412.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.102129 restraints weight = 4084.154| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.5118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13378 Z= 0.192 Angle : 0.633 6.062 19465 Z= 0.419 Chirality : 0.041 0.177 2212 Planarity : 0.005 0.055 1343 Dihedral : 30.080 89.179 4361 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.33 % Allowed : 0.00 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.30), residues: 726 helix: 1.69 (0.22), residues: 494 sheet: None (None), residues: 0 loop : -1.49 (0.36), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 32 TYR 0.019 0.001 TYR F 51 PHE 0.016 0.001 PHE E 104 HIS 0.012 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.19 (13378) covalent geometry : angle 0.63281 / 0.42 (19465) hydrogen bonds : bond 0.06482 / 7.26 ( 765) hydrogen bonds : angle 3.73025 / 4.87 ( 1882) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5126.49 seconds wall clock time: 87 minutes 47.23 seconds (5267.23 seconds total)