Starting phenix.real_space_refine on Sat Jul 4 18:21:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r5k_53590/07_2026/9r5k_53590.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r5k_53590/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9r5k_53590/07_2026/9r5k_53590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r5k_53590/07_2026/9r5k_53590.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9r5k_53590/07_2026/9r5k_53590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r5k_53590/07_2026/9r5k_53590.map" } 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-dev-6108/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: 3.64, per 1000 atoms: 0.16 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: 1.53 Conformation dependent library (CDL) restraints added in 438.3 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: 3.60 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: 4.78 Time building geometry restraints manager: 2.25 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: 40343 2.07 - 4.13: 1569 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: 16.100 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: 0.110 Extract box with map and model: 0.610 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 21.920 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.150 ------------------------------------------------------------------------------- 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 : 0.891 10.328 19465 Z= 0.785 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 0.89056 / 0.78 (19465) hydrogen bonds : bond 0.13045 / 14.57 ( 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 : 0.334 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 67 PHE cc_start: 0.8678 (t80) cc_final: 0.8199 (t80) REVERT: A 76 GLN cc_start: 0.8191 (tp-100) cc_final: 0.7437 (tp-100) REVERT: A 93 GLN cc_start: 0.8343 (tt0) cc_final: 0.7352 (tt0) REVERT: A 94 GLU cc_start: 0.8271 (mt-10) cc_final: 0.8048 (mt-10) REVERT: A 97 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7533 (mt-10) REVERT: A 117 VAL cc_start: 0.7937 (m) cc_final: 0.7605 (t) REVERT: A 131 ARG cc_start: 0.8227 (ttm170) cc_final: 0.7799 (ttm-80) REVERT: B 26 ILE cc_start: 0.8793 (tp) cc_final: 0.8581 (tp) REVERT: B 27 GLN cc_start: 0.8231 (mm110) cc_final: 0.7939 (mm110) REVERT: C 39 TYR cc_start: 0.8207 (m-10) cc_final: 0.7947 (m-80) REVERT: C 61 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7725 (mm-30) REVERT: C 64 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7235 (tm-30) REVERT: C 65 LEU cc_start: 0.8534 (mt) cc_final: 0.8102 (mt) REVERT: C 81 ARG cc_start: 0.8254 (ttt90) cc_final: 0.8006 (ttm-80) REVERT: C 92 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7383 (mt-10) REVERT: D 56 MET cc_start: 0.8575 (tpp) cc_final: 0.8264 (tpp) REVERT: D 65 ASP cc_start: 0.7521 (t0) cc_final: 0.7301 (t0) REVERT: D 73 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7729 (mm-30) REVERT: E 70 LEU cc_start: 0.7920 (tp) cc_final: 0.7666 (tp) REVERT: E 74 ILE cc_start: 0.8938 (mt) cc_final: 0.8696 (mt) REVERT: F 27 GLN cc_start: 0.8546 (mm-40) cc_final: 0.8294 (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: 0.7616 (mm-30) REVERT: F 91 LYS cc_start: 0.8674 (ttmt) cc_final: 0.8339 (ttmt) REVERT: G 29 ARG cc_start: 0.8055 (ttm170) cc_final: 0.7690 (mmm-85) REVERT: G 51 LEU cc_start: 0.8881 (tp) cc_final: 0.8423 (tt) REVERT: G 65 LEU cc_start: 0.7815 (mt) cc_final: 0.7508 (mm) REVERT: H 43 LYS cc_start: 0.8564 (mmtp) cc_final: 0.8106 (mmtp) REVERT: H 82 LYS cc_start: 0.8037 (mmtt) cc_final: 0.7740 (mmtt) outliers start: 0 outliers final: 0 residues processed: 328 average time/residue: 0.2929 time to fit residues: 123.6788 Evaluate side-chains 321 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS D 44 GLN D 46 HIS E 108 ASN H 79 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.116534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.095103 restraints weight = 60454.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.098929 restraints weight = 19502.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.101119 restraints weight = 8889.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.102484 restraints weight = 5328.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.103276 restraints weight = 3924.225| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 13378 Z= 0.291 Angle : 0.805 7.313 19465 Z= 0.511 Chirality : 0.050 0.201 2212 Planarity : 0.006 0.068 1343 Dihedral : 30.296 88.563 4361 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.33 % Allowed : 2.14 % Favored : 97.53 % 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: 1.18 (0.29), residues: 726 helix: 1.60 (0.22), residues: 485 sheet: None (None), residues: 0 loop : -0.89 (0.36), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 83 TYR 0.021 0.002 TYR H 80 PHE 0.012 0.002 PHE B 61 HIS 0.010 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.29 (13378) covalent geometry : angle 0.80547 / 0.51 (19465) hydrogen bonds : bond 0.07862 / 8.70 ( 765) hydrogen bonds : angle 4.23310 / 5.47 ( 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 352 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 350 time to evaluate : 0.339 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: 0.8122 (mm) cc_final: 0.7814 (mm) REVERT: A 62 ILE cc_start: 0.8324 (mm) cc_final: 0.8078 (mm) REVERT: A 67 PHE cc_start: 0.8790 (t80) cc_final: 0.8566 (t80) REVERT: A 72 ARG cc_start: 0.9105 (mmt90) cc_final: 0.8855 (mtt90) REVERT: A 76 GLN cc_start: 0.8206 (tp-100) cc_final: 0.7576 (tp-100) REVERT: A 93 GLN cc_start: 0.8575 (tt0) cc_final: 0.7628 (tt0) REVERT: A 94 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8131 (mt-10) REVERT: A 97 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7753 (mt-10) REVERT: A 105 GLU cc_start: 0.7563 (mp0) cc_final: 0.7233 (mp0) REVERT: A 117 VAL cc_start: 0.8489 (m) cc_final: 0.8248 (t) REVERT: A 131 ARG cc_start: 0.8147 (ttm170) cc_final: 0.7731 (ttm-80) REVERT: B 26 ILE cc_start: 0.8992 (tp) cc_final: 0.8769 (tp) REVERT: B 27 GLN cc_start: 0.8169 (mm110) cc_final: 0.7969 (mm110) REVERT: B 91 LYS cc_start: 0.8902 (ttmt) cc_final: 0.8455 (tppp) REVERT: C 39 TYR cc_start: 0.8342 (m-10) cc_final: 0.7912 (m-10) REVERT: C 50 TYR cc_start: 0.8302 (t80) cc_final: 0.8074 (t80) REVERT: C 61 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7732 (mm-30) REVERT: C 64 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7216 (tm-30) REVERT: C 65 LEU cc_start: 0.8521 (mt) cc_final: 0.7948 (mm) REVERT: D 48 ASP cc_start: 0.8755 (p0) cc_final: 0.8513 (p0) REVERT: D 51 ILE cc_start: 0.8156 (tt) cc_final: 0.7922 (tt) REVERT: D 56 MET cc_start: 0.8742 (tpp) cc_final: 0.8480 (tpp) REVERT: D 57 SER cc_start: 0.8722 (m) cc_final: 0.8168 (t) REVERT: D 59 MET cc_start: 0.8285 (mmm) cc_final: 0.7732 (mmm) REVERT: D 90 GLU cc_start: 0.7962 (mp0) cc_final: 0.7501 (mp0) REVERT: E 42 ARG cc_start: 0.8064 (mtp180) cc_final: 0.7813 (mtp180) REVERT: E 74 ILE cc_start: 0.8937 (mt) cc_final: 0.8687 (mt) REVERT: E 80 THR cc_start: 0.8185 (t) cc_final: 0.7972 (t) REVERT: F 27 GLN cc_start: 0.8580 (mm-40) cc_final: 0.8247 (mm110) REVERT: F 36 ARG cc_start: 0.8198 (mtm-85) cc_final: 0.7992 (mtm-85) REVERT: F 52 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7709 (mm-30) REVERT: G 51 LEU cc_start: 0.8948 (tp) cc_final: 0.8584 (tt) REVERT: G 59 THR cc_start: 0.8681 (t) cc_final: 0.8435 (p) REVERT: G 81 ARG cc_start: 0.8079 (ttt90) cc_final: 0.7681 (tpt170) REVERT: H 34 TYR cc_start: 0.8478 (m-10) cc_final: 0.8276 (m-10) REVERT: H 43 LYS cc_start: 0.8627 (mmtp) cc_final: 0.8176 (mmtp) REVERT: H 91 ILE cc_start: 0.8542 (mm) cc_final: 0.8315 (mm) REVERT: H 93 THR cc_start: 0.8647 (m) cc_final: 0.8356 (p) outliers start: 2 outliers final: 0 residues processed: 350 average time/residue: 0.3074 time to fit residues: 137.2357 Evaluate side-chains 343 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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: 2.9990 chunk 100 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 108 ASN H 79 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.116919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.095680 restraints weight = 60143.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.099377 restraints weight = 19722.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.101544 restraints weight = 9145.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.102878 restraints weight = 5562.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.103733 restraints weight = 4137.422| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3039 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= 0.254 Angle : 0.710 11.606 19465 Z= 0.470 Chirality : 0.045 0.189 2212 Planarity : 0.006 0.087 1343 Dihedral : 30.307 88.596 4361 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.16 % Allowed : 1.48 % 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: 1.20 (0.29), residues: 726 helix: 1.72 (0.22), residues: 487 sheet: None (None), residues: 0 loop : -1.17 (0.35), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 96 TYR 0.011 0.001 TYR H 80 PHE 0.007 0.001 PHE F 61 HIS 0.007 0.002 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.25 (13378) covalent geometry : angle 0.70954 / 0.47 (19465) hydrogen bonds : bond 0.07478 / 8.28 ( 765) hydrogen bonds : angle 4.03215 / 5.21 ( 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 369 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 368 time to evaluate : 0.464 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: A 60 LEU cc_start: 0.8171 (mm) cc_final: 0.7709 (mm) REVERT: A 62 ILE cc_start: 0.8350 (mm) cc_final: 0.8109 (mm) REVERT: A 69 ARG cc_start: 0.8138 (mtp180) cc_final: 0.7582 (ttm-80) REVERT: A 72 ARG cc_start: 0.9107 (mmt90) cc_final: 0.8816 (mtt90) REVERT: A 74 ILE cc_start: 0.8634 (mt) cc_final: 0.8432 (tp) REVERT: A 76 GLN cc_start: 0.8205 (tp-100) cc_final: 0.7655 (tp-100) REVERT: A 78 PHE cc_start: 0.8299 (m-80) cc_final: 0.8086 (m-80) REVERT: A 93 GLN cc_start: 0.8594 (tt0) cc_final: 0.7689 (tt0) REVERT: A 97 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7875 (mt-10) REVERT: A 105 GLU cc_start: 0.7827 (mp0) cc_final: 0.7442 (mp0) REVERT: A 117 VAL cc_start: 0.8522 (m) cc_final: 0.8257 (t) REVERT: A 129 ARG cc_start: 0.7740 (ttt180) cc_final: 0.7455 (ttt-90) REVERT: A 131 ARG cc_start: 0.8127 (ttm170) cc_final: 0.7668 (ttm-80) REVERT: B 27 GLN cc_start: 0.8132 (mm110) cc_final: 0.7931 (mm110) REVERT: B 57 VAL cc_start: 0.8485 (m) cc_final: 0.8264 (m) REVERT: C 17 ARG cc_start: 0.8456 (mtp180) cc_final: 0.8164 (mtp85) REVERT: C 29 ARG cc_start: 0.8603 (ttm170) cc_final: 0.8257 (mtp85) REVERT: C 39 TYR cc_start: 0.8174 (m-10) cc_final: 0.7744 (m-10) REVERT: C 50 TYR cc_start: 0.8295 (t80) cc_final: 0.7969 (t80) REVERT: C 58 LEU cc_start: 0.8874 (mp) cc_final: 0.8643 (mm) REVERT: C 61 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7652 (mm-30) REVERT: C 64 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7285 (tm-30) REVERT: C 110 ASN cc_start: 0.8562 (t0) cc_final: 0.8348 (t0) REVERT: D 48 ASP cc_start: 0.8692 (p0) cc_final: 0.8232 (p0) REVERT: D 51 ILE cc_start: 0.8237 (tt) cc_final: 0.8030 (tt) REVERT: D 56 MET cc_start: 0.8730 (tpp) cc_final: 0.8377 (tpp) REVERT: D 68 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7946 (mt-10) REVERT: D 83 ARG cc_start: 0.7629 (mtp85) cc_final: 0.7244 (mtp85) REVERT: D 90 GLU cc_start: 0.7955 (mp0) cc_final: 0.7611 (mp0) REVERT: D 96 ARG cc_start: 0.8597 (ttm110) cc_final: 0.8392 (ttm110) REVERT: E 62 ILE cc_start: 0.8339 (tt) cc_final: 0.8095 (tt) REVERT: E 70 LEU cc_start: 0.8192 (tp) cc_final: 0.7878 (tp) REVERT: E 74 ILE cc_start: 0.8866 (mt) cc_final: 0.8570 (mt) REVERT: E 93 GLN cc_start: 0.8495 (tt0) cc_final: 0.7895 (tt0) REVERT: E 97 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7653 (mt-10) REVERT: E 103 LEU cc_start: 0.8308 (tp) cc_final: 0.8085 (tp) REVERT: E 122 LYS cc_start: 0.8951 (mtmt) cc_final: 0.8625 (mtmt) REVERT: F 27 GLN cc_start: 0.8529 (mm-40) cc_final: 0.8112 (mm110) REVERT: F 35 ARG cc_start: 0.8224 (ttp-170) cc_final: 0.7992 (ttp80) REVERT: F 52 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7765 (mm-30) REVERT: F 58 LEU cc_start: 0.8835 (tp) cc_final: 0.8614 (tt) REVERT: F 78 ARG cc_start: 0.7593 (ptt180) cc_final: 0.7347 (ptt180) REVERT: F 84 MET cc_start: 0.6670 (tpt) cc_final: 0.6174 (tpp) REVERT: G 20 ARG cc_start: 0.8182 (ptp-170) cc_final: 0.7886 (mtm-85) REVERT: G 32 ARG cc_start: 0.8478 (ttp-170) cc_final: 0.8138 (ttp-170) REVERT: G 35 ARG cc_start: 0.8052 (ttm-80) cc_final: 0.7443 (ttm-80) REVERT: G 41 GLU cc_start: 0.7175 (tt0) cc_final: 0.6913 (tt0) REVERT: G 51 LEU cc_start: 0.8970 (tp) cc_final: 0.8691 (tt) REVERT: G 61 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7807 (mm-30) REVERT: G 81 ARG cc_start: 0.8239 (ttt90) cc_final: 0.7804 (tpt170) REVERT: G 83 LEU cc_start: 0.8793 (mp) cc_final: 0.8450 (mt) REVERT: H 44 GLN cc_start: 0.8490 (tm-30) cc_final: 0.8177 (tm-30) REVERT: H 54 LYS cc_start: 0.8435 (mmmm) cc_final: 0.8228 (mmmm) REVERT: H 73 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7639 (mm-30) REVERT: H 82 LYS cc_start: 0.8165 (mptt) cc_final: 0.7727 (mptt) REVERT: H 117 LYS cc_start: 0.8818 (tttm) cc_final: 0.8495 (tttm) outliers start: 1 outliers final: 0 residues processed: 368 average time/residue: 0.3424 time to fit residues: 160.4425 Evaluate side-chains 365 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 365 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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: 5.9990 chunk 43 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3551 r_free = 0.3551 target = 0.113502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.092040 restraints weight = 60571.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.095709 restraints weight = 19594.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.097835 restraints weight = 9082.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.099136 restraints weight = 5564.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.099944 restraints weight = 4162.412| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 13378 Z= 0.346 Angle : 0.799 8.011 19465 Z= 0.506 Chirality : 0.047 0.196 2212 Planarity : 0.005 0.043 1343 Dihedral : 30.241 89.374 4361 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.49 % Allowed : 2.14 % 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: 0.34 (0.28), residues: 726 helix: 1.10 (0.22), residues: 492 sheet: None (None), residues: 0 loop : -1.65 (0.34), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 92 TYR 0.021 0.002 TYR B 98 PHE 0.018 0.002 PHE D 67 HIS 0.009 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.35 (13378) covalent geometry : angle 0.79859 / 0.51 (19465) hydrogen bonds : bond 0.08424 / 9.27 ( 765) hydrogen bonds : angle 4.50741 / 5.82 ( 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 383 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 380 time to evaluate : 0.380 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: A 60 LEU cc_start: 0.8239 (mm) cc_final: 0.7720 (mm) REVERT: A 69 ARG cc_start: 0.8211 (mtp180) cc_final: 0.7668 (ttm-80) REVERT: A 71 VAL cc_start: 0.8973 (t) cc_final: 0.8763 (t) REVERT: A 72 ARG cc_start: 0.9129 (mmt90) cc_final: 0.8868 (mtt90) REVERT: A 76 GLN cc_start: 0.8305 (tp-100) cc_final: 0.7750 (tp-100) REVERT: A 93 GLN cc_start: 0.8667 (tt0) cc_final: 0.7696 (tt0) REVERT: A 97 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7930 (mt-10) REVERT: A 105 GLU cc_start: 0.7695 (mp0) cc_final: 0.7249 (mp0) REVERT: A 117 VAL cc_start: 0.8549 (m) cc_final: 0.8347 (t) REVERT: A 129 ARG cc_start: 0.7815 (ttt180) cc_final: 0.7519 (ttt-90) REVERT: A 131 ARG cc_start: 0.8104 (ttm170) cc_final: 0.7718 (ttm-80) REVERT: B 26 ILE cc_start: 0.9049 (tp) cc_final: 0.8792 (tp) REVERT: B 27 GLN cc_start: 0.8172 (mm110) cc_final: 0.7957 (mm110) REVERT: B 52 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8098 (mm-30) REVERT: B 61 PHE cc_start: 0.8626 (t80) cc_final: 0.8423 (t80) REVERT: B 91 LYS cc_start: 0.8892 (ttmt) cc_final: 0.8383 (tppp) REVERT: B 98 TYR cc_start: 0.7615 (m-10) cc_final: 0.7315 (m-80) REVERT: C 29 ARG cc_start: 0.8734 (ttm170) cc_final: 0.8311 (ttm170) REVERT: C 39 TYR cc_start: 0.8198 (m-10) cc_final: 0.7849 (m-10) REVERT: C 58 LEU cc_start: 0.8870 (mp) cc_final: 0.8617 (mm) REVERT: C 61 GLU cc_start: 0.8374 (mm-30) cc_final: 0.7895 (mm-30) REVERT: C 64 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7261 (tm-30) REVERT: C 71 ARG cc_start: 0.8390 (ttp-170) cc_final: 0.8178 (ttp-170) REVERT: C 81 ARG cc_start: 0.8771 (ttm-80) cc_final: 0.8301 (ttt-90) REVERT: C 110 ASN cc_start: 0.8586 (t0) cc_final: 0.8198 (t0) REVERT: D 40 LYS cc_start: 0.8364 (mtmm) cc_final: 0.7975 (mtmm) REVERT: D 48 ASP cc_start: 0.8703 (p0) cc_final: 0.8242 (p0) REVERT: D 56 MET cc_start: 0.8794 (tpp) cc_final: 0.8432 (tpp) REVERT: D 59 MET cc_start: 0.8400 (mmm) cc_final: 0.8003 (mmm) REVERT: D 68 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7952 (mt-10) REVERT: D 83 ARG cc_start: 0.7726 (mtp85) cc_final: 0.7329 (mtp85) REVERT: D 110 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7793 (mm-30) REVERT: E 42 ARG cc_start: 0.8115 (mtp180) cc_final: 0.7874 (mtp180) REVERT: E 48 LEU cc_start: 0.8685 (mt) cc_final: 0.8317 (mt) REVERT: E 62 ILE cc_start: 0.8365 (tt) cc_final: 0.8081 (tt) REVERT: E 74 ILE cc_start: 0.8891 (mt) cc_final: 0.8637 (mt) REVERT: E 92 LEU cc_start: 0.8812 (mp) cc_final: 0.8607 (mm) REVERT: E 93 GLN cc_start: 0.8621 (tt0) cc_final: 0.7877 (tt0) REVERT: E 97 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7670 (mt-10) REVERT: E 103 LEU cc_start: 0.8307 (tp) cc_final: 0.8088 (tp) REVERT: E 125 GLN cc_start: 0.8114 (mp10) cc_final: 0.7787 (mp10) REVERT: E 128 ARG cc_start: 0.8638 (mtp85) cc_final: 0.8392 (mtm180) REVERT: F 27 GLN cc_start: 0.8529 (mm-40) cc_final: 0.8128 (mm110) REVERT: F 35 ARG cc_start: 0.8216 (ttp-170) cc_final: 0.7981 (ttp80) REVERT: F 40 ARG cc_start: 0.8509 (ttm170) cc_final: 0.8271 (ttm-80) REVERT: F 52 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7874 (mm-30) REVERT: F 78 ARG cc_start: 0.7612 (ptt180) cc_final: 0.7370 (ptt180) REVERT: F 84 MET cc_start: 0.7235 (tpt) cc_final: 0.6843 (tpp) REVERT: G 26 PRO cc_start: 0.8319 (Cg_endo) cc_final: 0.8082 (Cg_exo) REVERT: G 41 GLU cc_start: 0.7468 (tt0) cc_final: 0.7095 (tt0) REVERT: G 61 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7860 (mm-30) REVERT: G 81 ARG cc_start: 0.8390 (ttt90) cc_final: 0.8073 (tpt170) REVERT: G 83 LEU cc_start: 0.8897 (mp) cc_final: 0.8685 (mt) REVERT: G 85 LEU cc_start: 0.8850 (mt) cc_final: 0.8591 (mt) REVERT: G 100 VAL cc_start: 0.9001 (t) cc_final: 0.8659 (p) REVERT: H 44 GLN cc_start: 0.8517 (tm-30) cc_final: 0.8252 (tm-30) REVERT: H 73 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7760 (mm-30) REVERT: H 82 LYS cc_start: 0.8296 (mptt) cc_final: 0.7784 (mptt) REVERT: H 83 ARG cc_start: 0.8437 (ttm-80) cc_final: 0.8081 (ttm110) REVERT: H 117 LYS cc_start: 0.8818 (tttm) cc_final: 0.8500 (tttm) outliers start: 3 outliers final: 1 residues processed: 381 average time/residue: 0.3293 time to fit residues: 160.1841 Evaluate side-chains 373 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 372 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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: 3.9990 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: 0.9990 chunk 82 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN E 108 ASN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.115253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.093739 restraints weight = 59445.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.097437 restraints weight = 19187.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.099575 restraints weight = 8866.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.100878 restraints weight = 5431.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.101672 restraints weight = 4078.688| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13378 Z= 0.256 Angle : 0.678 7.203 19465 Z= 0.450 Chirality : 0.043 0.151 2212 Planarity : 0.005 0.045 1343 Dihedral : 30.219 89.149 4361 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.16 % Allowed : 1.32 % Favored : 98.52 % 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: 0.93 (0.29), residues: 726 helix: 1.54 (0.22), residues: 490 sheet: None (None), residues: 0 loop : -1.38 (0.35), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 36 TYR 0.010 0.002 TYR C 50 PHE 0.011 0.001 PHE D 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.26 (13378) covalent geometry : angle 0.67814 / 0.45 (19465) hydrogen bonds : bond 0.07323 / 8.09 ( 765) hydrogen bonds : angle 4.10767 / 5.36 ( 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 377 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 376 time to evaluate : 0.424 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: A 60 LEU cc_start: 0.8219 (mm) cc_final: 0.7652 (mm) REVERT: A 69 ARG cc_start: 0.8190 (mtp180) cc_final: 0.7510 (ttm110) REVERT: A 72 ARG cc_start: 0.9062 (mmt90) cc_final: 0.8778 (mtt90) REVERT: A 93 GLN cc_start: 0.8642 (tt0) cc_final: 0.7666 (tt0) REVERT: A 97 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7889 (mt-10) REVERT: A 117 VAL cc_start: 0.8528 (m) cc_final: 0.8276 (t) REVERT: A 131 ARG cc_start: 0.8115 (ttm170) cc_final: 0.7639 (ttm-80) REVERT: B 52 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8021 (mm-30) REVERT: B 75 HIS cc_start: 0.8881 (t-90) cc_final: 0.8271 (t-90) REVERT: B 91 LYS cc_start: 0.8760 (ttmt) cc_final: 0.8290 (tppp) REVERT: C 29 ARG cc_start: 0.8635 (ttm170) cc_final: 0.8164 (mtp85) REVERT: C 39 TYR cc_start: 0.8094 (m-10) cc_final: 0.7748 (m-10) REVERT: C 58 LEU cc_start: 0.8867 (mp) cc_final: 0.8619 (mm) REVERT: C 61 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7763 (mm-30) REVERT: C 64 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7249 (tm-30) REVERT: C 81 ARG cc_start: 0.8721 (ttm-80) cc_final: 0.8247 (ttt-90) REVERT: C 110 ASN cc_start: 0.8496 (t0) cc_final: 0.8039 (t0) REVERT: D 48 ASP cc_start: 0.8684 (p0) cc_final: 0.8212 (p0) REVERT: D 56 MET cc_start: 0.8750 (tpp) cc_final: 0.8414 (tpp) REVERT: D 59 MET cc_start: 0.8337 (mmm) cc_final: 0.7987 (mmm) REVERT: D 68 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7889 (mt-10) REVERT: D 83 ARG cc_start: 0.7643 (mtp85) cc_final: 0.7362 (mtp85) REVERT: D 108 VAL cc_start: 0.7793 (m) cc_final: 0.7486 (m) REVERT: D 110 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7775 (mm-30) REVERT: D 112 THR cc_start: 0.8504 (m) cc_final: 0.8103 (m) REVERT: E 42 ARG cc_start: 0.8045 (mtp180) cc_final: 0.7804 (mtp180) REVERT: E 62 ILE cc_start: 0.8273 (tt) cc_final: 0.7988 (tt) REVERT: E 74 ILE cc_start: 0.8869 (mt) cc_final: 0.8625 (mt) REVERT: E 93 GLN cc_start: 0.8528 (tt0) cc_final: 0.7848 (tt0) REVERT: E 97 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7623 (mt-10) REVERT: E 103 LEU cc_start: 0.8311 (tp) cc_final: 0.8092 (tp) REVERT: E 115 LYS cc_start: 0.8999 (mtpp) cc_final: 0.8683 (mtpp) REVERT: E 125 GLN cc_start: 0.7912 (mp10) cc_final: 0.7654 (mp10) REVERT: F 27 GLN cc_start: 0.8468 (mm-40) cc_final: 0.8064 (mm110) REVERT: F 35 ARG cc_start: 0.8207 (ttp-170) cc_final: 0.7948 (ttp80) REVERT: F 52 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7840 (mm-30) REVERT: F 78 ARG cc_start: 0.7530 (ptt180) cc_final: 0.7267 (ptt180) REVERT: F 84 MET cc_start: 0.7163 (tpt) cc_final: 0.6752 (tpp) REVERT: G 29 ARG cc_start: 0.8291 (ttm170) cc_final: 0.7859 (ttp80) REVERT: G 61 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7917 (mm-30) REVERT: G 81 ARG cc_start: 0.8349 (ttt90) cc_final: 0.7954 (tpt170) REVERT: G 85 LEU cc_start: 0.8868 (mt) cc_final: 0.8593 (mt) REVERT: G 88 ARG cc_start: 0.8671 (mmt180) cc_final: 0.8371 (tpp-160) REVERT: G 100 VAL cc_start: 0.9006 (t) cc_final: 0.8684 (p) REVERT: H 43 LYS cc_start: 0.8476 (tppp) cc_final: 0.8110 (tppp) REVERT: H 54 LYS cc_start: 0.8501 (mmmm) cc_final: 0.8283 (mmmm) REVERT: H 73 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7723 (mm-30) REVERT: H 82 LYS cc_start: 0.8280 (mptt) cc_final: 0.7817 (mptt) REVERT: H 89 ARG cc_start: 0.8250 (mtp85) cc_final: 0.7995 (mtp85) REVERT: H 117 LYS cc_start: 0.8818 (tttm) cc_final: 0.8502 (tttm) outliers start: 1 outliers final: 0 residues processed: 376 average time/residue: 0.3191 time to fit residues: 153.1714 Evaluate side-chains 371 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 371 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.2888 > 50: distance: 85 - 99: 34.645 distance: 99 - 100: 40.434 distance: 99 - 104: 68.617 distance: 100 - 103: 40.255 distance: 100 - 105: 40.354 distance: 101 - 102: 70.167 distance: 101 - 109: 56.893 distance: 103 - 106: 55.797 distance: 103 - 107: 56.210 distance: 103 - 108: 69.974 distance: 109 - 110: 57.088 distance: 109 - 118: 40.206 distance: 110 - 111: 39.273 distance: 110 - 113: 39.043 distance: 110 - 119: 40.363 distance: 111 - 112: 56.099 distance: 111 - 126: 40.897 distance: 113 - 114: 57.447 distance: 113 - 120: 39.670 distance: 113 - 121: 68.602 distance: 114 - 115: 68.389 distance: 114 - 122: 40.713 distance: 114 - 123: 56.440 distance: 115 - 116: 39.712 distance: 115 - 117: 57.392 distance: 117 - 124: 40.207 distance: 117 - 125: 39.218 distance: 126 - 127: 39.779 distance: 126 - 130: 39.413 distance: 127 - 128: 55.864 distance: 127 - 131: 55.798 distance: 127 - 132: 57.352 distance: 128 - 129: 57.587 distance: 128 - 133: 56.764 distance: 133 - 134: 56.642 distance: 133 - 137: 40.064 distance: 134 - 135: 57.189 distance: 134 - 138: 55.914 distance: 134 - 139: 40.477 distance: 135 - 136: 38.908 distance: 135 - 140: 56.885 distance: 140 - 141: 70.609 distance: 141 - 142: 40.882 distance: 141 - 144: 41.038 distance: 141 - 148: 55.764 distance: 142 - 143: 68.646 distance: 142 - 156: 56.473 distance: 144 - 146: 56.817 distance: 144 - 149: 57.126 distance: 145 - 150: 55.817 distance: 145 - 151: 39.694 distance: 145 - 152: 69.143 distance: 146 - 153: 39.373 distance: 146 - 154: 40.377 distance: 146 - 155: 39.339 distance: 156 - 157: 55.895 distance: 156 - 164: 39.257 distance: 157 - 158: 69.823 distance: 157 - 160: 57.043 distance: 157 - 165: 39.788 distance: 158 - 159: 68.052 distance: 158 - 175: 69.875 distance: 160 - 161: 39.607 distance: 160 - 166: 40.788 distance: 160 - 167: 39.573 distance: 161 - 162: 56.906 distance: 161 - 163: 40.185 distance: 161 - 168: 48.635 distance: 162 - 169: 55.710 distance: 162 - 170: 40.585 distance: 162 - 171: 39.489 distance: 163 - 172: 69.910 distance: 163 - 173: 55.975 distance: 163 - 174: 56.802 distance: 175 - 176: 57.613 distance: 175 - 181: 69.723 distance: 176 - 177: 55.415 distance: 176 - 179: 38.740 distance: 176 - 182: 56.541 distance: 177 - 178: 40.188 distance: 177 - 189: 39.172 distance: 179 - 180: 56.646 distance: 179 - 183: 39.750 distance: 179 - 184: 39.496 distance: 180 - 185: 39.267 distance: 180 - 186: 57.250 distance: 181 - 187: 55.792 distance: 181 - 188: 57.290 distance: 189 - 190: 40.479 distance: 189 - 197: 57.255 distance: 190 - 191: 39.812 distance: 190 - 193: 39.028 distance: 190 - 198: 56.437 distance: 191 - 192: 70.315 distance: 191 - 203: 56.886 distance: 193 - 199: 56.783 distance: 193 - 200: 55.609 distance: 194 - 195: 56.222 distance: 196 - 201: 40.302 distance: 196 - 202: 57.144 distance: 203 - 204: 39.942 distance: 203 - 211: 40.435 distance: 204 - 205: 56.672 distance: 204 - 207: 39.914 distance: 204 - 212: 69.840 distance: 205 - 206: 41.156 distance: 205 - 222: 39.322 distance: 207 - 208: 41.048 distance: 207 - 209: 39.281 distance: 207 - 213: 40.654 distance: 208 - 210: 55.972 distance: 208 - 214: 69.048 distance: 208 - 215: 69.529 distance: 209 - 216: 56.381 distance: 209 - 217: 46.987 distance: 209 - 218: 40.612 distance: 210 - 220: 40.768 distance: 210 - 221: 55.918 distance: 222 - 231: 56.786 distance: 223 - 224: 41.221 distance: 223 - 226: 68.363 distance: 223 - 232: 69.094 distance: 224 - 225: 57.014 distance: 224 - 239: 34.724 distance: 226 - 227: 46.479 distance: 226 - 233: 69.193 distance: 226 - 234: 56.073 distance: 227 - 228: 43.489 distance: 227 - 235: 44.387 distance: 227 - 236: 43.118 distance: 228 - 229: 68.840 distance: 228 - 230: 3.493 distance: 230 - 237: 40.892 distance: 230 - 238: 56.071