Starting phenix.real_space_refine on Fri Feb 6 03:34:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r5k_53590/02_2026/9r5k_53590.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r5k_53590/02_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_53590/02_2026/9r5k_53590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r5k_53590/02_2026/9r5k_53590.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9r5k_53590/02_2026/9r5k_53590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r5k_53590/02_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-2.0-5952/lib/python3.9/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: 3.12, per 1000 atoms: 0.14 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: 1.63 Conformation dependent library (CDL) restraints added in 309.5 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: 3.96 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: 4.87 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=" C TYR A 41 " pdb=" N ARG A 42 " ideal model delta sigma weight residual 1.333 1.384 -0.051 2.74e-02 1.33e+03 3.52e+00 bond pdb=" C PRO G 80 " pdb=" O PRO G 80 " ideal model delta sigma weight residual 1.237 1.258 -0.020 1.26e-02 6.30e+03 2.60e+00 bond pdb=" N3 DC I 18 " pdb=" C4 DC I 18 " ideal model delta sigma weight residual 1.334 1.302 0.032 2.00e-02 2.50e+03 2.53e+00 bond pdb=" C ARG A 42 " pdb=" N PRO A 43 " ideal model delta sigma weight residual 1.334 1.371 -0.037 2.34e-02 1.83e+03 2.46e+00 bond pdb=" C1' DC I 7 " pdb=" N1 DC I 7 " ideal model delta sigma weight residual 1.490 1.535 -0.045 3.00e-02 1.11e+03 2.24e+00 ... (remaining 23137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 40782 2.07 - 4.13: 1140 4.13 - 6.20: 10 6.20 - 8.26: 3 8.26 - 10.33: 3 Bond angle restraints: 41938 Sorted by residual: angle pdb=" OP1 DT I -72 " pdb=" P DT I -72 " pdb=" OP2 DT I -72 " ideal model delta sigma weight residual 120.00 109.67 10.33 3.00e+00 1.11e-01 1.19e+01 angle pdb=" CB LYS B 31 " pdb=" CG LYS B 31 " pdb=" CD LYS B 31 " ideal model delta sigma weight residual 111.30 119.13 -7.83 2.30e+00 1.89e-01 1.16e+01 angle pdb=" OP1 DC I -73 " pdb=" P DC I -73 " pdb=" OP2 DC I -73 " ideal model delta sigma weight residual 120.00 109.83 10.17 3.00e+00 1.11e-01 1.15e+01 angle pdb=" O3' DC I -73 " pdb=" P DT I -72 " pdb=" OP1 DT I -72 " ideal model delta sigma weight residual 108.00 116.59 -8.59 3.00e+00 1.11e-01 8.20e+00 angle pdb=" O4' DG I 70 " pdb=" C1' DG I 70 " pdb=" N9 DG I 70 " ideal model delta sigma weight residual 108.40 112.64 -4.24 1.50e+00 4.44e-01 8.00e+00 ... (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 - 0.078: 2099 0.078 - 0.155: 111 0.155 - 0.232: 0 0.232 - 0.310: 0 0.310 - 0.387: 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 2.35 -2.73 -0.39 2.00e-01 2.50e+01 3.75e+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 2.35 -2.72 -0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" C1' DC I 66 " pdb=" O4' DC I 66 " pdb=" C2' DC I 66 " pdb=" N1 DC I 66 " both_signs ideal model delta sigma weight residual False 2.47 2.31 0.15 2.00e-01 2.50e+01 5.96e-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: 13.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 0.450 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 21.110 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 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 : 0.005 0.051 13378 Z= 0.219 Angle : 0.746 10.328 19465 Z= 0.466 Chirality : 0.041 0.387 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 covalent geometry : bond 0.00451 (13378) covalent geometry : angle 0.74636 (19465) hydrogen bonds : bond 0.13045 ( 765) hydrogen bonds : angle 4.88042 ( 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 : 0.473 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: 0.3573 time to fit residues: 147.6057 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 : 0.444 ------------------------------------------------------------------------------- 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: 4.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 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: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3551 r_free = 0.3551 target = 0.114165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.093246 restraints weight = 60461.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.097076 restraints weight = 19493.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.099281 restraints weight = 8829.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.100677 restraints weight = 5238.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.101532 restraints weight = 3803.605| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 13378 Z= 0.281 Angle : 0.706 6.165 19465 Z= 0.444 Chirality : 0.045 0.152 2212 Planarity : 0.005 0.038 1343 Dihedral : 29.853 89.518 4361 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.33 % Allowed : 1.97 % Favored : 97.70 % 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: 1.75 (0.30), residues: 726 helix: 2.05 (0.22), residues: 486 sheet: None (None), residues: 0 loop : -0.71 (0.36), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 83 TYR 0.014 0.002 TYR H 80 PHE 0.008 0.001 PHE G 25 HIS 0.009 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00572 (13378) covalent geometry : angle 0.70587 (19465) hydrogen bonds : bond 0.06677 ( 765) hydrogen bonds : angle 3.80347 ( 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 359 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 357 time to evaluate : 0.381 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: 0.8118 (mm) cc_final: 0.7796 (mm) REVERT: A 67 PHE cc_start: 0.8786 (t80) cc_final: 0.8577 (t80) REVERT: A 69 ARG cc_start: 0.8140 (mtp180) cc_final: 0.7458 (ttm110) REVERT: A 72 ARG cc_start: 0.9119 (mmt90) cc_final: 0.8814 (mtt90) REVERT: A 76 GLN cc_start: 0.8199 (tp-100) cc_final: 0.7606 (tp-100) REVERT: A 93 GLN cc_start: 0.8594 (tt0) cc_final: 0.7635 (tt0) REVERT: A 97 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7785 (mt-10) REVERT: A 105 GLU cc_start: 0.7624 (mp0) cc_final: 0.7377 (mp0) REVERT: A 109 LEU cc_start: 0.8726 (mp) cc_final: 0.8487 (mp) REVERT: A 117 VAL cc_start: 0.8522 (m) cc_final: 0.8267 (t) REVERT: B 26 ILE cc_start: 0.9009 (tp) cc_final: 0.8787 (tp) REVERT: B 27 GLN cc_start: 0.8143 (mm110) cc_final: 0.7931 (mm110) REVERT: C 17 ARG cc_start: 0.8451 (mtp180) cc_final: 0.8181 (mtp85) REVERT: C 29 ARG cc_start: 0.8544 (ttm170) cc_final: 0.8317 (mtp85) REVERT: C 39 TYR cc_start: 0.8273 (m-10) cc_final: 0.7851 (m-10) REVERT: C 58 LEU cc_start: 0.8806 (mt) cc_final: 0.8523 (mm) REVERT: C 61 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7670 (mm-30) REVERT: C 64 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7215 (tm-30) REVERT: C 81 ARG cc_start: 0.8442 (ttt90) cc_final: 0.8233 (ttm-80) REVERT: C 102 ILE cc_start: 0.8712 (mt) cc_final: 0.8499 (mm) REVERT: C 110 ASN cc_start: 0.8573 (t0) cc_final: 0.8308 (t0) REVERT: D 48 ASP cc_start: 0.8772 (p0) cc_final: 0.8453 (p0) REVERT: D 56 MET cc_start: 0.8727 (tpp) cc_final: 0.8327 (tpp) REVERT: D 57 SER cc_start: 0.8665 (m) cc_final: 0.8096 (t) REVERT: D 59 MET cc_start: 0.8286 (mmm) cc_final: 0.7718 (mmm) REVERT: D 83 ARG cc_start: 0.7693 (mtp85) cc_final: 0.7355 (mtp85) REVERT: D 106 HIS cc_start: 0.8793 (m170) cc_final: 0.8428 (m-70) REVERT: D 110 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7720 (mm-30) REVERT: E 60 LEU cc_start: 0.8417 (mt) cc_final: 0.7989 (mt) REVERT: E 62 ILE cc_start: 0.8344 (tt) cc_final: 0.8061 (tt) REVERT: E 70 LEU cc_start: 0.8193 (tp) cc_final: 0.7919 (tp) REVERT: E 74 ILE cc_start: 0.8906 (mt) cc_final: 0.8597 (mt) REVERT: E 93 GLN cc_start: 0.8554 (tt0) cc_final: 0.7861 (tt0) REVERT: E 97 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7495 (mt-10) REVERT: E 103 LEU cc_start: 0.8301 (tp) cc_final: 0.8094 (tp) REVERT: E 129 ARG cc_start: 0.8098 (ttt180) cc_final: 0.7860 (ttt180) REVERT: F 27 GLN cc_start: 0.8558 (mm-40) cc_final: 0.8134 (mm110) REVERT: F 52 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7770 (mm-30) REVERT: F 78 ARG cc_start: 0.7571 (ptt180) cc_final: 0.7358 (ptt180) REVERT: G 20 ARG cc_start: 0.8221 (ptp-170) cc_final: 0.7914 (ptp-110) REVERT: G 41 GLU cc_start: 0.7157 (tt0) cc_final: 0.6884 (tt0) REVERT: G 51 LEU cc_start: 0.8961 (tp) cc_final: 0.8571 (tt) REVERT: G 65 LEU cc_start: 0.7889 (mt) cc_final: 0.7617 (mm) REVERT: G 81 ARG cc_start: 0.8200 (ttt90) cc_final: 0.7754 (tpt170) REVERT: H 34 TYR cc_start: 0.8570 (m-10) cc_final: 0.8358 (m-10) REVERT: H 43 LYS cc_start: 0.8572 (mmtp) cc_final: 0.8084 (mmtp) REVERT: H 73 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7653 (mm-30) REVERT: H 76 ARG cc_start: 0.8032 (ttm110) cc_final: 0.7797 (ttm110) REVERT: H 117 LYS cc_start: 0.8804 (tttm) cc_final: 0.8480 (tttm) outliers start: 2 outliers final: 2 residues processed: 357 average time/residue: 0.3451 time to fit residues: 153.9830 Evaluate side-chains 349 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 347 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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: 2.9990 chunk 75 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN H 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.118114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.096938 restraints weight = 59484.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.100719 restraints weight = 19178.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.102927 restraints weight = 8848.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.104262 restraints weight = 5388.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.105116 restraints weight = 4008.709| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 13378 Z= 0.251 Angle : 0.671 7.383 19465 Z= 0.420 Chirality : 0.043 0.134 2212 Planarity : 0.005 0.049 1343 Dihedral : 29.639 86.816 4361 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.66 % Allowed : 2.80 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.92 (0.30), residues: 726 helix: 2.21 (0.22), residues: 492 sheet: None (None), residues: 0 loop : -0.79 (0.37), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 36 TYR 0.011 0.001 TYR H 80 PHE 0.009 0.001 PHE A 78 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00512 (13378) covalent geometry : angle 0.67106 (19465) hydrogen bonds : bond 0.06025 ( 765) hydrogen bonds : angle 3.62243 ( 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 377 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 373 time to evaluate : 0.323 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: 0.8238 (mm) cc_final: 0.7729 (mm) REVERT: A 69 ARG cc_start: 0.8162 (mtp180) cc_final: 0.7486 (ttm110) REVERT: A 71 VAL cc_start: 0.8962 (t) cc_final: 0.8754 (t) REVERT: A 72 ARG cc_start: 0.9089 (mmt90) cc_final: 0.8775 (mtt-85) REVERT: A 76 GLN cc_start: 0.8185 (tp-100) cc_final: 0.7694 (tp-100) REVERT: A 93 GLN cc_start: 0.8614 (tt0) cc_final: 0.7538 (tt0) REVERT: A 97 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7864 (mt-10) REVERT: A 105 GLU cc_start: 0.7652 (mp0) cc_final: 0.7266 (mp0) REVERT: A 117 VAL cc_start: 0.8549 (m) cc_final: 0.8271 (t) REVERT: A 131 ARG cc_start: 0.8124 (ttm170) cc_final: 0.7659 (ttm-80) REVERT: B 52 GLU cc_start: 0.8440 (mm-30) cc_final: 0.7971 (mm-30) REVERT: B 64 ASN cc_start: 0.8686 (m-40) cc_final: 0.8434 (m-40) REVERT: B 91 LYS cc_start: 0.8745 (ttmt) cc_final: 0.8218 (tppp) REVERT: C 29 ARG cc_start: 0.8654 (ttm170) cc_final: 0.8141 (mtp85) REVERT: C 58 LEU cc_start: 0.8845 (mt) cc_final: 0.8560 (mm) REVERT: C 61 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7696 (mm-30) REVERT: C 64 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7405 (tm-30) REVERT: C 102 ILE cc_start: 0.8825 (mt) cc_final: 0.8604 (mm) REVERT: C 110 ASN cc_start: 0.8588 (t0) cc_final: 0.8192 (t0) REVERT: D 48 ASP cc_start: 0.8703 (p0) cc_final: 0.8154 (p0) REVERT: D 56 MET cc_start: 0.8654 (tpp) cc_final: 0.8262 (tpp) REVERT: D 57 SER cc_start: 0.8711 (m) cc_final: 0.8168 (t) REVERT: D 59 MET cc_start: 0.8315 (mmm) cc_final: 0.7847 (mmm) REVERT: D 110 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7739 (mm-30) REVERT: E 42 ARG cc_start: 0.8021 (mtp180) cc_final: 0.7803 (mtp180) REVERT: E 60 LEU cc_start: 0.8507 (mt) cc_final: 0.7752 (mt) REVERT: E 62 ILE cc_start: 0.8291 (tt) cc_final: 0.7946 (tt) REVERT: E 74 ILE cc_start: 0.8833 (mt) cc_final: 0.8571 (mt) REVERT: E 93 GLN cc_start: 0.8485 (tt0) cc_final: 0.7977 (tt0) REVERT: E 97 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7542 (mt-10) REVERT: E 103 LEU cc_start: 0.8312 (tp) cc_final: 0.7967 (tp) REVERT: F 26 ILE cc_start: 0.8683 (tp) cc_final: 0.8466 (tp) REVERT: F 27 GLN cc_start: 0.8494 (mm-40) cc_final: 0.8037 (mm110) REVERT: F 31 LYS cc_start: 0.8860 (ttpt) cc_final: 0.8621 (ttpt) REVERT: F 35 ARG cc_start: 0.8220 (ttp-170) cc_final: 0.7936 (ttp80) REVERT: F 78 ARG cc_start: 0.7421 (ptt180) cc_final: 0.7145 (ptt180) REVERT: G 20 ARG cc_start: 0.8155 (ptp-170) cc_final: 0.7893 (ptp-110) REVERT: G 29 ARG cc_start: 0.8331 (ttm170) cc_final: 0.8108 (tpp80) REVERT: G 41 GLU cc_start: 0.7454 (tt0) cc_final: 0.7231 (tt0) REVERT: G 61 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7864 (mm-30) REVERT: G 64 GLU cc_start: 0.6719 (tm-30) cc_final: 0.6148 (tm-30) REVERT: G 65 LEU cc_start: 0.8152 (mt) cc_final: 0.7651 (mm) REVERT: G 81 ARG cc_start: 0.8375 (ttt90) cc_final: 0.7991 (tpt170) REVERT: G 83 LEU cc_start: 0.8844 (mp) cc_final: 0.8634 (mt) REVERT: G 85 LEU cc_start: 0.8802 (mt) cc_final: 0.8548 (mt) REVERT: H 54 LYS cc_start: 0.8468 (mmmm) cc_final: 0.8236 (mmmm) REVERT: H 73 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7762 (mm-30) REVERT: H 76 ARG cc_start: 0.8153 (ttm110) cc_final: 0.7854 (ttm-80) REVERT: H 82 LYS cc_start: 0.8286 (mptt) cc_final: 0.7887 (mptt) REVERT: H 117 LYS cc_start: 0.8774 (tttm) cc_final: 0.8486 (tttm) outliers start: 4 outliers final: 2 residues processed: 375 average time/residue: 0.3430 time to fit residues: 161.5145 Evaluate side-chains 367 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 365 time to evaluate : 0.288 ------------------------------------------------------------------------------- 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: 3.9990 chunk 33 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS E 108 ASN F 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.110889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.089676 restraints weight = 60073.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.093367 restraints weight = 19219.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.095498 restraints weight = 8828.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.096772 restraints weight = 5362.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.097578 restraints weight = 4004.607| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 13378 Z= 0.314 Angle : 0.679 6.322 19465 Z= 0.429 Chirality : 0.047 0.150 2212 Planarity : 0.005 0.072 1343 Dihedral : 29.540 87.789 4361 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.16 % Allowed : 1.15 % 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: 1.47 (0.29), residues: 726 helix: 1.92 (0.22), residues: 495 sheet: None (None), residues: 0 loop : -1.16 (0.35), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 36 TYR 0.012 0.001 TYR B 72 PHE 0.015 0.001 PHE E 104 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00640 (13378) covalent geometry : angle 0.67869 (19465) hydrogen bonds : bond 0.06625 ( 765) hydrogen bonds : angle 3.86322 ( 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 380 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 379 time to evaluate : 0.450 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: A 59 GLU cc_start: 0.7338 (pm20) cc_final: 0.7115 (pm20) REVERT: A 60 LEU cc_start: 0.8246 (mm) cc_final: 0.7793 (mm) REVERT: A 69 ARG cc_start: 0.8224 (mtp180) cc_final: 0.7536 (ttm110) REVERT: A 72 ARG cc_start: 0.9070 (mmt90) cc_final: 0.8751 (mtt90) REVERT: A 93 GLN cc_start: 0.8625 (tt0) cc_final: 0.7661 (tt0) REVERT: A 97 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7916 (mt-10) REVERT: A 117 VAL cc_start: 0.8560 (m) cc_final: 0.8305 (t) REVERT: A 131 ARG cc_start: 0.8152 (ttm170) cc_final: 0.7606 (ttm-80) REVERT: B 26 ILE cc_start: 0.9091 (tp) cc_final: 0.8657 (tp) REVERT: B 52 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8187 (mm-30) REVERT: B 64 ASN cc_start: 0.8771 (m-40) cc_final: 0.8532 (m-40) REVERT: B 75 HIS cc_start: 0.9020 (OUTLIER) cc_final: 0.8238 (t-90) REVERT: B 91 LYS cc_start: 0.8719 (ttmt) cc_final: 0.8241 (tppp) REVERT: C 29 ARG cc_start: 0.8670 (ttm170) cc_final: 0.8138 (ttm170) REVERT: C 58 LEU cc_start: 0.8860 (mt) cc_final: 0.8609 (mm) REVERT: C 61 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7755 (mm-30) REVERT: C 64 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7428 (tm-30) REVERT: C 65 LEU cc_start: 0.8487 (mt) cc_final: 0.8184 (mt) REVERT: C 81 ARG cc_start: 0.8825 (ttm-80) cc_final: 0.8566 (tpt-90) REVERT: C 110 ASN cc_start: 0.8535 (t0) cc_final: 0.8177 (t0) REVERT: D 48 ASP cc_start: 0.8749 (p0) cc_final: 0.8171 (p0) REVERT: D 56 MET cc_start: 0.8686 (tpp) cc_final: 0.8350 (tpp) REVERT: D 59 MET cc_start: 0.8346 (mmm) cc_final: 0.7939 (mmm) REVERT: D 68 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7878 (mt-10) REVERT: D 110 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7675 (mm-30) REVERT: D 112 THR cc_start: 0.8463 (m) cc_final: 0.8125 (m) REVERT: E 42 ARG cc_start: 0.8076 (mtp180) cc_final: 0.7843 (mtp180) REVERT: E 60 LEU cc_start: 0.8503 (mt) cc_final: 0.7945 (mt) REVERT: E 62 ILE cc_start: 0.8259 (tt) cc_final: 0.7941 (tt) REVERT: E 74 ILE cc_start: 0.8809 (mt) cc_final: 0.8608 (mt) REVERT: E 93 GLN cc_start: 0.8599 (tt0) cc_final: 0.7952 (tt0) REVERT: E 97 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7517 (mt-10) REVERT: E 122 LYS cc_start: 0.9121 (mtmt) cc_final: 0.8916 (mtmt) REVERT: E 125 GLN cc_start: 0.7843 (mp10) cc_final: 0.7478 (mp10) REVERT: F 27 GLN cc_start: 0.8429 (mm-40) cc_final: 0.8148 (mm110) REVERT: F 35 ARG cc_start: 0.8229 (ttp-170) cc_final: 0.7939 (ttp80) REVERT: F 55 ARG cc_start: 0.8418 (mtt180) cc_final: 0.8099 (mtt180) REVERT: G 29 ARG cc_start: 0.8362 (ttm170) cc_final: 0.8008 (ttp80) REVERT: G 61 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7822 (mm-30) REVERT: G 64 GLU cc_start: 0.7041 (tm-30) cc_final: 0.6311 (tm-30) REVERT: G 65 LEU cc_start: 0.8227 (mt) cc_final: 0.7628 (mm) REVERT: G 100 VAL cc_start: 0.9023 (t) cc_final: 0.8766 (p) REVERT: G 107 VAL cc_start: 0.9021 (m) cc_final: 0.8666 (t) REVERT: H 43 LYS cc_start: 0.8443 (tppp) cc_final: 0.8081 (tppp) REVERT: H 73 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7673 (mm-30) REVERT: H 76 ARG cc_start: 0.8177 (ttm110) cc_final: 0.7813 (ttm-80) REVERT: H 82 LYS cc_start: 0.8438 (mptt) cc_final: 0.7932 (mptt) REVERT: H 117 LYS cc_start: 0.8795 (tttm) cc_final: 0.8499 (tttm) outliers start: 1 outliers final: 0 residues processed: 379 average time/residue: 0.3517 time to fit residues: 166.4508 Evaluate side-chains 371 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 370 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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: 1.9990 chunk 102 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN D 46 HIS 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 = 0.3617 r_free = 0.3617 target = 0.117973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.096585 restraints weight = 59289.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.100303 restraints weight = 19264.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.102455 restraints weight = 8954.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.103773 restraints weight = 5521.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.104552 restraints weight = 4152.568| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13378 Z= 0.225 Angle : 0.631 4.302 19465 Z= 0.400 Chirality : 0.042 0.127 2212 Planarity : 0.004 0.049 1343 Dihedral : 29.440 88.377 4361 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.33 % Allowed : 1.81 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.79 (0.29), residues: 726 helix: 2.13 (0.22), residues: 499 sheet: None (None), residues: 0 loop : -1.01 (0.36), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 36 TYR 0.009 0.001 TYR B 88 PHE 0.005 0.001 PHE H 62 HIS 0.006 0.001 HIS H 79 Details of bonding type rmsd covalent geometry : bond 0.00459 (13378) covalent geometry : angle 0.63125 (19465) hydrogen bonds : bond 0.05675 ( 765) hydrogen bonds : angle 3.50956 ( 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: 2 poor density : 377 time to evaluate : 0.355 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 59 GLU cc_start: 0.7377 (pm20) cc_final: 0.7101 (pm20) REVERT: A 60 LEU cc_start: 0.8258 (mm) cc_final: 0.7865 (mm) REVERT: A 63 ARG cc_start: 0.7588 (mmm160) cc_final: 0.7370 (mmm160) REVERT: A 69 ARG cc_start: 0.8190 (mtp180) cc_final: 0.7505 (ttm110) REVERT: A 70 LEU cc_start: 0.8302 (tp) cc_final: 0.8062 (tp) REVERT: A 72 ARG cc_start: 0.8991 (mmt90) cc_final: 0.8636 (mtt-85) REVERT: A 93 GLN cc_start: 0.8624 (tt0) cc_final: 0.7649 (tt0) REVERT: A 97 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7865 (mt-10) REVERT: A 117 VAL cc_start: 0.8531 (m) cc_final: 0.8269 (t) REVERT: A 131 ARG cc_start: 0.8108 (ttm170) cc_final: 0.7742 (ttm-80) REVERT: B 64 ASN cc_start: 0.8734 (m-40) cc_final: 0.8340 (m-40) REVERT: B 67 ARG cc_start: 0.8483 (ttp-110) cc_final: 0.8094 (ttp80) REVERT: B 91 LYS cc_start: 0.8709 (ttmt) cc_final: 0.8219 (tppp) REVERT: C 29 ARG cc_start: 0.8626 (ttm170) cc_final: 0.8087 (mtp85) REVERT: C 51 LEU cc_start: 0.8759 (tp) cc_final: 0.8556 (tp) REVERT: C 58 LEU cc_start: 0.8856 (mt) cc_final: 0.8592 (mm) REVERT: C 61 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7673 (mm-30) REVERT: C 64 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7406 (tm-30) REVERT: C 65 LEU cc_start: 0.8426 (mt) cc_final: 0.8132 (mt) REVERT: C 71 ARG cc_start: 0.8173 (ttp80) cc_final: 0.7900 (ttp80) REVERT: C 81 ARG cc_start: 0.8790 (ttm-80) cc_final: 0.8526 (tpt-90) REVERT: C 110 ASN cc_start: 0.8525 (t0) cc_final: 0.8265 (t0) REVERT: D 42 LEU cc_start: 0.8300 (tp) cc_final: 0.8081 (tp) REVERT: D 48 ASP cc_start: 0.8732 (p0) cc_final: 0.8126 (p0) REVERT: D 56 MET cc_start: 0.8628 (tpp) cc_final: 0.8288 (tpp) REVERT: D 59 MET cc_start: 0.8330 (mmm) cc_final: 0.7879 (mmm) REVERT: D 68 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7875 (mt-10) REVERT: D 110 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7604 (mm-30) REVERT: E 42 ARG cc_start: 0.8067 (mtp180) cc_final: 0.7829 (mtp180) REVERT: E 60 LEU cc_start: 0.8511 (mt) cc_final: 0.7714 (mt) REVERT: E 62 ILE cc_start: 0.8218 (tt) cc_final: 0.7903 (tt) REVERT: E 74 ILE cc_start: 0.8802 (mt) cc_final: 0.8566 (mt) REVERT: E 76 GLN cc_start: 0.8461 (tp40) cc_final: 0.7991 (tp-100) REVERT: E 93 GLN cc_start: 0.8612 (tt0) cc_final: 0.7918 (tt0) REVERT: E 97 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7517 (mt-10) REVERT: E 103 LEU cc_start: 0.8281 (tp) cc_final: 0.8041 (tp) REVERT: E 125 GLN cc_start: 0.7920 (mp10) cc_final: 0.7532 (mp10) REVERT: F 35 ARG cc_start: 0.8241 (ttp-170) cc_final: 0.7903 (ttp80) REVERT: F 52 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7819 (mm-30) REVERT: G 20 ARG cc_start: 0.8151 (ptp-170) cc_final: 0.7856 (ptp-170) REVERT: G 29 ARG cc_start: 0.8321 (ttm170) cc_final: 0.7961 (ttp80) REVERT: G 61 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7788 (mm-30) REVERT: G 64 GLU cc_start: 0.6906 (tm-30) cc_final: 0.6172 (tm-30) REVERT: G 65 LEU cc_start: 0.8152 (mt) cc_final: 0.7528 (mm) REVERT: G 100 VAL cc_start: 0.9010 (t) cc_final: 0.8768 (p) REVERT: G 107 VAL cc_start: 0.8947 (m) cc_final: 0.8718 (t) REVERT: H 43 LYS cc_start: 0.8360 (tppp) cc_final: 0.7999 (tppp) REVERT: H 54 LYS cc_start: 0.8436 (mmmm) cc_final: 0.8213 (mmmm) REVERT: H 73 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7643 (mm-30) REVERT: H 82 LYS cc_start: 0.8465 (mptt) cc_final: 0.7909 (mptt) REVERT: H 117 LYS cc_start: 0.8751 (tttm) cc_final: 0.8507 (tttm) outliers start: 2 outliers final: 0 residues processed: 377 average time/residue: 0.3334 time to fit residues: 157.7407 Evaluate side-chains 377 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 377 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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: 1.9990 chunk 102 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 HIS E 108 ASN G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.113898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.092015 restraints weight = 60407.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.095777 restraints weight = 19689.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.097948 restraints weight = 9213.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.099251 restraints weight = 5677.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.100078 restraints weight = 4268.759| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.5368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 13378 Z= 0.355 Angle : 0.698 6.758 19465 Z= 0.442 Chirality : 0.050 0.161 2212 Planarity : 0.005 0.046 1343 Dihedral : 29.477 88.848 4361 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % 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: 0.98 (0.29), residues: 726 helix: 1.55 (0.22), residues: 494 sheet: None (None), residues: 0 loop : -1.34 (0.35), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 36 TYR 0.011 0.002 TYR C 39 PHE 0.016 0.002 PHE E 104 HIS 0.008 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00719 (13378) covalent geometry : angle 0.69795 (19465) hydrogen bonds : bond 0.07347 ( 765) hydrogen bonds : angle 4.15352 ( 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 380 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 380 time to evaluate : 0.436 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 59 GLU cc_start: 0.7619 (pm20) cc_final: 0.7277 (pm20) REVERT: A 60 LEU cc_start: 0.8306 (mm) cc_final: 0.7978 (mm) REVERT: A 69 ARG cc_start: 0.8264 (mtp180) cc_final: 0.7708 (ttm-80) REVERT: A 70 LEU cc_start: 0.8417 (tp) cc_final: 0.8196 (tp) REVERT: A 72 ARG cc_start: 0.9064 (mmt90) cc_final: 0.8794 (mtt-85) REVERT: A 74 ILE cc_start: 0.8657 (tp) cc_final: 0.8435 (tp) REVERT: A 93 GLN cc_start: 0.8659 (tt0) cc_final: 0.7904 (tt0) REVERT: A 97 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7938 (mt-10) REVERT: A 117 VAL cc_start: 0.8523 (m) cc_final: 0.8272 (t) REVERT: A 131 ARG cc_start: 0.8128 (ttm170) cc_final: 0.7633 (ttm-80) REVERT: B 52 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8322 (mm-30) REVERT: B 64 ASN cc_start: 0.8804 (m-40) cc_final: 0.8458 (m-40) REVERT: B 67 ARG cc_start: 0.8531 (ttp-110) cc_final: 0.8153 (ttp80) REVERT: B 91 LYS cc_start: 0.8792 (ttmt) cc_final: 0.8316 (tppp) REVERT: C 17 ARG cc_start: 0.8335 (mtp180) cc_final: 0.7990 (mtp85) REVERT: C 24 GLN cc_start: 0.8473 (mp10) cc_final: 0.7931 (mp10) REVERT: C 29 ARG cc_start: 0.8687 (ttm170) cc_final: 0.8046 (ttm170) REVERT: C 56 GLU cc_start: 0.8226 (tt0) cc_final: 0.7657 (tt0) REVERT: C 58 LEU cc_start: 0.8887 (mt) cc_final: 0.8657 (mm) REVERT: C 61 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7787 (mm-30) REVERT: C 64 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7392 (tm-30) REVERT: C 65 LEU cc_start: 0.8452 (mt) cc_final: 0.8051 (mt) REVERT: C 71 ARG cc_start: 0.8259 (ttp80) cc_final: 0.7969 (ttp80) REVERT: C 81 ARG cc_start: 0.8855 (ttm-80) cc_final: 0.8637 (tpt-90) REVERT: C 110 ASN cc_start: 0.8547 (t0) cc_final: 0.8247 (t0) REVERT: D 42 LEU cc_start: 0.8368 (tp) cc_final: 0.8151 (tp) REVERT: D 48 ASP cc_start: 0.8812 (p0) cc_final: 0.8194 (p0) REVERT: D 56 MET cc_start: 0.8703 (tpp) cc_final: 0.8360 (tpp) REVERT: D 68 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7901 (mt-10) REVERT: D 110 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7634 (mm-30) REVERT: E 42 ARG cc_start: 0.8146 (mtp180) cc_final: 0.7891 (mtp180) REVERT: E 60 LEU cc_start: 0.8512 (mt) cc_final: 0.7986 (mt) REVERT: E 74 ILE cc_start: 0.8836 (mt) cc_final: 0.8616 (mt) REVERT: E 76 GLN cc_start: 0.8741 (tp40) cc_final: 0.8057 (tp-100) REVERT: E 93 GLN cc_start: 0.8630 (tt0) cc_final: 0.8257 (tt0) REVERT: E 94 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7979 (mm-30) REVERT: E 97 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7583 (mt-10) REVERT: E 116 ARG cc_start: 0.8666 (mtm-85) cc_final: 0.8399 (mtm-85) REVERT: E 129 ARG cc_start: 0.8522 (ttt180) cc_final: 0.8241 (ttt180) REVERT: F 35 ARG cc_start: 0.8283 (ttp-170) cc_final: 0.7871 (tpp80) REVERT: F 52 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7941 (mm-30) REVERT: F 88 TYR cc_start: 0.8381 (m-80) cc_final: 0.8078 (m-80) REVERT: G 20 ARG cc_start: 0.8181 (ptp-170) cc_final: 0.7893 (ptp-170) REVERT: G 61 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7811 (mm-30) REVERT: G 100 VAL cc_start: 0.9003 (t) cc_final: 0.8762 (p) REVERT: H 43 LYS cc_start: 0.8360 (tppp) cc_final: 0.8017 (tppp) REVERT: H 73 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7684 (mm-30) REVERT: H 82 LYS cc_start: 0.8462 (mptt) cc_final: 0.7912 (mptt) REVERT: H 117 LYS cc_start: 0.8775 (tttm) cc_final: 0.8554 (tttm) outliers start: 0 outliers final: 0 residues processed: 380 average time/residue: 0.3421 time to fit residues: 162.9221 Evaluate side-chains 373 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 373 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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: 0.0370 chunk 102 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 91 optimal weight: 0.0970 chunk 6 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN D 64 ASN F 75 HIS F 93 GLN H 79 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.121239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.099772 restraints weight = 59001.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.103620 restraints weight = 19204.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.105841 restraints weight = 8887.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.107197 restraints weight = 5434.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.108014 restraints weight = 4056.869| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.5508 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= 0.176 Angle : 0.614 4.359 19465 Z= 0.386 Chirality : 0.039 0.137 2212 Planarity : 0.005 0.083 1343 Dihedral : 29.346 89.888 4361 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % 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: 1.93 (0.30), residues: 726 helix: 2.29 (0.22), residues: 494 sheet: None (None), residues: 0 loop : -1.03 (0.36), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 36 TYR 0.007 0.001 TYR A 99 PHE 0.009 0.001 PHE G 25 HIS 0.007 0.001 HIS H 79 Details of bonding type rmsd covalent geometry : bond 0.00371 (13378) covalent geometry : angle 0.61405 (19465) hydrogen bonds : bond 0.04953 ( 765) hydrogen bonds : angle 3.22469 ( 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 366 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 365 time to evaluate : 0.273 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: 0.8314 (mm) cc_final: 0.7936 (mm) REVERT: A 69 ARG cc_start: 0.8202 (mtp180) cc_final: 0.7509 (ttm110) REVERT: A 72 ARG cc_start: 0.8949 (mmt90) cc_final: 0.8646 (mtt-85) REVERT: A 93 GLN cc_start: 0.8642 (tt0) cc_final: 0.7854 (tt0) REVERT: A 97 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7823 (mt-10) REVERT: A 131 ARG cc_start: 0.8119 (ttm170) cc_final: 0.7655 (ttm-80) REVERT: B 45 ARG cc_start: 0.7979 (mtp180) cc_final: 0.7518 (mtp180) REVERT: B 52 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8231 (mm-30) REVERT: B 64 ASN cc_start: 0.8700 (m-40) cc_final: 0.8405 (m-40) REVERT: B 67 ARG cc_start: 0.8443 (ttp-110) cc_final: 0.8029 (ttp80) REVERT: B 91 LYS cc_start: 0.8675 (ttmt) cc_final: 0.8426 (ttmt) REVERT: C 29 ARG cc_start: 0.8592 (ttm170) cc_final: 0.8086 (mtp85) REVERT: C 58 LEU cc_start: 0.8832 (mt) cc_final: 0.8599 (mm) REVERT: C 61 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7753 (mm-30) REVERT: C 81 ARG cc_start: 0.8738 (ttm-80) cc_final: 0.8514 (tpt-90) REVERT: C 110 ASN cc_start: 0.8484 (t0) cc_final: 0.8231 (t0) REVERT: D 42 LEU cc_start: 0.8266 (tp) cc_final: 0.8027 (tp) REVERT: D 48 ASP cc_start: 0.8785 (p0) cc_final: 0.8190 (p0) REVERT: D 56 MET cc_start: 0.8538 (tpp) cc_final: 0.8220 (tpp) REVERT: D 68 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7847 (mt-10) REVERT: D 103 LEU cc_start: 0.9029 (mp) cc_final: 0.8700 (mm) REVERT: E 42 ARG cc_start: 0.8070 (mtp180) cc_final: 0.7838 (mtp180) REVERT: E 53 ARG cc_start: 0.8429 (ttp-170) cc_final: 0.8167 (ttp-170) REVERT: E 60 LEU cc_start: 0.8475 (mt) cc_final: 0.7724 (mt) REVERT: E 74 ILE cc_start: 0.8769 (mt) cc_final: 0.8543 (mt) REVERT: E 76 GLN cc_start: 0.8482 (tp40) cc_final: 0.7766 (tp-100) REVERT: E 93 GLN cc_start: 0.8509 (tt0) cc_final: 0.8248 (tt0) REVERT: E 97 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7514 (mt-10) REVERT: E 126 LEU cc_start: 0.8661 (tp) cc_final: 0.8451 (tp) REVERT: E 129 ARG cc_start: 0.8431 (ttt180) cc_final: 0.8146 (ttt180) REVERT: F 35 ARG cc_start: 0.8193 (ttp-170) cc_final: 0.7848 (ttm-80) REVERT: F 52 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7796 (mm-30) REVERT: G 61 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7764 (mm-30) REVERT: H 43 LYS cc_start: 0.8246 (tppp) cc_final: 0.7906 (tppp) REVERT: H 54 LYS cc_start: 0.8412 (mmmm) cc_final: 0.8190 (mmmm) REVERT: H 73 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7577 (mm-30) REVERT: H 76 ARG cc_start: 0.8092 (ttm110) cc_final: 0.7601 (ttm-80) REVERT: H 82 LYS cc_start: 0.8452 (mptt) cc_final: 0.7898 (mptt) outliers start: 1 outliers final: 0 residues processed: 365 average time/residue: 0.3393 time to fit residues: 156.3073 Evaluate side-chains 364 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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: 3.9990 chunk 17 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 91 optimal weight: 0.4980 chunk 86 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.115204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.093653 restraints weight = 59703.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.097458 restraints weight = 19293.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.099658 restraints weight = 8932.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.101004 restraints weight = 5459.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.101840 restraints weight = 4071.175| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.5777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 13378 Z= 0.310 Angle : 0.661 5.292 19465 Z= 0.419 Chirality : 0.048 0.147 2212 Planarity : 0.005 0.058 1343 Dihedral : 29.344 88.168 4361 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % 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: 1.34 (0.29), residues: 726 helix: 1.86 (0.22), residues: 499 sheet: None (None), residues: 0 loop : -1.37 (0.35), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 69 TYR 0.013 0.001 TYR B 51 PHE 0.009 0.002 PHE E 78 HIS 0.005 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00631 (13378) covalent geometry : angle 0.66106 (19465) hydrogen bonds : bond 0.06538 ( 765) hydrogen bonds : angle 3.85458 ( 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 374 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 0.378 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: 0.8288 (mm) cc_final: 0.7912 (mm) REVERT: A 69 ARG cc_start: 0.8277 (mtp180) cc_final: 0.7605 (ttm110) REVERT: A 72 ARG cc_start: 0.9004 (mmt90) cc_final: 0.8729 (mtt-85) REVERT: A 93 GLN cc_start: 0.8655 (tt0) cc_final: 0.7892 (tt0) REVERT: A 97 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7916 (mt-10) REVERT: A 115 LYS cc_start: 0.8585 (mttm) cc_final: 0.8192 (mmmm) REVERT: A 131 ARG cc_start: 0.8147 (ttm170) cc_final: 0.7636 (ttm-80) REVERT: B 52 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8339 (mm-30) REVERT: B 64 ASN cc_start: 0.8776 (m-40) cc_final: 0.8383 (m-40) REVERT: B 67 ARG cc_start: 0.8481 (ttp-110) cc_final: 0.8053 (ttp80) REVERT: B 91 LYS cc_start: 0.8742 (ttmt) cc_final: 0.8471 (ttmt) REVERT: C 24 GLN cc_start: 0.8421 (mp10) cc_final: 0.7951 (mp10) REVERT: C 29 ARG cc_start: 0.8683 (ttm170) cc_final: 0.7840 (ttm170) REVERT: C 56 GLU cc_start: 0.8092 (tt0) cc_final: 0.7657 (tt0) REVERT: C 58 LEU cc_start: 0.8871 (mt) cc_final: 0.8643 (mm) REVERT: C 61 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7733 (mm-30) REVERT: C 64 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7353 (tm-30) REVERT: C 71 ARG cc_start: 0.8205 (ttp80) cc_final: 0.7885 (ttp80) REVERT: C 110 ASN cc_start: 0.8527 (t0) cc_final: 0.8268 (t0) REVERT: D 42 LEU cc_start: 0.8353 (tp) cc_final: 0.8137 (tp) REVERT: D 48 ASP cc_start: 0.8831 (p0) cc_final: 0.8230 (p0) REVERT: D 56 MET cc_start: 0.8642 (tpp) cc_final: 0.8337 (tpp) REVERT: D 68 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7876 (mt-10) REVERT: D 102 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7090 (mm-30) REVERT: D 103 LEU cc_start: 0.9067 (mp) cc_final: 0.8410 (mm) REVERT: D 110 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7558 (mm-30) REVERT: E 42 ARG cc_start: 0.8124 (mtp180) cc_final: 0.7880 (mtp180) REVERT: E 60 LEU cc_start: 0.8501 (mt) cc_final: 0.7894 (mt) REVERT: E 64 LYS cc_start: 0.8415 (mmmm) cc_final: 0.7947 (mmmm) REVERT: E 74 ILE cc_start: 0.8876 (mt) cc_final: 0.8660 (mt) REVERT: E 76 GLN cc_start: 0.8690 (tp40) cc_final: 0.8044 (tp-100) REVERT: E 93 GLN cc_start: 0.8591 (tt0) cc_final: 0.7926 (tt0) REVERT: E 97 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7449 (mt-10) REVERT: E 129 ARG cc_start: 0.8491 (ttt180) cc_final: 0.8181 (ttt180) REVERT: F 27 GLN cc_start: 0.8378 (mm-40) cc_final: 0.7930 (mm110) REVERT: F 35 ARG cc_start: 0.8252 (ttp-170) cc_final: 0.7891 (ttm-80) REVERT: F 52 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7912 (mm-30) REVERT: F 88 TYR cc_start: 0.8335 (m-80) cc_final: 0.7991 (m-80) REVERT: G 61 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7759 (mm-30) REVERT: G 100 VAL cc_start: 0.9032 (t) cc_final: 0.8774 (p) REVERT: H 43 LYS cc_start: 0.8271 (tppp) cc_final: 0.7959 (tppp) REVERT: H 73 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7652 (mm-30) REVERT: H 76 ARG cc_start: 0.8260 (ttm110) cc_final: 0.7792 (ttm-80) REVERT: H 82 LYS cc_start: 0.8408 (mptt) cc_final: 0.7890 (mptt) outliers start: 0 outliers final: 0 residues processed: 374 average time/residue: 0.3195 time to fit residues: 149.5869 Evaluate side-chains 370 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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: 1.9990 chunk 12 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN H 79 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.117527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.096054 restraints weight = 59640.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.099897 restraints weight = 19291.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.102107 restraints weight = 8901.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.103464 restraints weight = 5445.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.104277 restraints weight = 4059.995| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.5885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 13378 Z= 0.249 Angle : 0.642 7.727 19465 Z= 0.405 Chirality : 0.044 0.136 2212 Planarity : 0.005 0.066 1343 Dihedral : 29.269 88.229 4361 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % 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: 1.31 (0.29), residues: 726 helix: 1.83 (0.22), residues: 498 sheet: None (None), residues: 0 loop : -1.34 (0.35), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 69 TYR 0.012 0.001 TYR B 51 PHE 0.010 0.001 PHE E 78 HIS 0.004 0.001 HIS H 79 Details of bonding type rmsd covalent geometry : bond 0.00508 (13378) covalent geometry : angle 0.64246 (19465) hydrogen bonds : bond 0.05902 ( 765) hydrogen bonds : angle 3.64839 ( 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 376 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 375 time to evaluate : 0.378 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: 0.8282 (mm) cc_final: 0.7930 (mm) REVERT: A 69 ARG cc_start: 0.8274 (mtp180) cc_final: 0.7582 (ttm110) REVERT: A 72 ARG cc_start: 0.8998 (mmt90) cc_final: 0.8697 (mtt-85) REVERT: A 76 GLN cc_start: 0.8231 (tp-100) cc_final: 0.7832 (tp-100) REVERT: A 93 GLN cc_start: 0.8648 (tt0) cc_final: 0.7912 (tt0) REVERT: A 97 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7895 (mt-10) REVERT: A 115 LYS cc_start: 0.8592 (mttm) cc_final: 0.8204 (mmmm) REVERT: A 131 ARG cc_start: 0.8148 (ttm170) cc_final: 0.7629 (ttm-80) REVERT: B 52 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8350 (mm-30) REVERT: B 64 ASN cc_start: 0.8736 (m-40) cc_final: 0.8369 (m-40) REVERT: B 67 ARG cc_start: 0.8477 (ttp-110) cc_final: 0.8043 (ttp80) REVERT: B 91 LYS cc_start: 0.8725 (ttmt) cc_final: 0.8476 (ttmt) REVERT: C 24 GLN cc_start: 0.8440 (mp10) cc_final: 0.7962 (mp10) REVERT: C 29 ARG cc_start: 0.8666 (ttm170) cc_final: 0.7945 (ttm170) REVERT: C 58 LEU cc_start: 0.8853 (mt) cc_final: 0.8622 (mm) REVERT: C 61 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7821 (mm-30) REVERT: C 92 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7793 (mt-10) REVERT: C 110 ASN cc_start: 0.8502 (t0) cc_final: 0.8245 (t0) REVERT: D 40 LYS cc_start: 0.8319 (mppt) cc_final: 0.8108 (mtmm) REVERT: D 42 LEU cc_start: 0.8322 (tp) cc_final: 0.8091 (tp) REVERT: D 48 ASP cc_start: 0.8866 (p0) cc_final: 0.8260 (p0) REVERT: D 56 MET cc_start: 0.8640 (tpp) cc_final: 0.8320 (tpp) REVERT: D 102 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7065 (mm-30) REVERT: D 103 LEU cc_start: 0.9076 (mp) cc_final: 0.8392 (mm) REVERT: D 110 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7529 (mm-30) REVERT: E 42 ARG cc_start: 0.8147 (mtp180) cc_final: 0.7912 (mtp180) REVERT: E 60 LEU cc_start: 0.8476 (mt) cc_final: 0.7963 (mt) REVERT: E 64 LYS cc_start: 0.8370 (mmmm) cc_final: 0.7909 (mmmm) REVERT: E 74 ILE cc_start: 0.8848 (mt) cc_final: 0.8638 (mt) REVERT: E 76 GLN cc_start: 0.8643 (tp40) cc_final: 0.7992 (tp-100) REVERT: E 93 GLN cc_start: 0.8631 (tt0) cc_final: 0.8232 (tt0) REVERT: E 94 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7905 (mm-30) REVERT: E 97 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7476 (mt-10) REVERT: E 126 LEU cc_start: 0.8719 (tp) cc_final: 0.8518 (tp) REVERT: E 129 ARG cc_start: 0.8500 (ttt180) cc_final: 0.8215 (ttt180) REVERT: F 35 ARG cc_start: 0.8234 (ttp-170) cc_final: 0.7861 (ttm-80) REVERT: F 52 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7900 (mm-30) REVERT: F 88 TYR cc_start: 0.8305 (m-80) cc_final: 0.7999 (m-80) REVERT: G 61 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7760 (mm-30) REVERT: H 43 LYS cc_start: 0.8258 (tppp) cc_final: 0.7937 (tppp) REVERT: H 73 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7656 (mm-30) REVERT: H 82 LYS cc_start: 0.8365 (mptt) cc_final: 0.7864 (mptt) outliers start: 1 outliers final: 0 residues processed: 375 average time/residue: 0.3387 time to fit residues: 159.1901 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 : 0.383 ------------------------------------------------------------------------------- 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: 4.9990 chunk 22 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.115007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.093562 restraints weight = 60222.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.097367 restraints weight = 19552.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.099558 restraints weight = 9073.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.100895 restraints weight = 5547.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.101750 restraints weight = 4132.276| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.6021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 13378 Z= 0.317 Angle : 0.670 5.797 19465 Z= 0.424 Chirality : 0.048 0.146 2212 Planarity : 0.005 0.059 1343 Dihedral : 29.306 89.517 4361 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % 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: 0.93 (0.29), residues: 726 helix: 1.53 (0.22), residues: 497 sheet: None (None), residues: 0 loop : -1.47 (0.35), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 36 TYR 0.013 0.001 TYR B 51 PHE 0.011 0.002 PHE D 67 HIS 0.003 0.001 HIS C 82 Details of bonding type rmsd covalent geometry : bond 0.00645 (13378) covalent geometry : angle 0.67043 (19465) hydrogen bonds : bond 0.06787 ( 765) hydrogen bonds : angle 3.96353 ( 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 374 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 0.427 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: 0.8259 (mm) cc_final: 0.7903 (mm) REVERT: A 69 ARG cc_start: 0.8298 (mtp180) cc_final: 0.7624 (ttm110) REVERT: A 72 ARG cc_start: 0.9000 (mmt90) cc_final: 0.8717 (mtt-85) REVERT: A 76 GLN cc_start: 0.8228 (tp-100) cc_final: 0.7828 (tp-100) REVERT: A 93 GLN cc_start: 0.8605 (tt0) cc_final: 0.7909 (tt0) REVERT: A 94 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8053 (mt-10) REVERT: A 97 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7869 (mt-10) REVERT: A 115 LYS cc_start: 0.8566 (mttm) cc_final: 0.8213 (mmmm) REVERT: A 131 ARG cc_start: 0.8177 (ttm170) cc_final: 0.7637 (ttm-80) REVERT: B 52 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8357 (mm-30) REVERT: B 64 ASN cc_start: 0.8826 (m-40) cc_final: 0.8612 (m-40) REVERT: B 91 LYS cc_start: 0.8746 (ttmt) cc_final: 0.8500 (ttmt) REVERT: C 24 GLN cc_start: 0.8465 (mp10) cc_final: 0.7970 (mp10) REVERT: C 29 ARG cc_start: 0.8690 (ttm170) cc_final: 0.8082 (ttm170) REVERT: C 58 LEU cc_start: 0.8878 (mt) cc_final: 0.8641 (mm) REVERT: C 61 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7837 (mm-30) REVERT: C 110 ASN cc_start: 0.8514 (t0) cc_final: 0.8285 (t0) REVERT: D 42 LEU cc_start: 0.8372 (tp) cc_final: 0.8162 (tp) REVERT: D 48 ASP cc_start: 0.8885 (p0) cc_final: 0.8253 (p0) REVERT: D 56 MET cc_start: 0.8638 (tpp) cc_final: 0.8325 (tpp) REVERT: D 68 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7828 (mt-10) REVERT: D 102 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7089 (mm-30) REVERT: D 103 LEU cc_start: 0.9087 (mp) cc_final: 0.8362 (mm) REVERT: D 110 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7438 (mm-30) REVERT: E 42 ARG cc_start: 0.8142 (mtp180) cc_final: 0.7916 (mtp180) REVERT: E 60 LEU cc_start: 0.8473 (mt) cc_final: 0.7970 (mt) REVERT: E 64 LYS cc_start: 0.8410 (mmmm) cc_final: 0.7944 (mmmm) REVERT: E 76 GLN cc_start: 0.8688 (tp40) cc_final: 0.8091 (tp-100) REVERT: E 93 GLN cc_start: 0.8608 (tt0) cc_final: 0.8205 (tt0) REVERT: E 94 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7899 (mm-30) REVERT: E 97 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7505 (mt-10) REVERT: E 129 ARG cc_start: 0.8477 (ttt180) cc_final: 0.8200 (ttt180) REVERT: F 27 GLN cc_start: 0.8365 (mm-40) cc_final: 0.8032 (mm-40) REVERT: F 35 ARG cc_start: 0.8246 (ttp-170) cc_final: 0.7921 (ttm-80) REVERT: F 52 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7855 (mm-30) REVERT: F 77 LYS cc_start: 0.8498 (mttt) cc_final: 0.8279 (mttt) REVERT: F 88 TYR cc_start: 0.8327 (m-80) cc_final: 0.7993 (m-80) REVERT: G 61 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7756 (mm-30) REVERT: G 85 LEU cc_start: 0.8977 (mt) cc_final: 0.8775 (mt) REVERT: H 43 LYS cc_start: 0.8265 (tppp) cc_final: 0.7945 (tppp) REVERT: H 73 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7623 (mm-30) REVERT: H 82 LYS cc_start: 0.8377 (mptt) cc_final: 0.7899 (mptt) REVERT: H 117 LYS cc_start: 0.8735 (tttm) cc_final: 0.8514 (tttm) outliers start: 0 outliers final: 0 residues processed: 374 average time/residue: 0.3438 time to fit residues: 161.7101 Evaluate side-chains 370 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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: 1.9990 chunk 81 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN E 108 ASN F 93 GLN H 79 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.117170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.095714 restraints weight = 59290.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.099571 restraints weight = 19279.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.101802 restraints weight = 8901.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.103160 restraints weight = 5409.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.103992 restraints weight = 4020.983| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.6073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13378 Z= 0.235 Angle : 0.638 5.875 19465 Z= 0.403 Chirality : 0.043 0.132 2212 Planarity : 0.005 0.057 1343 Dihedral : 29.227 89.206 4361 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.33 % Allowed : 0.16 % 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: 1.26 (0.29), residues: 726 helix: 1.81 (0.22), residues: 498 sheet: None (None), residues: 0 loop : -1.41 (0.35), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 36 TYR 0.012 0.001 TYR B 51 PHE 0.011 0.001 PHE D 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00482 (13378) covalent geometry : angle 0.63813 (19465) hydrogen bonds : bond 0.05805 ( 765) hydrogen bonds : angle 3.60642 ( 1882) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5055.15 seconds wall clock time: 86 minutes 16.94 seconds (5176.94 seconds total)