Starting phenix.real_space_refine on Sat Jul 4 14:46:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mln_48376/07_2026/9mln_48376.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mln_48376/07_2026/9mln_48376.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mln_48376/07_2026/9mln_48376.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mln_48376/07_2026/9mln_48376.map" model { file = "/net/cci-nas-00/data/ceres_data/9mln_48376/07_2026/9mln_48376.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mln_48376/07_2026/9mln_48376.cif" } resolution = 3.3 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= 0.001 sd= 0.013 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 286 5.49 5 S 14 5.16 5 C 6524 2.51 5 N 2211 2.21 5 O 2765 1.98 5 H 9457 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21257 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1626 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1291 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1715 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1460 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1616 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1291 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1691 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1494 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 4518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 4518 Classifications: {'DNA': 143} Link IDs: {'rna3p': 142} Chain: "J" Number of atoms: 4555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 4555 Classifications: {'DNA': 143} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 142} Time building chain proxies: 3.63, per 1000 atoms: 0.17 Number of scatterers: 21257 At special positions: 0 Unit cell: (80.84, 123.84, 118.68, 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 14 16.00 P 286 15.00 O 2765 8.00 N 2211 7.00 C 6524 6.00 H 9457 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 422.6 milliseconds 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1394 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 72.7% alpha, 2.9% beta 143 base pairs and 243 stacking pairs defined. Time for finding SS restraints: 3.67 Creating SS restraints... Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 64 through 78 removed outlier: 3.612A pdb=" N PHE A 68 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASP A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 115 removed outlier: 3.926A pdb=" N VAL A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N MET A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 31 through 42 removed outlier: 3.582A pdb=" N LEU B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 77 removed outlier: 4.087A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ASP B 69 " --> pdb=" O ASN B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 94 removed outlier: 3.662A pdb=" N VAL B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 27 through 38 Processing helix chain 'C' and resid 46 through 74 removed outlier: 4.396A pdb=" N VAL C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR C 51 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU C 66 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN C 69 " --> pdb=" O GLU C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 91 Processing helix chain 'C' and resid 93 through 98 Processing helix chain 'D' and resid 38 through 50 removed outlier: 3.616A pdb=" N GLN D 48 " --> pdb=" O LYS D 44 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL D 49 " --> pdb=" O VAL D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 85 removed outlier: 3.729A pdb=" N ASN D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN D 85 " --> pdb=" O LEU D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 103 Processing helix chain 'D' and resid 104 through 124 Processing helix chain 'E' and resid 45 through 58 removed outlier: 3.728A pdb=" N ARG E 50 " --> pdb=" O THR E 46 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER E 58 " --> pdb=" O ARG E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 80 removed outlier: 4.367A pdb=" N ASP E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N PHE E 79 " --> pdb=" O ILE E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 115 removed outlier: 3.790A pdb=" N VAL E 90 " --> pdb=" O GLN E 86 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N MET E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 132 removed outlier: 3.777A pdb=" N ILE E 125 " --> pdb=" O MET E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 30 removed outlier: 3.569A pdb=" N ILE F 30 " --> pdb=" O ILE F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 42 Processing helix chain 'F' and resid 50 through 77 removed outlier: 3.749A pdb=" N GLU F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 95 removed outlier: 3.586A pdb=" N VAL F 87 " --> pdb=" O THR F 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 23 Processing helix chain 'G' and resid 27 through 38 removed outlier: 3.610A pdb=" N VAL G 31 " --> pdb=" O PRO G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 74 removed outlier: 3.704A pdb=" N LEU G 66 " --> pdb=" O GLU G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 89 removed outlier: 3.650A pdb=" N LEU G 84 " --> pdb=" O ILE G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 98 removed outlier: 3.565A pdb=" N LYS G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 50 Processing helix chain 'H' and resid 56 through 85 removed outlier: 3.819A pdb=" N ASN H 85 " --> pdb=" O LEU H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 103 removed outlier: 3.540A pdb=" N ILE H 95 " --> pdb=" O THR H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 126 removed outlier: 3.561A pdb=" N LYS H 109 " --> pdb=" O GLY H 105 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N HIS H 110 " --> pdb=" O GLU H 106 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.718A pdb=" N ARG A 84 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.215A pdb=" N ARG C 43 " --> pdb=" O ILE D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'C' and resid 102 through 103 removed outlier: 6.922A pdb=" N THR C 102 " --> pdb=" O TYR F 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85 removed outlier: 7.056A pdb=" N ARG E 84 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 119 through 120 Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.303A pdb=" N ARG G 43 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79 383 hydrogen bonds defined for protein. 1134 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 366 hydrogen bonds 732 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 243 stacking parallelities Total time for adding SS restraints: 4.81 Time building geometry restraints manager: 2.78 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: 9453 1.03 - 1.23: 103 1.23 - 1.42: 5399 1.42 - 1.62: 7072 1.62 - 1.81: 24 Bond restraints: 22051 Sorted by residual: bond pdb=" C3' DT I 43 " pdb=" C2' DT I 43 " ideal model delta sigma weight residual 1.516 1.569 -0.053 8.00e-03 1.56e+04 4.32e+01 bond pdb=" C3' DT J 33 " pdb=" C2' DT J 33 " ideal model delta sigma weight residual 1.516 1.554 -0.038 8.00e-03 1.56e+04 2.27e+01 bond pdb=" C3' DG J -69 " pdb=" C2' DG J -69 " ideal model delta sigma weight residual 1.516 1.553 -0.037 8.00e-03 1.56e+04 2.12e+01 bond pdb=" C3' DG I -7 " pdb=" C2' DG I -7 " ideal model delta sigma weight residual 1.516 1.551 -0.035 8.00e-03 1.56e+04 1.97e+01 bond pdb=" C3' DC J 53 " pdb=" C2' DC J 53 " ideal model delta sigma weight residual 1.516 1.551 -0.035 8.00e-03 1.56e+04 1.94e+01 ... (remaining 22046 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 34971 1.41 - 2.81: 4408 2.81 - 4.22: 419 4.22 - 5.62: 155 5.62 - 7.03: 19 Bond angle restraints: 39972 Sorted by residual: angle pdb=" O5' DT J -16 " pdb=" C5' DT J -16 " pdb=" C4' DT J -16 " ideal model delta sigma weight residual 109.40 116.21 -6.81 8.00e-01 1.56e+00 7.26e+01 angle pdb=" O4' DG J 27 " pdb=" C1' DG J 27 " pdb=" N9 DG J 27 " ideal model delta sigma weight residual 108.00 113.49 -5.49 7.00e-01 2.04e+00 6.15e+01 angle pdb=" O4' DT I 64 " pdb=" C1' DT I 64 " pdb=" N1 DT I 64 " ideal model delta sigma weight residual 108.00 113.39 -5.39 7.00e-01 2.04e+00 5.92e+01 angle pdb=" O4' DA I -54 " pdb=" C1' DA I -54 " pdb=" N9 DA I -54 " ideal model delta sigma weight residual 108.00 102.89 5.11 7.00e-01 2.04e+00 5.34e+01 angle pdb=" O4' DT I 43 " pdb=" C1' DT I 43 " pdb=" N1 DT I 43 " ideal model delta sigma weight residual 108.00 102.95 5.05 7.00e-01 2.04e+00 5.20e+01 ... (remaining 39967 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 6489 17.96 - 35.91: 1166 35.91 - 53.87: 995 53.87 - 71.83: 477 71.83 - 89.78: 29 Dihedral angle restraints: 9156 sinusoidal: 6725 harmonic: 2431 Sorted by residual: dihedral pdb=" CA PRO G 110 " pdb=" C PRO G 110 " pdb=" N ASN G 111 " pdb=" CA ASN G 111 " ideal model delta harmonic sigma weight residual -180.00 -152.58 -27.42 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA SER D 88 " pdb=" C SER D 88 " pdb=" N THR D 89 " pdb=" CA THR D 89 " ideal model delta harmonic sigma weight residual -180.00 -154.26 -25.74 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA PRO H 104 " pdb=" C PRO H 104 " pdb=" N GLY H 105 " pdb=" CA GLY H 105 " ideal model delta harmonic sigma weight residual -180.00 -156.01 -23.99 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 9153 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1249 0.049 - 0.098: 527 0.098 - 0.147: 218 0.147 - 0.196: 70 0.196 - 0.245: 7 Chirality restraints: 2071 Sorted by residual: 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 2.43 2.19 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" C3' DA J 39 " pdb=" C4' DA J 39 " pdb=" O3' DA J 39 " pdb=" C2' DA J 39 " both_signs ideal model delta sigma weight residual False -2.73 -2.51 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C3' DA I -15 " pdb=" C4' DA I -15 " pdb=" O3' DA I -15 " pdb=" C2' DA I -15 " both_signs ideal model delta sigma weight residual False -2.73 -2.51 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 2068 not shown) Planarity restraints: 2262 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC I -12 " 0.047 2.00e-02 2.50e+03 3.86e-02 4.11e+01 pdb=" N1 DC I -12 " -0.106 2.00e-02 2.50e+03 pdb=" C2 DC I -12 " 0.053 2.00e-02 2.50e+03 pdb=" O2 DC I -12 " -0.010 2.00e-02 2.50e+03 pdb=" N3 DC I -12 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DC I -12 " -0.002 2.00e-02 2.50e+03 pdb=" N4 DC I -12 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DC I -12 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DC I -12 " -0.001 2.00e-02 2.50e+03 pdb=" H5 DC I -12 " 0.009 2.00e-02 2.50e+03 pdb=" H6 DC I -12 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 89 " 0.004 9.50e-02 1.11e+02 4.05e-02 3.68e+01 pdb=" NE ARG C 89 " -0.001 2.00e-02 2.50e+03 pdb=" CZ ARG C 89 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG C 89 " -0.057 2.00e-02 2.50e+03 pdb=" NH2 ARG C 89 " 0.063 2.00e-02 2.50e+03 pdb="HH11 ARG C 89 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG C 89 " 0.059 2.00e-02 2.50e+03 pdb="HH21 ARG C 89 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG C 89 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I -51 " -0.038 2.00e-02 2.50e+03 3.29e-02 2.98e+01 pdb=" N1 DC I -51 " 0.091 2.00e-02 2.50e+03 pdb=" C2 DC I -51 " -0.045 2.00e-02 2.50e+03 pdb=" O2 DC I -51 " 0.007 2.00e-02 2.50e+03 pdb=" N3 DC I -51 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DC I -51 " -0.003 2.00e-02 2.50e+03 pdb=" N4 DC I -51 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DC I -51 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DC I -51 " 0.001 2.00e-02 2.50e+03 pdb=" H5 DC I -51 " -0.007 2.00e-02 2.50e+03 pdb=" H6 DC I -51 " -0.006 2.00e-02 2.50e+03 ... (remaining 2259 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.13: 484 2.13 - 2.75: 32231 2.75 - 3.37: 54591 3.37 - 3.98: 73708 3.98 - 4.60: 114627 Nonbonded interactions: 275641 Sorted by model distance: nonbonded pdb=" H VAL A 118 " pdb=" OP1 DG I -3 " model vdw 1.515 2.450 nonbonded pdb=" H GLY B 49 " pdb=" OP1 DC J 7 " model vdw 1.583 2.450 nonbonded pdb=" HZ1 LYS E 80 " pdb=" OE2 GLU F 75 " model vdw 1.599 2.450 nonbonded pdb=" O SER C 17 " pdb=" HG SER C 20 " model vdw 1.612 2.450 nonbonded pdb=" O ARG E 130 " pdb="HH11 ARG E 130 " model vdw 1.630 2.450 ... (remaining 275636 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 40 through 134) selection = (chain 'E' and resid 40 through 134) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 13 through 119) selection = chain 'G' } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 34 through 125) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.460 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: 0.120 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 23.310 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 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 : 0.007 0.072 12594 Z= 0.646 Angle : 1.077 7.028 18233 Z= 0.896 Chirality : 0.066 0.245 2071 Planarity : 0.013 0.137 1318 Dihedral : 27.082 89.784 5434 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.11 (0.28), residues: 735 helix: 0.16 (0.21), residues: 525 sheet: None (None), residues: 0 loop : -0.33 (0.39), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.003 ARG G 18 TYR 0.030 0.005 TYR G 58 PHE 0.016 0.002 PHE A 105 HIS 0.013 0.003 HIS D 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00714 / 0.65 (12594) covalent geometry : angle 1.07725 / 0.90 (18233) hydrogen bonds : bond 0.11668 / 7.66 ( 749) hydrogen bonds : angle 4.50994 / 3.27 ( 1866) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.465 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: A 91 MET cc_start: 0.7312 (mmp) cc_final: 0.6564 (mmt) REVERT: C 40 TYR cc_start: 0.8114 (m-80) cc_final: 0.7216 (m-80) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.3731 time to fit residues: 89.6104 Evaluate side-chains 122 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 GLN B 26 ASN B 65 ASN C 39 HIS ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 ASN D 96 GLN E 86 GLN F 26 ASN G 69 ASN H 50 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.078258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.059758 restraints weight = 104949.867| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.53 r_work: 0.3106 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12594 Z= 0.211 Angle : 0.756 7.648 18233 Z= 0.487 Chirality : 0.048 0.188 2071 Planarity : 0.006 0.038 1318 Dihedral : 29.919 112.302 3962 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.45 % Allowed : 12.60 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.30 (0.30), residues: 735 helix: 1.47 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -0.63 (0.40), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 87 TYR 0.012 0.002 TYR H 41 PHE 0.012 0.001 PHE D 66 HIS 0.007 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.21 (12594) covalent geometry : angle 0.75616 / 0.49 (18233) hydrogen bonds : bond 0.07309 / 4.87 ( 749) hydrogen bonds : angle 3.75067 / 2.74 ( 1866) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.414 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 outliers start: 9 outliers final: 5 residues processed: 127 average time/residue: 0.2724 time to fit residues: 46.3641 Evaluate side-chains 116 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 111 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 72 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.077334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.058298 restraints weight = 105301.194| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.51 r_work: 0.3064 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12594 Z= 0.205 Angle : 0.662 6.686 18233 Z= 0.440 Chirality : 0.043 0.158 2071 Planarity : 0.005 0.049 1318 Dihedral : 30.298 119.740 3962 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.42 % Allowed : 12.76 % Favored : 84.81 % 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: 1.49 (0.30), residues: 735 helix: 1.72 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -0.92 (0.40), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 132 TYR 0.011 0.001 TYR H 41 PHE 0.010 0.001 PHE D 66 HIS 0.005 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.20 (12594) covalent geometry : angle 0.66170 / 0.44 (18233) hydrogen bonds : bond 0.06644 / 4.42 ( 749) hydrogen bonds : angle 3.57026 / 2.60 ( 1866) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 11 residues processed: 122 average time/residue: 0.2470 time to fit residues: 41.8275 Evaluate side-chains 116 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain D residue 83 HIS Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain G residue 16 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 52 optimal weight: 0.0970 chunk 42 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 97 optimal weight: 20.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.078724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.059815 restraints weight = 105387.442| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.55 r_work: 0.3088 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 12594 Z= 0.159 Angle : 0.633 7.036 18233 Z= 0.416 Chirality : 0.042 0.166 2071 Planarity : 0.004 0.036 1318 Dihedral : 30.310 120.800 3962 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.13 % Allowed : 14.38 % Favored : 84.49 % 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: 1.99 (0.30), residues: 735 helix: 2.14 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -0.93 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 135 TYR 0.010 0.001 TYR H 41 PHE 0.007 0.001 PHE F 62 HIS 0.003 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.16 (12594) covalent geometry : angle 0.63251 / 0.42 (18233) hydrogen bonds : bond 0.05523 / 3.67 ( 749) hydrogen bonds : angle 3.20824 / 2.34 ( 1866) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 121 LYS cc_start: 0.9171 (tptp) cc_final: 0.8724 (mtpp) outliers start: 7 outliers final: 6 residues processed: 120 average time/residue: 0.2493 time to fit residues: 41.1339 Evaluate side-chains 117 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 111 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain D residue 83 HIS Chi-restraints excluded: chain G residue 16 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 65 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 57 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 70 optimal weight: 20.0000 chunk 77 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 25 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.076282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.057192 restraints weight = 105629.427| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.51 r_work: 0.3039 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12594 Z= 0.222 Angle : 0.654 6.787 18233 Z= 0.424 Chirality : 0.042 0.184 2071 Planarity : 0.004 0.038 1318 Dihedral : 30.339 121.516 3962 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.10 % Allowed : 15.02 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.30), residues: 735 helix: 2.03 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.16 (0.38), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 72 TYR 0.015 0.001 TYR F 99 PHE 0.011 0.001 PHE A 105 HIS 0.005 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.22 (12594) covalent geometry : angle 0.65380 / 0.42 (18233) hydrogen bonds : bond 0.06384 / 4.25 ( 749) hydrogen bonds : angle 3.49874 / 2.54 ( 1866) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 77 GLU cc_start: 0.8736 (tp30) cc_final: 0.8283 (mm-30) REVERT: D 121 LYS cc_start: 0.9247 (tptp) cc_final: 0.8759 (mtpp) REVERT: F 94 GLN cc_start: 0.8895 (tt0) cc_final: 0.8656 (mm-40) REVERT: H 94 GLU cc_start: 0.9048 (mp0) cc_final: 0.8611 (mp0) outliers start: 13 outliers final: 11 residues processed: 112 average time/residue: 0.2450 time to fit residues: 37.5448 Evaluate side-chains 111 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain D residue 83 HIS Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain H residue 48 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 10.0000 chunk 40 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 82 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.076810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.057990 restraints weight = 107102.984| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.51 r_work: 0.3062 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12594 Z= 0.162 Angle : 0.617 6.657 18233 Z= 0.405 Chirality : 0.041 0.164 2071 Planarity : 0.004 0.036 1318 Dihedral : 30.388 121.504 3962 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.45 % Allowed : 15.19 % Favored : 83.36 % 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: 2.05 (0.30), residues: 735 helix: 2.27 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.20 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 135 TYR 0.010 0.001 TYR H 41 PHE 0.008 0.001 PHE D 66 HIS 0.003 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.16 (12594) covalent geometry : angle 0.61679 / 0.40 (18233) hydrogen bonds : bond 0.05511 / 3.66 ( 749) hydrogen bonds : angle 3.24080 / 2.35 ( 1866) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 77 GLU cc_start: 0.8713 (tp30) cc_final: 0.8287 (mm-30) REVERT: D 121 LYS cc_start: 0.9250 (tptp) cc_final: 0.8776 (mtpp) REVERT: H 94 GLU cc_start: 0.9030 (mp0) cc_final: 0.8636 (mp0) outliers start: 9 outliers final: 8 residues processed: 114 average time/residue: 0.2439 time to fit residues: 38.6499 Evaluate side-chains 116 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain D residue 83 HIS Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain H residue 48 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 52 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.076999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.057992 restraints weight = 107038.104| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.53 r_work: 0.3049 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12594 Z= 0.179 Angle : 0.626 6.822 18233 Z= 0.405 Chirality : 0.040 0.162 2071 Planarity : 0.004 0.037 1318 Dihedral : 30.392 123.176 3962 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.62 % Allowed : 15.19 % Favored : 83.20 % 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: 2.09 (0.30), residues: 735 helix: 2.36 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.36 (0.38), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 53 TYR 0.012 0.001 TYR C 40 PHE 0.013 0.001 PHE E 79 HIS 0.004 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.18 (12594) covalent geometry : angle 0.62576 / 0.41 (18233) hydrogen bonds : bond 0.05545 / 3.68 ( 749) hydrogen bonds : angle 3.27050 / 2.37 ( 1866) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 121 LYS cc_start: 0.9253 (tptp) cc_final: 0.8765 (mtpp) REVERT: F 64 GLU cc_start: 0.9276 (mm-30) cc_final: 0.8740 (mm-30) REVERT: G 65 GLU cc_start: 0.9374 (tt0) cc_final: 0.9164 (tm-30) REVERT: H 94 GLU cc_start: 0.9023 (mp0) cc_final: 0.8566 (mp0) outliers start: 10 outliers final: 8 residues processed: 112 average time/residue: 0.2407 time to fit residues: 37.7812 Evaluate side-chains 112 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain D residue 83 HIS Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain H residue 48 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 8 optimal weight: 0.7980 chunk 9 optimal weight: 0.3980 chunk 26 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 84 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.077748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.058859 restraints weight = 106351.976| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.61 r_work: 0.3074 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12594 Z= 0.147 Angle : 0.601 6.778 18233 Z= 0.393 Chirality : 0.040 0.158 2071 Planarity : 0.004 0.036 1318 Dihedral : 30.414 123.515 3962 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.97 % Allowed : 16.48 % Favored : 82.55 % 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: 2.40 (0.31), residues: 735 helix: 2.62 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.35 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 100 TYR 0.013 0.001 TYR C 40 PHE 0.011 0.001 PHE E 79 HIS 0.005 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.15 (12594) covalent geometry : angle 0.60100 / 0.39 (18233) hydrogen bonds : bond 0.04892 / 3.25 ( 749) hydrogen bonds : angle 2.98923 / 2.17 ( 1866) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 112 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 121 LYS cc_start: 0.9265 (tptp) cc_final: 0.8760 (mtpp) REVERT: H 94 GLU cc_start: 0.9026 (mp0) cc_final: 0.8574 (mp0) outliers start: 6 outliers final: 4 residues processed: 114 average time/residue: 0.2477 time to fit residues: 38.9848 Evaluate side-chains 112 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain D residue 83 HIS Chi-restraints excluded: chain G residue 16 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 30 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 87 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.075776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.057204 restraints weight = 106566.085| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.56 r_work: 0.3035 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12594 Z= 0.205 Angle : 0.638 7.000 18233 Z= 0.407 Chirality : 0.040 0.161 2071 Planarity : 0.004 0.040 1318 Dihedral : 30.413 124.097 3962 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.97 % Allowed : 16.80 % Favored : 82.23 % 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: 2.05 (0.31), residues: 735 helix: 2.39 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.53 (0.38), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 36 TYR 0.010 0.001 TYR F 99 PHE 0.010 0.001 PHE E 79 HIS 0.003 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.20 (12594) covalent geometry : angle 0.63779 / 0.41 (18233) hydrogen bonds : bond 0.05743 / 3.82 ( 749) hydrogen bonds : angle 3.30969 / 2.39 ( 1866) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 102 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 77 GLU cc_start: 0.8790 (tp30) cc_final: 0.8324 (tp30) REVERT: D 121 LYS cc_start: 0.9269 (tptp) cc_final: 0.8776 (mtpp) REVERT: F 64 GLU cc_start: 0.9271 (mm-30) cc_final: 0.8704 (mm-30) REVERT: H 94 GLU cc_start: 0.9030 (mp0) cc_final: 0.8527 (mp0) outliers start: 6 outliers final: 6 residues processed: 104 average time/residue: 0.2505 time to fit residues: 36.0699 Evaluate side-chains 107 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain D residue 83 HIS Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain G residue 16 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 20.0000 chunk 40 optimal weight: 3.9990 chunk 25 optimal weight: 0.0060 chunk 38 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.077325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.058526 restraints weight = 107057.483| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.61 r_work: 0.3068 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12594 Z= 0.147 Angle : 0.604 6.745 18233 Z= 0.392 Chirality : 0.040 0.155 2071 Planarity : 0.004 0.039 1318 Dihedral : 30.448 124.313 3962 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.65 % Allowed : 17.29 % Favored : 82.07 % 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: 2.40 (0.31), residues: 735 helix: 2.64 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -1.44 (0.39), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 53 TYR 0.010 0.001 TYR C 40 PHE 0.009 0.001 PHE E 79 HIS 0.004 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.15 (12594) covalent geometry : angle 0.60428 / 0.39 (18233) hydrogen bonds : bond 0.04840 / 3.22 ( 749) hydrogen bonds : angle 3.00737 / 2.18 ( 1866) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 77 GLU cc_start: 0.8759 (tp30) cc_final: 0.8388 (tp30) REVERT: D 121 LYS cc_start: 0.9271 (tptp) cc_final: 0.8786 (mtpp) REVERT: F 64 GLU cc_start: 0.9236 (mm-30) cc_final: 0.8675 (mm-30) outliers start: 4 outliers final: 4 residues processed: 109 average time/residue: 0.2456 time to fit residues: 36.8258 Evaluate side-chains 107 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 103 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain D residue 83 HIS Chi-restraints excluded: chain G residue 16 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 70 optimal weight: 20.0000 chunk 82 optimal weight: 20.0000 chunk 69 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.076354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.057584 restraints weight = 107336.502| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.56 r_work: 0.3049 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12594 Z= 0.169 Angle : 0.616 6.966 18233 Z= 0.395 Chirality : 0.039 0.154 2071 Planarity : 0.004 0.042 1318 Dihedral : 30.429 125.223 3962 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.65 % Allowed : 17.12 % Favored : 82.23 % 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: 2.29 (0.31), residues: 735 helix: 2.56 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -1.49 (0.38), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 68 TYR 0.009 0.001 TYR H 41 PHE 0.009 0.001 PHE E 79 HIS 0.003 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.17 (12594) covalent geometry : angle 0.61560 / 0.40 (18233) hydrogen bonds : bond 0.05185 / 3.45 ( 749) hydrogen bonds : angle 3.14144 / 2.28 ( 1866) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4493.57 seconds wall clock time: 76 minutes 54.36 seconds (4614.36 seconds total)