Starting phenix.real_space_refine on Fri Aug 7 12:09:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mln_48376/08_2026/9mln_48376.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mln_48376/08_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_48376/08_2026/9mln_48376.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mln_48376/08_2026/9mln_48376.map" model { file = "/net/cci-nas-00/data/ceres_data/9mln_48376/08_2026/9mln_48376.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mln_48376/08_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-2.2rc3-6140/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: 3.50, per 1000 atoms: 0.16 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: 2.06 Conformation dependent library (CDL) restraints added in 411.0 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: 3.56 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: 4.89 Time building geometry restraints manager: 2.79 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: 34899 1.41 - 2.81: 4470 2.81 - 4.22: 429 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: 2.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.130 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.880 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.650 ------------------------------------------------------------------------------- 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= 0.647 Angle : 1.088 7.028 18233 Z= 0.907 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 1.08766 / 0.91 (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 : 0.469 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: A 91 MET cc_start: 0.7312 (mmp) cc_final: 0.6567 (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: 0.3619 time to fit residues: 87.6027 Evaluate side-chains 121 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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: 2.9990 chunk 97 optimal weight: 20.0000 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: 2.3588 ------------------------------------------------------------------------------- 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 = 0.3744 r_free = 0.3744 target = 0.077860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.058979 restraints weight = 106355.480| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.52 r_work: 0.3087 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12594 Z= 0.226 Angle : 0.781 7.957 18233 Z= 0.492 Chirality : 0.049 0.179 2071 Planarity : 0.005 0.038 1318 Dihedral : 30.012 115.097 3962 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 11.25 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: 1.20 (0.30), residues: 735 helix: 1.42 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -0.77 (0.40), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 87 TYR 0.012 0.002 TYR H 41 PHE 0.011 0.001 PHE F 62 HIS 0.008 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.23 (12594) covalent geometry : angle 0.78075 / 0.49 (18233) hydrogen bonds : bond 0.07486 / 4.99 ( 749) hydrogen bonds : angle 3.80357 / 2.78 ( 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 : 0.385 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: A 121 MET cc_start: 0.7325 (mmt) cc_final: 0.7065 (mtt) REVERT: G 91 ASP cc_start: 0.8312 (t0) cc_final: 0.8068 (t0) REVERT: G 93 GLU cc_start: 0.8642 (mp0) cc_final: 0.8370 (mp0) outliers start: 9 outliers final: 6 residues processed: 127 average time/residue: 0.2671 time to fit residues: 46.3994 Evaluate side-chains 116 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 C residue 86 LEU 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: 2.9990 chunk 24 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 23 optimal weight: 0.3980 chunk 77 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 95 optimal weight: 9.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 = 0.077569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.058844 restraints weight = 106744.784| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.53 r_work: 0.3076 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12594 Z= 0.185 Angle : 0.660 6.870 18233 Z= 0.440 Chirality : 0.043 0.171 2071 Planarity : 0.005 0.046 1318 Dihedral : 30.216 116.798 3962 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.10 % Allowed : 13.25 % Favored : 84.65 % 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: 1.67 (0.30), residues: 735 helix: 1.86 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -0.87 (0.40), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 53 TYR 0.011 0.001 TYR H 41 PHE 0.011 0.001 PHE D 66 HIS 0.005 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.19 (12594) covalent geometry : angle 0.65950 / 0.44 (18233) hydrogen bonds : bond 0.06331 / 4.21 ( 749) hydrogen bonds : angle 3.45768 / 2.52 ( 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 130 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.7601 (mmt) cc_final: 0.7281 (mmt) REVERT: F 94 GLN cc_start: 0.8850 (tt0) cc_final: 0.8542 (mm-40) REVERT: G 91 ASP cc_start: 0.8262 (t0) cc_final: 0.7851 (t0) REVERT: G 93 GLU cc_start: 0.8668 (mp0) cc_final: 0.8284 (mp0) outliers start: 13 outliers final: 8 residues processed: 122 average time/residue: 0.2584 time to fit residues: 43.7467 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 : 0.473 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 52 optimal weight: 0.5980 chunk 42 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 overall best weight: 2.1188 ------------------------------------------------------------------------------- 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 = 0.3720 r_free = 0.3720 target = 0.077097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.058676 restraints weight = 105728.946| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.56 r_work: 0.3054 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3174 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= 0.198 Angle : 0.665 7.950 18233 Z= 0.428 Chirality : 0.042 0.173 2071 Planarity : 0.004 0.038 1318 Dihedral : 30.288 119.069 3962 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.94 % Allowed : 14.05 % Favored : 84.01 % 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: 1.72 (0.30), residues: 735 helix: 1.97 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.09 (0.39), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 53 TYR 0.012 0.001 TYR H 41 PHE 0.009 0.001 PHE A 105 HIS 0.005 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.20 (12594) covalent geometry : angle 0.66496 / 0.43 (18233) hydrogen bonds : bond 0.06214 / 4.14 ( 749) hydrogen bonds : angle 3.45416 / 2.52 ( 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 126 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.7889 (mmt) cc_final: 0.7317 (mmp) REVERT: D 121 LYS cc_start: 0.9204 (tptp) cc_final: 0.8756 (mtpp) REVERT: E 121 MET cc_start: 0.6506 (mtt) cc_final: 0.6305 (mtt) REVERT: G 91 ASP cc_start: 0.8390 (t0) cc_final: 0.8148 (t0) outliers start: 12 outliers final: 11 residues processed: 119 average time/residue: 0.2661 time to fit residues: 43.4862 Evaluate side-chains 119 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 65 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 57 optimal weight: 0.2980 chunk 50 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 70 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 overall best weight: 3.0588 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.075581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.056487 restraints weight = 108730.885| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.56 r_work: 0.3018 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12594 Z= 0.229 Angle : 0.669 7.148 18233 Z= 0.431 Chirality : 0.042 0.174 2071 Planarity : 0.005 0.039 1318 Dihedral : 30.366 118.099 3962 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.26 % Allowed : 14.70 % Favored : 83.04 % 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: 1.48 (0.30), residues: 735 helix: 1.84 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.35 (0.38), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 135 TYR 0.011 0.001 TYR F 99 PHE 0.010 0.001 PHE E 85 HIS 0.004 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.23 (12594) covalent geometry : angle 0.66906 / 0.43 (18233) hydrogen bonds : bond 0.06676 / 4.44 ( 749) hydrogen bonds : angle 3.63494 / 2.63 ( 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 119 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8357 (mp) REVERT: D 77 GLU cc_start: 0.8767 (tp30) cc_final: 0.8310 (mm-30) REVERT: D 121 LYS cc_start: 0.9253 (tptp) cc_final: 0.8750 (mtpp) REVERT: G 91 ASP cc_start: 0.8439 (t0) cc_final: 0.8128 (t0) REVERT: H 94 GLU cc_start: 0.9048 (mp0) cc_final: 0.8614 (mp0) outliers start: 14 outliers final: 11 residues processed: 115 average time/residue: 0.2751 time to fit residues: 43.3616 Evaluate side-chains 112 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 B residue 47 ILE Chi-restraints excluded: chain D residue 83 HIS Chi-restraints excluded: chain D residue 123 THR 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: 20.0000 chunk 40 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 44 optimal weight: 0.1980 chunk 45 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.3715 r_free = 0.3715 target = 0.076547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.057939 restraints weight = 106718.238| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.57 r_work: 0.3048 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12594 Z= 0.157 Angle : 0.629 7.138 18233 Z= 0.408 Chirality : 0.041 0.170 2071 Planarity : 0.004 0.034 1318 Dihedral : 30.389 119.486 3962 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.45 % Allowed : 16.32 % 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: 1.92 (0.30), residues: 735 helix: 2.21 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.34 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 43 TYR 0.010 0.001 TYR C 40 PHE 0.008 0.001 PHE D 66 HIS 0.003 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.16 (12594) covalent geometry : angle 0.62942 / 0.41 (18233) hydrogen bonds : bond 0.05647 / 3.75 ( 749) hydrogen bonds : angle 3.25297 / 2.36 ( 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 : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 77 GLU cc_start: 0.8731 (tp30) cc_final: 0.8316 (mm-30) REVERT: D 121 LYS cc_start: 0.9260 (tptp) cc_final: 0.8780 (mtpp) REVERT: G 91 ASP cc_start: 0.8404 (t0) cc_final: 0.8078 (t0) REVERT: H 94 GLU cc_start: 0.9009 (mp0) cc_final: 0.8614 (mp0) outliers start: 9 outliers final: 8 residues processed: 113 average time/residue: 0.2427 time to fit residues: 37.1756 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 : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 103 ILE Chi-restraints excluded: chain D residue 83 HIS Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain H residue 102 LEU 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: 4.9990 chunk 11 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 44 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3710 r_free = 0.3710 target = 0.076260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.057846 restraints weight = 106533.857| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.56 r_work: 0.3049 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12594 Z= 0.169 Angle : 0.625 7.024 18233 Z= 0.405 Chirality : 0.040 0.165 2071 Planarity : 0.004 0.036 1318 Dihedral : 30.366 120.419 3962 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.45 % Allowed : 16.80 % Favored : 81.74 % 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 (0.31), residues: 735 helix: 2.38 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.40 (0.39), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 53 TYR 0.010 0.001 TYR C 40 PHE 0.008 0.001 PHE A 105 HIS 0.004 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.17 (12594) covalent geometry : angle 0.62478 / 0.40 (18233) hydrogen bonds : bond 0.05452 / 3.61 ( 749) hydrogen bonds : angle 3.23689 / 2.35 ( 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 115 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 121 LYS cc_start: 0.9260 (tptp) cc_final: 0.8764 (mtpp) REVERT: F 64 GLU cc_start: 0.9251 (mm-30) cc_final: 0.8668 (mm-30) REVERT: G 91 ASP cc_start: 0.8430 (t0) cc_final: 0.8205 (t0) REVERT: H 94 GLU cc_start: 0.9028 (mp0) cc_final: 0.8560 (mp0) outliers start: 9 outliers final: 7 residues processed: 110 average time/residue: 0.2575 time to fit residues: 40.0134 Evaluate side-chains 110 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Chi-restraints excluded: chain H residue 102 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 8 optimal weight: 0.9990 chunk 9 optimal weight: 0.3980 chunk 26 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 73 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.076842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.058047 restraints weight = 107344.887| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.58 r_work: 0.3051 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12594 Z= 0.157 Angle : 0.618 7.116 18233 Z= 0.400 Chirality : 0.040 0.164 2071 Planarity : 0.004 0.036 1318 Dihedral : 30.387 120.782 3962 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.29 % Allowed : 17.77 % Favored : 80.94 % 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: 2.22 (0.31), residues: 735 helix: 2.51 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.48 (0.39), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 53 TYR 0.008 0.001 TYR F 99 PHE 0.008 0.001 PHE D 66 HIS 0.004 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.16 (12594) covalent geometry : angle 0.61849 / 0.40 (18233) hydrogen bonds : bond 0.05157 / 3.43 ( 749) hydrogen bonds : angle 3.14378 / 2.28 ( 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 114 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 121 LYS cc_start: 0.9277 (tptp) cc_final: 0.8779 (mtpp) REVERT: G 91 ASP cc_start: 0.8427 (t0) cc_final: 0.8141 (t0) outliers start: 8 outliers final: 7 residues processed: 108 average time/residue: 0.2597 time to fit residues: 38.8917 Evaluate side-chains 108 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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 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 102 LEU 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: 10.0000 chunk 56 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3697 r_free = 0.3697 target = 0.075402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.056762 restraints weight = 106901.219| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.56 r_work: 0.3031 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12594 Z= 0.193 Angle : 0.638 7.169 18233 Z= 0.407 Chirality : 0.040 0.164 2071 Planarity : 0.004 0.039 1318 Dihedral : 30.392 121.059 3962 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.13 % Allowed : 17.77 % Favored : 81.10 % 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 (0.31), residues: 735 helix: 2.28 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.60 (0.38), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 68 TYR 0.010 0.001 TYR F 99 PHE 0.010 0.001 PHE A 105 HIS 0.004 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.19 (12594) covalent geometry : angle 0.63757 / 0.41 (18233) hydrogen bonds : bond 0.05817 / 3.87 ( 749) hydrogen bonds : angle 3.34802 / 2.43 ( 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 106 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8344 (mp) REVERT: D 77 GLU cc_start: 0.8850 (tp30) cc_final: 0.8415 (tp30) REVERT: D 121 LYS cc_start: 0.9270 (tptp) cc_final: 0.8780 (mtpp) REVERT: G 91 ASP cc_start: 0.8531 (t0) cc_final: 0.8210 (t0) outliers start: 7 outliers final: 6 residues processed: 102 average time/residue: 0.2775 time to fit residues: 38.8734 Evaluate side-chains 105 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 B residue 31 THR Chi-restraints excluded: chain B residue 47 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 82 optimal weight: 20.0000 chunk 40 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.075720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.057017 restraints weight = 107626.146| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.59 r_work: 0.3037 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12594 Z= 0.168 Angle : 0.622 7.153 18233 Z= 0.399 Chirality : 0.040 0.162 2071 Planarity : 0.004 0.040 1318 Dihedral : 30.423 120.892 3962 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.45 % Allowed : 17.29 % Favored : 81.26 % 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: 2.02 (0.31), residues: 735 helix: 2.39 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.64 (0.38), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 68 TYR 0.010 0.001 TYR F 99 PHE 0.009 0.001 PHE D 66 HIS 0.004 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.17 (12594) covalent geometry : angle 0.62185 / 0.40 (18233) hydrogen bonds : bond 0.05353 / 3.55 ( 749) hydrogen bonds : angle 3.25560 / 2.36 ( 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 113 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 121 LYS cc_start: 0.9267 (tptp) cc_final: 0.8784 (mtpp) REVERT: F 64 GLU cc_start: 0.9275 (mm-30) cc_final: 0.8801 (mm-30) REVERT: G 91 ASP cc_start: 0.8501 (t0) cc_final: 0.8259 (t0) outliers start: 9 outliers final: 9 residues processed: 108 average time/residue: 0.2821 time to fit residues: 41.7361 Evaluate side-chains 110 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.463 ------------------------------------------------------------------------------- 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 B residue 31 THR Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 83 HIS Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 102 LEU 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: 0.6980 chunk 32 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3722 r_free = 0.3722 target = 0.076535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.057688 restraints weight = 107737.538| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.58 r_work: 0.3054 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.4554 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= 0.151 Angle : 0.606 6.942 18233 Z= 0.391 Chirality : 0.039 0.156 2071 Planarity : 0.004 0.039 1318 Dihedral : 30.397 122.333 3962 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.81 % Allowed : 18.09 % Favored : 81.10 % 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: 2.30 (0.31), residues: 735 helix: 2.60 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.54 (0.39), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 80 TYR 0.008 0.001 TYR C 40 PHE 0.007 0.001 PHE D 66 HIS 0.004 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.15 (12594) covalent geometry : angle 0.60643 / 0.39 (18233) hydrogen bonds : bond 0.04800 / 3.20 ( 749) hydrogen bonds : angle 3.07679 / 2.23 ( 1866) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4572.13 seconds wall clock time: 78 minutes 27.90 seconds (4707.90 seconds total)