Starting phenix.real_space_refine on Fri Feb 6 00:16:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mln_48376/02_2026/9mln_48376.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mln_48376/02_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_48376/02_2026/9mln_48376.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mln_48376/02_2026/9mln_48376.map" model { file = "/net/cci-nas-00/data/ceres_data/9mln_48376/02_2026/9mln_48376.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mln_48376/02_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-2.0-5952/lib/python3.9/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: 3.76, per 1000 atoms: 0.18 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: 2.08 Conformation dependent library (CDL) restraints added in 599.5 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: 4.21 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: 5.04 Time building geometry restraints manager: 2.89 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 1.525 1.569 -0.044 2.00e-02 2.50e+03 4.75e+00 bond pdb=" CG1 ILE A 52 " pdb=" CD1 ILE A 52 " ideal model delta sigma weight residual 1.513 1.441 0.072 3.90e-02 6.57e+02 3.39e+00 bond pdb=" C4' DT I 43 " pdb=" O4' DT I 43 " ideal model delta sigma weight residual 1.450 1.414 0.036 2.00e-02 2.50e+03 3.30e+00 bond pdb=" CB ILE A 52 " pdb=" CG2 ILE A 52 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.97e+00 bond pdb=" C3' DT J 33 " pdb=" C2' DT J 33 " ideal model delta sigma weight residual 1.525 1.554 -0.029 2.00e-02 2.50e+03 2.12e+00 ... (remaining 22046 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 35151 1.41 - 2.81: 4355 2.81 - 4.22: 403 4.22 - 5.62: 58 5.62 - 7.03: 5 Bond angle restraints: 39972 Sorted by residual: angle pdb=" C2' DT I 43 " pdb=" C1' DT I 43 " pdb=" N1 DT I 43 " ideal model delta sigma weight residual 113.50 120.42 -6.92 1.50e+00 4.44e-01 2.13e+01 angle pdb=" C2' DG J -69 " pdb=" C1' DG J -69 " pdb=" N9 DG J -69 " ideal model delta sigma weight residual 113.50 119.09 -5.59 1.50e+00 4.44e-01 1.39e+01 angle pdb=" C4' DT I 68 " pdb=" O4' DT I 68 " pdb=" C1' DT I 68 " ideal model delta sigma weight residual 109.70 104.15 5.55 1.50e+00 4.44e-01 1.37e+01 angle pdb=" O4' DA I -54 " pdb=" C1' DA I -54 " pdb=" N9 DA I -54 " ideal model delta sigma weight residual 108.40 102.89 5.51 1.50e+00 4.44e-01 1.35e+01 angle pdb=" C4' DG J 21 " pdb=" O4' DG J 21 " pdb=" C1' DG J 21 " ideal model delta sigma weight residual 109.70 104.23 5.47 1.50e+00 4.44e-01 1.33e+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 - 0.056: 1532 0.056 - 0.113: 443 0.113 - 0.169: 86 0.169 - 0.226: 8 0.226 - 0.282: 2 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 2.47 2.19 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" C1' DT I 64 " pdb=" O4' DT I 64 " pdb=" C2' DT I 64 " pdb=" N1 DT I 64 " both_signs ideal model delta sigma weight residual False 2.47 2.23 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" C1' DC J -2 " pdb=" O4' DC J -2 " pdb=" C2' DC J -2 " pdb=" N1 DC J -2 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.22 2.00e-01 2.50e+01 1.21e+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: 3.220 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: 0.080 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 24.480 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.700 ------------------------------------------------------------------------------- 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 : 0.006 0.072 12594 Z= 0.268 Angle : 0.989 7.028 18233 Z= 0.634 Chirality : 0.053 0.282 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 covalent geometry : bond 0.00568 (12594) covalent geometry : angle 0.98921 (18233) hydrogen bonds : bond 0.11668 ( 749) hydrogen bonds : angle 4.50994 ( 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 : 0.420 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: 0.3886 time to fit residues: 91.6279 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 : 0.372 ------------------------------------------------------------------------------- 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: 5.9990 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: 3.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN B 26 ASN B 65 ASN C 39 HIS ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN E 86 GLN F 26 ASN G 25 GLN G 69 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.077273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.058439 restraints weight = 106714.811| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.52 r_work: 0.3087 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12594 Z= 0.224 Angle : 0.689 5.884 18233 Z= 0.425 Chirality : 0.041 0.131 2071 Planarity : 0.005 0.042 1318 Dihedral : 29.960 116.127 3962 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.62 % Allowed : 12.28 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.30), residues: 735 helix: 1.88 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -0.60 (0.40), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 53 TYR 0.011 0.001 TYR H 41 PHE 0.010 0.001 PHE D 66 HIS 0.004 0.001 HIS F 76 Details of bonding type rmsd covalent geometry : bond 0.00480 (12594) covalent geometry : angle 0.68919 (18233) hydrogen bonds : bond 0.06060 ( 749) hydrogen bonds : angle 3.41364 ( 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 140 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.457 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: C 105 GLN cc_start: 0.8319 (mm-40) cc_final: 0.8078 (mp10) REVERT: D 121 LYS cc_start: 0.9236 (tptp) cc_final: 0.8823 (mtpp) REVERT: G 91 ASP cc_start: 0.8369 (t0) cc_final: 0.8106 (t0) REVERT: G 93 GLU cc_start: 0.8674 (mp0) cc_final: 0.8307 (mp0) outliers start: 10 outliers final: 6 residues processed: 135 average time/residue: 0.2949 time to fit residues: 52.8696 Evaluate side-chains 122 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 86 LEU Chi-restraints excluded: chain D residue 83 HIS Chi-restraints excluded: chain G residue 16 LYS 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: 2.9990 chunk 11 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.075416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.056921 restraints weight = 107459.020| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.58 r_work: 0.3026 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12594 Z= 0.227 Angle : 0.662 7.244 18233 Z= 0.409 Chirality : 0.041 0.137 2071 Planarity : 0.004 0.033 1318 Dihedral : 29.766 108.329 3962 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.78 % Allowed : 13.89 % Favored : 84.33 % 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: 1.91 (0.30), residues: 735 helix: 2.09 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.00 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 68 TYR 0.011 0.001 TYR D 84 PHE 0.010 0.001 PHE D 66 HIS 0.004 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00482 (12594) covalent geometry : angle 0.66209 (18233) hydrogen bonds : bond 0.05839 ( 749) hydrogen bonds : angle 3.41295 ( 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 121 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 105 GLN cc_start: 0.8504 (mm-40) cc_final: 0.8221 (mp10) REVERT: D 121 LYS cc_start: 0.9251 (tptp) cc_final: 0.8784 (mtpp) REVERT: F 64 GLU cc_start: 0.9278 (mm-30) cc_final: 0.8662 (mm-30) REVERT: G 91 ASP cc_start: 0.8433 (t0) cc_final: 0.8181 (t0) outliers start: 11 outliers final: 10 residues processed: 115 average time/residue: 0.3414 time to fit residues: 50.6856 Evaluate side-chains 112 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 42 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 97 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.077384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.058508 restraints weight = 107114.294| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.58 r_work: 0.3078 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12594 Z= 0.168 Angle : 0.616 7.463 18233 Z= 0.382 Chirality : 0.037 0.127 2071 Planarity : 0.004 0.035 1318 Dihedral : 29.748 108.583 3962 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.97 % Allowed : 15.35 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.67 (0.31), residues: 735 helix: 2.75 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.00 (0.40), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 135 TYR 0.009 0.001 TYR H 41 PHE 0.007 0.001 PHE A 105 HIS 0.005 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00358 (12594) covalent geometry : angle 0.61625 (18233) hydrogen bonds : bond 0.04145 ( 749) hydrogen bonds : angle 2.88982 ( 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 120 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 114 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 105 GLN cc_start: 0.8426 (mm-40) cc_final: 0.8190 (mp10) REVERT: D 77 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8433 (tp30) REVERT: D 121 LYS cc_start: 0.9252 (tptp) cc_final: 0.8746 (mtpp) REVERT: E 74 GLU cc_start: 0.9049 (tm-30) cc_final: 0.8617 (tm-30) REVERT: F 64 GLU cc_start: 0.9181 (mm-30) cc_final: 0.8480 (mm-30) REVERT: G 91 ASP cc_start: 0.8420 (t0) cc_final: 0.8094 (t0) REVERT: G 93 GLU cc_start: 0.8827 (mp0) cc_final: 0.8616 (mp0) outliers start: 6 outliers final: 3 residues processed: 117 average time/residue: 0.2778 time to fit residues: 43.4440 Evaluate side-chains 111 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 108 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 61 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.073656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.054814 restraints weight = 109156.895| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.56 r_work: 0.2987 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 12594 Z= 0.265 Angle : 0.666 8.156 18233 Z= 0.410 Chirality : 0.043 0.145 2071 Planarity : 0.005 0.038 1318 Dihedral : 29.838 101.409 3962 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.26 % Allowed : 15.35 % Favored : 82.39 % 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: 1.85 (0.30), residues: 735 helix: 2.16 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.37 (0.39), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 53 TYR 0.012 0.001 TYR D 84 PHE 0.011 0.001 PHE D 66 HIS 0.005 0.001 HIS G 39 Details of bonding type rmsd covalent geometry : bond 0.00567 (12594) covalent geometry : angle 0.66570 (18233) hydrogen bonds : bond 0.06459 ( 749) hydrogen bonds : angle 3.58441 ( 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 115 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 121 LYS cc_start: 0.9283 (tptp) cc_final: 0.8771 (mtpp) REVERT: E 74 GLU cc_start: 0.9102 (tm-30) cc_final: 0.8655 (tm-30) REVERT: F 64 GLU cc_start: 0.9243 (mm-30) cc_final: 0.8521 (mm-30) REVERT: G 91 ASP cc_start: 0.8518 (t0) cc_final: 0.8099 (t0) outliers start: 14 outliers final: 11 residues processed: 108 average time/residue: 0.2745 time to fit residues: 40.0236 Evaluate side-chains 110 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 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 C residue 79 ILE 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 86 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.075522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.056717 restraints weight = 108205.336| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.53 r_work: 0.3040 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12594 Z= 0.178 Angle : 0.617 7.912 18233 Z= 0.382 Chirality : 0.038 0.132 2071 Planarity : 0.004 0.037 1318 Dihedral : 29.770 101.777 3962 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.65 % Allowed : 16.96 % Favored : 82.39 % 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: 2.32 (0.31), residues: 735 helix: 2.54 (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 0.004 0.000 ARG E 53 TYR 0.009 0.001 TYR H 41 PHE 0.008 0.001 PHE A 105 HIS 0.005 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00376 (12594) covalent geometry : angle 0.61678 (18233) hydrogen bonds : bond 0.04592 ( 749) hydrogen bonds : angle 3.07945 ( 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 105 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 101 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 121 LYS cc_start: 0.9246 (tptp) cc_final: 0.8711 (mtpp) REVERT: E 74 GLU cc_start: 0.9072 (tm-30) cc_final: 0.8654 (tm-30) REVERT: F 64 GLU cc_start: 0.9217 (mm-30) cc_final: 0.8485 (mm-30) REVERT: G 91 ASP cc_start: 0.8468 (t0) cc_final: 0.8160 (t0) outliers start: 4 outliers final: 3 residues processed: 103 average time/residue: 0.3044 time to fit residues: 41.9569 Evaluate side-chains 103 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 100 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain D residue 83 HIS Chi-restraints excluded: chain G residue 16 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 52 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.075425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.056557 restraints weight = 107676.834| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.52 r_work: 0.3033 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.4944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12594 Z= 0.190 Angle : 0.619 7.917 18233 Z= 0.383 Chirality : 0.039 0.133 2071 Planarity : 0.004 0.039 1318 Dihedral : 29.747 100.397 3962 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.89 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: 2.29 (0.31), residues: 735 helix: 2.54 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.41 (0.38), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 53 TYR 0.009 0.001 TYR F 52 PHE 0.007 0.001 PHE D 66 HIS 0.005 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00402 (12594) covalent geometry : angle 0.61869 (18233) hydrogen bonds : bond 0.04896 ( 749) hydrogen bonds : angle 3.14028 ( 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 107 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 121 LYS cc_start: 0.9254 (tptp) cc_final: 0.8706 (mtpp) REVERT: E 74 GLU cc_start: 0.9102 (tm-30) cc_final: 0.8673 (tm-30) REVERT: F 64 GLU cc_start: 0.9223 (mm-30) cc_final: 0.8477 (mm-30) REVERT: G 91 ASP cc_start: 0.8492 (t0) cc_final: 0.8119 (t0) outliers start: 9 outliers final: 7 residues processed: 103 average time/residue: 0.2955 time to fit residues: 40.7567 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 : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain C residue 79 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 8 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 84 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.076224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.057353 restraints weight = 106574.063| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.52 r_work: 0.3054 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.5198 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= 0.175 Angle : 0.611 7.363 18233 Z= 0.378 Chirality : 0.038 0.131 2071 Planarity : 0.004 0.037 1318 Dihedral : 29.703 99.460 3962 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.13 % Allowed : 17.45 % Favored : 81.42 % 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: 2.50 (0.31), residues: 735 helix: 2.76 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.51 (0.38), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 53 TYR 0.007 0.001 TYR C 40 PHE 0.007 0.001 PHE A 105 HIS 0.006 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00373 (12594) covalent geometry : angle 0.61127 (18233) hydrogen bonds : bond 0.04205 ( 749) hydrogen bonds : angle 2.96196 ( 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 112 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 105 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 121 LYS cc_start: 0.9233 (tptp) cc_final: 0.8667 (mtpp) REVERT: E 74 GLU cc_start: 0.9095 (tm-30) cc_final: 0.8719 (tm-30) REVERT: F 64 GLU cc_start: 0.9189 (mm-30) cc_final: 0.8478 (mm-30) REVERT: G 91 ASP cc_start: 0.8489 (t0) cc_final: 0.8199 (t0) outliers start: 7 outliers final: 6 residues processed: 109 average time/residue: 0.3098 time to fit residues: 44.7782 Evaluate side-chains 102 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 83 HIS Chi-restraints excluded: chain E residue 64 ARG 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: 2.9990 chunk 78 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 72 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.073761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.055018 restraints weight = 107532.484| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.49 r_work: 0.2996 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.5383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12594 Z= 0.237 Angle : 0.649 7.818 18233 Z= 0.399 Chirality : 0.041 0.138 2071 Planarity : 0.004 0.040 1318 Dihedral : 29.794 97.034 3962 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.62 % Allowed : 16.80 % Favored : 81.58 % 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: 1.86 (0.30), residues: 735 helix: 2.27 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.72 (0.37), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 53 TYR 0.013 0.001 TYR D 84 PHE 0.010 0.001 PHE D 66 HIS 0.005 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00504 (12594) covalent geometry : angle 0.64949 (18233) hydrogen bonds : bond 0.05967 ( 749) hydrogen bonds : angle 3.44159 ( 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: 10 poor density : 96 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 74 GLU cc_start: 0.9097 (tm-30) cc_final: 0.8638 (tm-30) REVERT: F 64 GLU cc_start: 0.9206 (mm-30) cc_final: 0.8578 (mm-30) REVERT: G 91 ASP cc_start: 0.8540 (t0) cc_final: 0.8242 (t0) outliers start: 10 outliers final: 9 residues processed: 103 average time/residue: 0.2960 time to fit residues: 40.1522 Evaluate side-chains 103 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 83 HIS Chi-restraints excluded: chain E residue 64 ARG 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: 6.9990 chunk 40 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.075091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.055991 restraints weight = 106834.980| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.50 r_work: 0.3024 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.5478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12594 Z= 0.192 Angle : 0.626 7.573 18233 Z= 0.385 Chirality : 0.039 0.137 2071 Planarity : 0.004 0.039 1318 Dihedral : 29.741 98.122 3962 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.45 % Allowed : 16.96 % Favored : 81.58 % 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: 2.12 (0.31), residues: 735 helix: 2.50 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.71 (0.38), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 53 TYR 0.007 0.001 TYR F 99 PHE 0.008 0.001 PHE A 105 HIS 0.005 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00408 (12594) covalent geometry : angle 0.62647 (18233) hydrogen bonds : bond 0.04729 ( 749) hydrogen bonds : angle 3.15352 ( 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 106 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 121 LYS cc_start: 0.9209 (tptp) cc_final: 0.8624 (mtpp) REVERT: E 74 GLU cc_start: 0.9124 (tm-30) cc_final: 0.8691 (tm-30) REVERT: F 64 GLU cc_start: 0.9202 (mm-30) cc_final: 0.8566 (mm-30) REVERT: G 91 ASP cc_start: 0.8495 (t0) cc_final: 0.8072 (t0) REVERT: G 93 GLU cc_start: 0.8675 (mp0) cc_final: 0.8013 (mp0) outliers start: 9 outliers final: 7 residues processed: 104 average time/residue: 0.3206 time to fit residues: 43.9920 Evaluate side-chains 101 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 83 HIS Chi-restraints excluded: chain E residue 64 ARG 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 70 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.074610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.055887 restraints weight = 107635.057| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.50 r_work: 0.3026 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.5527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12594 Z= 0.199 Angle : 0.633 8.157 18233 Z= 0.388 Chirality : 0.039 0.139 2071 Planarity : 0.004 0.039 1318 Dihedral : 29.734 97.777 3962 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.45 % Allowed : 16.64 % Favored : 81.91 % 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: 2.49 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.77 (0.38), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 53 TYR 0.007 0.001 TYR F 52 PHE 0.007 0.001 PHE D 66 HIS 0.005 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00423 (12594) covalent geometry : angle 0.63310 (18233) hydrogen bonds : bond 0.04867 ( 749) hydrogen bonds : angle 3.18226 ( 1866) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4970.32 seconds wall clock time: 85 minutes 0.39 seconds (5100.39 seconds total)