Starting phenix.real_space_refine on Thu Aug 6 00:13:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e0r_47367/08_2026/9e0r_47367.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e0r_47367/08_2026/9e0r_47367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e0r_47367/08_2026/9e0r_47367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e0r_47367/08_2026/9e0r_47367.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e0r_47367/08_2026/9e0r_47367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e0r_47367/08_2026/9e0r_47367.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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: 5 Type Number sf(0) Gaussians P 310 5.49 5 S 13 5.16 5 C 6751 2.51 5 N 2321 2.21 5 O 2910 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s 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: 12305 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 795 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 764 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 755 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 3190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 3190 Classifications: {'DNA': 155} Link IDs: {'rna3p': 154} Chain: "J" Number of atoms: 3165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 3165 Classifications: {'DNA': 155} Link IDs: {'rna3p': 154} Chain: "L" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 84 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "K" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Time building chain proxies: 2.55, per 1000 atoms: 0.21 Number of scatterers: 12305 At special positions: 0 Unit cell: (120.06, 115.092, 124.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 13 16.00 P 310 15.00 O 2910 8.00 N 2321 7.00 C 6751 6.00 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: 0.62 Conformation dependent library (CDL) restraints added in 335.8 milliseconds 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1402 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 8 sheets defined 72.9% alpha, 2.4% beta 155 base pairs and 276 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 removed outlier: 3.541A pdb=" N GLN A 55 " --> pdb=" O ILE A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.635A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.644A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.622A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.639A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 74 removed outlier: 4.297A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA C 53 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.558A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL C 87 " --> pdb=" O LEU C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.522A pdb=" N ARG D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.586A pdb=" N LYS D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 removed outlier: 3.711A pdb=" N GLN E 55 " --> pdb=" O ILE E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.510A pdb=" N ILE E 74 " --> pdb=" O LEU E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.673A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.509A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.822A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.601A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.642A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG G 35 " --> pdb=" O HIS G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.337A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.568A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 removed outlier: 3.650A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.679A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 741 through 746 removed outlier: 3.744A pdb=" N LYS L 745 " --> pdb=" O GLY L 741 " (cutoff:3.500A) Processing helix chain 'K' and resid 741 through 746 removed outlier: 3.941A pdb=" N LYS K 745 " --> pdb=" O GLY K 741 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.167A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.382A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.833A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.682A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 372 hydrogen bonds defined for protein. 1110 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 399 hydrogen bonds 794 hydrogen bond angles 0 basepair planarities 155 basepair parallelities 276 stacking parallelities Total time for adding SS restraints: 2.25 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2426 1.34 - 1.46: 4357 1.46 - 1.58: 5729 1.58 - 1.70: 617 1.70 - 1.82: 24 Bond restraints: 13153 Sorted by residual: bond pdb=" N PRO H 100 " pdb=" CA PRO H 100 " ideal model delta sigma weight residual 1.471 1.529 -0.057 1.29e-02 6.01e+03 1.99e+01 bond pdb=" C LEU H 99 " pdb=" N PRO H 100 " ideal model delta sigma weight residual 1.336 1.386 -0.050 1.20e-02 6.94e+03 1.71e+01 bond pdb=" C3' DC I 153 " pdb=" O3' DC I 153 " ideal model delta sigma weight residual 1.435 1.391 0.044 1.30e-02 5.92e+03 1.14e+01 bond pdb=" N MET A 120 " pdb=" CA MET A 120 " ideal model delta sigma weight residual 1.453 1.483 -0.029 9.20e-03 1.18e+04 1.02e+01 bond pdb=" O3' DC I 153 " pdb=" P DC I 154 " ideal model delta sigma weight residual 1.607 1.570 0.037 1.20e-02 6.94e+03 9.74e+00 ... (remaining 13148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 17570 2.18 - 4.36: 1491 4.36 - 6.53: 21 6.53 - 8.71: 4 8.71 - 10.89: 2 Bond angle restraints: 19088 Sorted by residual: angle pdb=" C LEU H 99 " pdb=" N PRO H 100 " pdb=" CA PRO H 100 " ideal model delta sigma weight residual 118.85 129.74 -10.89 1.09e+00 8.42e-01 9.98e+01 angle pdb=" C4' DC I 154 " pdb=" O4' DC I 154 " pdb=" C1' DC I 154 " ideal model delta sigma weight residual 110.10 104.88 5.22 1.00e+00 1.00e+00 2.72e+01 angle pdb=" O5' DA I 10 " pdb=" C5' DA I 10 " pdb=" C4' DA I 10 " ideal model delta sigma weight residual 109.40 113.47 -4.07 8.00e-01 1.56e+00 2.59e+01 angle pdb=" N PRO H 100 " pdb=" CA PRO H 100 " pdb=" C PRO H 100 " ideal model delta sigma weight residual 113.40 119.94 -6.54 1.34e+00 5.57e-01 2.38e+01 angle pdb=" N PRO D 100 " pdb=" CA PRO D 100 " pdb=" C PRO D 100 " ideal model delta sigma weight residual 113.40 119.24 -5.84 1.34e+00 5.57e-01 1.90e+01 ... (remaining 19083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.83: 5651 34.83 - 69.67: 1420 69.67 - 104.50: 19 104.50 - 139.33: 0 139.33 - 174.17: 2 Dihedral angle restraints: 7092 sinusoidal: 4921 harmonic: 2171 Sorted by residual: dihedral pdb=" C4' DG I 3 " pdb=" C3' DG I 3 " pdb=" O3' DG I 3 " pdb=" P DG I 4 " ideal model delta sinusoidal sigma weight residual -140.00 34.17 -174.17 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DC I 144 " pdb=" C3' DC I 144 " pdb=" O3' DC I 144 " pdb=" P DG I 145 " ideal model delta sinusoidal sigma weight residual 220.00 70.20 149.80 1 3.50e+01 8.16e-04 1.46e+01 dihedral pdb=" CA ILE F 29 " pdb=" C ILE F 29 " pdb=" N THR F 30 " pdb=" CA THR F 30 " ideal model delta harmonic sigma weight residual 180.00 -164.23 -15.77 0 5.00e+00 4.00e-02 9.94e+00 ... (remaining 7089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1550 0.066 - 0.132: 547 0.132 - 0.197: 65 0.197 - 0.263: 4 0.263 - 0.329: 3 Chirality restraints: 2169 Sorted by residual: chirality pdb=" C3' DG I 3 " pdb=" C4' DG I 3 " pdb=" O3' DG I 3 " pdb=" C2' DG I 3 " both_signs ideal model delta sigma weight residual False -2.73 -2.40 -0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" C3' DC I 144 " pdb=" C4' DC I 144 " pdb=" O3' DC I 144 " pdb=" C2' DC I 144 " both_signs ideal model delta sigma weight residual False -2.73 -2.42 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" C3' DC I 74 " pdb=" C4' DC I 74 " pdb=" O3' DC I 74 " pdb=" C2' DC I 74 " both_signs ideal model delta sigma weight residual False -2.73 -2.46 -0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 2166 not shown) Planarity restraints: 1342 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC I 154 " 0.027 2.00e-02 2.50e+03 1.72e-02 6.63e+00 pdb=" N1 DC I 154 " -0.043 2.00e-02 2.50e+03 pdb=" C2 DC I 154 " 0.002 2.00e-02 2.50e+03 pdb=" O2 DC I 154 " -0.000 2.00e-02 2.50e+03 pdb=" N3 DC I 154 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 154 " 0.007 2.00e-02 2.50e+03 pdb=" N4 DC I 154 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DC I 154 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DC I 154 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 130 " 0.030 2.00e-02 2.50e+03 1.36e-02 5.12e+00 pdb=" N9 DA I 130 " -0.031 2.00e-02 2.50e+03 pdb=" C8 DA I 130 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DA I 130 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA I 130 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DA I 130 " 0.007 2.00e-02 2.50e+03 pdb=" N6 DA I 130 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DA I 130 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DA I 130 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DA I 130 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DA I 130 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 48 " 0.026 2.00e-02 2.50e+03 1.10e-02 3.65e+00 pdb=" N9 DG I 48 " -0.026 2.00e-02 2.50e+03 pdb=" C8 DG I 48 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DG I 48 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG I 48 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DG I 48 " 0.005 2.00e-02 2.50e+03 pdb=" O6 DG I 48 " 0.005 2.00e-02 2.50e+03 pdb=" N1 DG I 48 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 48 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 48 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DG I 48 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DG I 48 " -0.002 2.00e-02 2.50e+03 ... (remaining 1339 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 3039 2.85 - 3.37: 10466 3.37 - 3.88: 24657 3.88 - 4.39: 27772 4.39 - 4.90: 37471 Nonbonded interactions: 103405 Sorted by model distance: nonbonded pdb=" OH TYR D 37 " pdb=" OP1 DG J 121 " model vdw 2.343 3.040 nonbonded pdb=" O2 DC I 8 " pdb=" N2 DG J 148 " model vdw 2.346 2.496 nonbonded pdb=" OE2 GLU G 61 " pdb=" NE2 GLN L 744 " model vdw 2.373 3.120 nonbonded pdb=" OE1 GLU D 68 " pdb=" NZ LYS F 91 " model vdw 2.410 3.120 nonbonded pdb=" O ARG A 69 " pdb=" ND2 ASN B 25 " model vdw 2.413 3.120 ... (remaining 103400 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' selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = (chain 'B' and resid 24 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 14 through 111) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 7.440 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: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.290 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 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 : 0.009 0.057 13153 Z= 0.624 Angle : 1.146 10.890 19088 Z= 0.883 Chirality : 0.063 0.329 2169 Planarity : 0.003 0.023 1342 Dihedral : 27.231 174.166 5690 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.16 % Allowed : 0.16 % Favored : 99.68 % 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: -2.48 (0.25), residues: 729 helix: -1.46 (0.17), residues: 524 sheet: None (None), residues: 0 loop : -1.65 (0.38), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 72 TYR 0.022 0.002 TYR G 57 PHE 0.023 0.003 PHE C 25 HIS 0.006 0.002 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00861 / 0.62 (13153) covalent geometry : angle 1.14646 / 0.88 (19088) hydrogen bonds : bond 0.15780 / 10.30 ( 771) hydrogen bonds : angle 5.37817 / 3.86 ( 1904) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.304 Fit side-chains REVERT: C 33 LEU cc_start: 0.7198 (mt) cc_final: 0.6962 (mp) REVERT: C 107 VAL cc_start: 0.7844 (m) cc_final: 0.7611 (p) REVERT: D 34 TYR cc_start: 0.7960 (m-80) cc_final: 0.7692 (m-10) REVERT: E 59 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7315 (mt-10) REVERT: H 59 MET cc_start: 0.8024 (mmm) cc_final: 0.7744 (mmp) outliers start: 1 outliers final: 1 residues processed: 77 average time/residue: 0.1367 time to fit residues: 14.3253 Evaluate side-chains 69 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.1980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.1980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 31 HIS D 81 ASN E 68 GLN F 25 ASN G 31 HIS H 81 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.164391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.133857 restraints weight = 18706.448| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.47 r_work: 0.3468 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13153 Z= 0.196 Angle : 0.693 8.441 19088 Z= 0.399 Chirality : 0.046 0.255 2169 Planarity : 0.005 0.042 1342 Dihedral : 31.407 169.446 4212 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.65 % Allowed : 3.06 % Favored : 96.29 % 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: 0.09 (0.29), residues: 729 helix: 0.52 (0.21), residues: 541 sheet: None (None), residues: 0 loop : -1.03 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 35 TYR 0.020 0.002 TYR G 57 PHE 0.020 0.003 PHE G 25 HIS 0.010 0.002 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.20 (13153) covalent geometry : angle 0.69259 / 0.40 (19088) hydrogen bonds : bond 0.05934 / 3.99 ( 771) hydrogen bonds : angle 3.21942 / 2.34 ( 1904) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.246 Fit side-chains REVERT: A 83 ARG cc_start: 0.8070 (mtp85) cc_final: 0.7557 (mtp85) REVERT: A 90 MET cc_start: 0.8102 (mmm) cc_final: 0.7886 (tpp) REVERT: D 34 TYR cc_start: 0.8576 (m-80) cc_final: 0.8169 (m-80) REVERT: D 98 LEU cc_start: 0.7952 (tp) cc_final: 0.7710 (tp) REVERT: E 112 ILE cc_start: 0.8963 (mm) cc_final: 0.8757 (mt) outliers start: 4 outliers final: 3 residues processed: 90 average time/residue: 0.2256 time to fit residues: 24.3285 Evaluate side-chains 84 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain F residue 26 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 37 optimal weight: 0.7980 chunk 19 optimal weight: 0.1980 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 0.3980 chunk 24 optimal weight: 0.9980 chunk 2 optimal weight: 0.2980 chunk 62 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.159427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.127876 restraints weight = 18509.970| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.48 r_work: 0.3387 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13153 Z= 0.174 Angle : 0.627 7.642 19088 Z= 0.375 Chirality : 0.044 0.237 2169 Planarity : 0.005 0.054 1342 Dihedral : 31.338 173.240 4212 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.65 % Allowed : 4.35 % Favored : 95.00 % 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: 1.10 (0.29), residues: 729 helix: 1.40 (0.21), residues: 534 sheet: None (None), residues: 0 loop : -1.10 (0.40), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 72 TYR 0.015 0.002 TYR F 72 PHE 0.023 0.003 PHE A 84 HIS 0.004 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.17 (13153) covalent geometry : angle 0.62657 / 0.38 (19088) hydrogen bonds : bond 0.05913 / 3.96 ( 771) hydrogen bonds : angle 2.84593 / 2.05 ( 1904) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.299 Fit side-chains REVERT: C 88 ARG cc_start: 0.8717 (mpt180) cc_final: 0.8449 (mmt-90) REVERT: E 60 LEU cc_start: 0.8313 (mt) cc_final: 0.7991 (mt) REVERT: F 84 MET cc_start: 0.8180 (mmm) cc_final: 0.7855 (mmm) outliers start: 4 outliers final: 3 residues processed: 73 average time/residue: 0.2193 time to fit residues: 19.7073 Evaluate side-chains 67 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 47 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 1 optimal weight: 0.2980 chunk 51 optimal weight: 0.6980 chunk 11 optimal weight: 0.1980 chunk 36 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 16 optimal weight: 0.0770 chunk 80 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS D 81 ASN E 68 GLN H 106 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.153539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.121218 restraints weight = 18319.696| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.44 r_work: 0.3362 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13153 Z= 0.168 Angle : 0.620 8.174 19088 Z= 0.361 Chirality : 0.043 0.231 2169 Planarity : 0.004 0.047 1342 Dihedral : 31.424 167.738 4210 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.45 % Allowed : 4.03 % Favored : 94.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.30), residues: 729 helix: 2.01 (0.21), residues: 535 sheet: None (None), residues: 0 loop : -1.07 (0.40), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 72 TYR 0.010 0.001 TYR G 57 PHE 0.012 0.001 PHE C 25 HIS 0.006 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.17 (13153) covalent geometry : angle 0.61954 / 0.36 (19088) hydrogen bonds : bond 0.05199 / 3.49 ( 771) hydrogen bonds : angle 2.60586 / 1.89 ( 1904) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.302 Fit side-chains REVERT: D 98 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7992 (mp) REVERT: F 84 MET cc_start: 0.8189 (mmm) cc_final: 0.7943 (mmm) REVERT: H 56 MET cc_start: 0.8211 (tpp) cc_final: 0.7965 (tpp) outliers start: 9 outliers final: 2 residues processed: 81 average time/residue: 0.2772 time to fit residues: 26.6936 Evaluate side-chains 75 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 112 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 60 optimal weight: 0.0980 chunk 43 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 44 optimal weight: 0.2980 chunk 2 optimal weight: 0.2980 chunk 21 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.152456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.120604 restraints weight = 18381.881| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.34 r_work: 0.3356 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13153 Z= 0.154 Angle : 0.596 7.859 19088 Z= 0.353 Chirality : 0.043 0.238 2169 Planarity : 0.004 0.053 1342 Dihedral : 31.337 168.838 4210 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.13 % Allowed : 5.00 % Favored : 93.87 % 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: 2.19 (0.30), residues: 729 helix: 2.25 (0.21), residues: 537 sheet: None (None), residues: 0 loop : -0.93 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 72 TYR 0.008 0.001 TYR D 37 PHE 0.010 0.001 PHE C 25 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.15 (13153) covalent geometry : angle 0.59646 / 0.35 (19088) hydrogen bonds : bond 0.05011 / 3.38 ( 771) hydrogen bonds : angle 2.53446 / 1.84 ( 1904) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.252 Fit side-chains REVERT: C 33 LEU cc_start: 0.8499 (mt) cc_final: 0.8221 (mp) REVERT: D 59 MET cc_start: 0.8404 (mmm) cc_final: 0.7884 (mmm) REVERT: D 98 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8063 (mp) REVERT: E 131 ARG cc_start: 0.8484 (mtt180) cc_final: 0.8231 (mtt180) outliers start: 7 outliers final: 5 residues processed: 69 average time/residue: 0.2432 time to fit residues: 20.2397 Evaluate side-chains 69 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 129 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 59 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 83 optimal weight: 50.0000 chunk 28 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 98 optimal weight: 30.0000 chunk 19 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 81 ASN E 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.147484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.115579 restraints weight = 18251.042| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.33 r_work: 0.3283 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13153 Z= 0.213 Angle : 0.687 13.840 19088 Z= 0.385 Chirality : 0.046 0.246 2169 Planarity : 0.005 0.050 1342 Dihedral : 31.601 164.906 4210 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.65 % Allowed : 5.48 % Favored : 93.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.30), residues: 729 helix: 2.12 (0.21), residues: 537 sheet: None (None), residues: 0 loop : -1.05 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 35 TYR 0.020 0.002 TYR H 80 PHE 0.015 0.002 PHE A 84 HIS 0.008 0.002 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.21 (13153) covalent geometry : angle 0.68691 / 0.39 (19088) hydrogen bonds : bond 0.05864 / 3.97 ( 771) hydrogen bonds : angle 2.71942 / 1.98 ( 1904) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.298 Fit side-chains REVERT: A 90 MET cc_start: 0.8056 (mmm) cc_final: 0.7740 (mmm) REVERT: C 33 LEU cc_start: 0.8531 (mt) cc_final: 0.8229 (mp) REVERT: D 59 MET cc_start: 0.8283 (mmm) cc_final: 0.7875 (mmm) REVERT: E 48 LEU cc_start: 0.8544 (mt) cc_final: 0.8306 (mp) REVERT: E 60 LEU cc_start: 0.8170 (mm) cc_final: 0.7932 (mt) REVERT: E 131 ARG cc_start: 0.8521 (mtt180) cc_final: 0.8223 (mtt180) outliers start: 4 outliers final: 2 residues processed: 69 average time/residue: 0.2662 time to fit residues: 21.9097 Evaluate side-chains 66 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 117 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 45 optimal weight: 0.7980 chunk 56 optimal weight: 0.0470 chunk 31 optimal weight: 0.4980 chunk 13 optimal weight: 0.1980 chunk 92 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 28 optimal weight: 0.1980 chunk 86 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 overall best weight: 0.3478 ------------------------------------------------------------------------------- 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 = 0.3890 r_free = 0.3890 target = 0.149902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.117525 restraints weight = 18043.051| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.46 r_work: 0.3292 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13153 Z= 0.147 Angle : 0.601 7.802 19088 Z= 0.354 Chirality : 0.042 0.253 2169 Planarity : 0.004 0.051 1342 Dihedral : 31.431 163.927 4210 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.81 % Allowed : 5.48 % Favored : 93.71 % 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: 2.37 (0.30), residues: 729 helix: 2.40 (0.21), residues: 541 sheet: None (None), residues: 0 loop : -0.99 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 128 TYR 0.010 0.001 TYR D 37 PHE 0.007 0.001 PHE A 84 HIS 0.002 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.15 (13153) covalent geometry : angle 0.60053 / 0.35 (19088) hydrogen bonds : bond 0.04919 / 3.31 ( 771) hydrogen bonds : angle 2.49216 / 1.80 ( 1904) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.330 Fit side-chains REVERT: C 33 LEU cc_start: 0.8502 (mt) cc_final: 0.8176 (mp) REVERT: D 59 MET cc_start: 0.8246 (mmm) cc_final: 0.7748 (mmm) REVERT: E 48 LEU cc_start: 0.8494 (mt) cc_final: 0.8257 (mp) REVERT: E 60 LEU cc_start: 0.8180 (mm) cc_final: 0.7900 (mt) REVERT: E 131 ARG cc_start: 0.8490 (mtt180) cc_final: 0.8138 (mtt180) REVERT: F 91 LYS cc_start: 0.8790 (tttt) cc_final: 0.8525 (ttmt) REVERT: F 100 PHE cc_start: 0.8688 (m-80) cc_final: 0.8483 (m-80) outliers start: 5 outliers final: 2 residues processed: 70 average time/residue: 0.2519 time to fit residues: 20.7736 Evaluate side-chains 66 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 117 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 52 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 41 optimal weight: 0.3980 chunk 11 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 chunk 89 optimal weight: 2.9990 chunk 48 optimal weight: 0.3980 chunk 87 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 31 HIS ** 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 = 0.3869 r_free = 0.3869 target = 0.148051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.114876 restraints weight = 17824.676| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.41 r_work: 0.3259 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13153 Z= 0.183 Angle : 0.628 7.595 19088 Z= 0.363 Chirality : 0.044 0.261 2169 Planarity : 0.004 0.053 1342 Dihedral : 31.495 161.033 4210 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.65 % Allowed : 6.13 % Favored : 93.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.30), residues: 729 helix: 2.44 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -1.04 (0.39), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 35 TYR 0.008 0.001 TYR G 57 PHE 0.010 0.001 PHE G 25 HIS 0.005 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.18 (13153) covalent geometry : angle 0.62848 / 0.36 (19088) hydrogen bonds : bond 0.05253 / 3.54 ( 771) hydrogen bonds : angle 2.56004 / 1.85 ( 1904) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.263 Fit side-chains REVERT: C 33 LEU cc_start: 0.8482 (mt) cc_final: 0.8153 (mp) REVERT: D 59 MET cc_start: 0.8242 (mmm) cc_final: 0.7799 (mmm) REVERT: E 48 LEU cc_start: 0.8505 (mt) cc_final: 0.8259 (mp) REVERT: E 60 LEU cc_start: 0.8208 (mm) cc_final: 0.7922 (mt) REVERT: E 131 ARG cc_start: 0.8489 (mtt180) cc_final: 0.8151 (mtt180) REVERT: G 35 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7822 (mpp80) REVERT: H 56 MET cc_start: 0.8260 (tpp) cc_final: 0.7923 (tpp) outliers start: 4 outliers final: 2 residues processed: 66 average time/residue: 0.2441 time to fit residues: 19.2438 Evaluate side-chains 67 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain G residue 35 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 37 optimal weight: 0.0060 chunk 73 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 46 optimal weight: 0.3980 chunk 57 optimal weight: 0.0040 chunk 97 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 62 optimal weight: 0.2980 chunk 31 optimal weight: 0.6980 chunk 84 optimal weight: 6.9990 chunk 18 optimal weight: 0.2980 overall best weight: 0.2008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 31 HIS ** 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 = 0.3895 r_free = 0.3895 target = 0.150280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.117951 restraints weight = 18083.525| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.46 r_work: 0.3301 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.4899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13153 Z= 0.131 Angle : 0.578 7.664 19088 Z= 0.344 Chirality : 0.041 0.268 2169 Planarity : 0.004 0.052 1342 Dihedral : 31.360 157.190 4210 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.76 (0.30), residues: 729 helix: 2.73 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -0.98 (0.40), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 35 TYR 0.009 0.001 TYR D 37 PHE 0.007 0.001 PHE E 67 HIS 0.002 0.000 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.13 (13153) covalent geometry : angle 0.57818 / 0.34 (19088) hydrogen bonds : bond 0.04638 / 3.13 ( 771) hydrogen bonds : angle 2.37774 / 1.71 ( 1904) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: C 33 LEU cc_start: 0.8480 (mt) cc_final: 0.8147 (mp) REVERT: D 59 MET cc_start: 0.8243 (mmm) cc_final: 0.7797 (mmm) REVERT: E 48 LEU cc_start: 0.8491 (mt) cc_final: 0.8246 (mp) REVERT: E 60 LEU cc_start: 0.8171 (mm) cc_final: 0.7876 (mt) REVERT: E 131 ARG cc_start: 0.8497 (mtt180) cc_final: 0.8131 (mtt180) REVERT: F 84 MET cc_start: 0.8200 (tpp) cc_final: 0.7932 (mmm) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.2636 time to fit residues: 21.8764 Evaluate side-chains 69 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 47 optimal weight: 0.5980 chunk 82 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 26 optimal weight: 0.3980 chunk 67 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.146331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.113216 restraints weight = 17916.391| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.44 r_work: 0.3246 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.5121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13153 Z= 0.202 Angle : 0.638 7.536 19088 Z= 0.365 Chirality : 0.045 0.272 2169 Planarity : 0.004 0.053 1342 Dihedral : 31.516 155.583 4210 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.16 % Allowed : 7.10 % Favored : 92.74 % 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: 2.38 (0.30), residues: 729 helix: 2.44 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -1.07 (0.40), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 35 TYR 0.010 0.001 TYR D 118 PHE 0.010 0.002 PHE G 25 HIS 0.006 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.20 (13153) covalent geometry : angle 0.63816 / 0.37 (19088) hydrogen bonds : bond 0.05319 / 3.58 ( 771) hydrogen bonds : angle 2.56878 / 1.85 ( 1904) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.293 Fit side-chains REVERT: C 33 LEU cc_start: 0.8503 (mt) cc_final: 0.8198 (mp) REVERT: D 59 MET cc_start: 0.8254 (mmm) cc_final: 0.7818 (mmm) REVERT: E 48 LEU cc_start: 0.8579 (mt) cc_final: 0.8335 (mp) REVERT: E 60 LEU cc_start: 0.8223 (mm) cc_final: 0.7931 (mt) REVERT: E 131 ARG cc_start: 0.8462 (mtt180) cc_final: 0.8115 (mtt180) REVERT: F 84 MET cc_start: 0.8247 (tpp) cc_final: 0.7972 (mmm) outliers start: 1 outliers final: 0 residues processed: 66 average time/residue: 0.2954 time to fit residues: 23.1511 Evaluate side-chains 65 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 36 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 68 optimal weight: 20.0000 chunk 90 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 39 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.144855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.113000 restraints weight = 17872.620| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.31 r_work: 0.3246 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.5344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13153 Z= 0.198 Angle : 0.638 7.410 19088 Z= 0.366 Chirality : 0.045 0.238 2169 Planarity : 0.004 0.053 1342 Dihedral : 31.576 155.846 4210 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.32 % Allowed : 6.61 % Favored : 93.06 % 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: 2.33 (0.30), residues: 729 helix: 2.37 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -0.95 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 20 TYR 0.009 0.001 TYR A 99 PHE 0.009 0.001 PHE F 100 HIS 0.003 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.20 (13153) covalent geometry : angle 0.63819 / 0.37 (19088) hydrogen bonds : bond 0.05207 / 3.51 ( 771) hydrogen bonds : angle 2.54776 / 1.84 ( 1904) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3368.02 seconds wall clock time: 58 minutes 5.91 seconds (3485.91 seconds total)