Starting phenix.real_space_refine on Fri Jul 3 06:02:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e0r_47367/07_2026/9e0r_47367.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e0r_47367/07_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_47367/07_2026/9e0r_47367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e0r_47367/07_2026/9e0r_47367.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e0r_47367/07_2026/9e0r_47367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e0r_47367/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.80, per 1000 atoms: 0.23 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: 0.93 Conformation dependent library (CDL) restraints added in 323.6 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: 1.68 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: 2.23 Time building geometry restraints manager: 1.30 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=" N MET E 120 " pdb=" CA MET E 120 " ideal model delta sigma weight residual 1.453 1.481 -0.027 9.20e-03 1.18e+04 8.74e+00 ... (remaining 13148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 17572 2.18 - 4.36: 1489 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: 9.330 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: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 12.880 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.990 ------------------------------------------------------------------------------- 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= 0.620 Angle : 1.142 10.890 19088 Z= 0.881 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 1.14208 / 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 : 0.301 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: 0.1439 time to fit residues: 15.1491 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 : 0.334 ------------------------------------------------------------------------------- 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: 4.9990 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 = 0.164345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.133926 restraints weight = 18701.906| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.45 r_work: 0.3474 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13153 Z= 0.200 Angle : 0.675 8.344 19088 Z= 0.395 Chirality : 0.046 0.253 2169 Planarity : 0.005 0.045 1342 Dihedral : 31.480 168.882 4212 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.90 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: 0.03 (0.28), residues: 729 helix: 0.47 (0.20), residues: 541 sheet: None (None), residues: 0 loop : -1.05 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 35 TYR 0.019 0.002 TYR G 57 PHE 0.017 0.003 PHE G 25 HIS 0.010 0.002 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.20 (13153) covalent geometry : angle 0.67459 / 0.39 (19088) hydrogen bonds : bond 0.06009 / 4.04 ( 771) hydrogen bonds : angle 3.22617 / 2.35 ( 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 86 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.304 Fit side-chains REVERT: A 83 ARG cc_start: 0.8056 (mtp85) cc_final: 0.7547 (mtp85) REVERT: A 90 MET cc_start: 0.8084 (mmm) cc_final: 0.7857 (tpp) REVERT: D 34 TYR cc_start: 0.8574 (m-80) cc_final: 0.8146 (m-80) REVERT: D 98 LEU cc_start: 0.7972 (tp) cc_final: 0.7731 (tp) REVERT: E 112 ILE cc_start: 0.8979 (mm) cc_final: 0.8768 (mt) outliers start: 4 outliers final: 3 residues processed: 85 average time/residue: 0.2298 time to fit residues: 23.7423 Evaluate side-chains 80 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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: 0.6980 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 2 optimal weight: 0.0570 chunk 62 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.157265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.125721 restraints weight = 18447.808| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.48 r_work: 0.3352 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3203 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= 0.188 Angle : 0.651 7.622 19088 Z= 0.387 Chirality : 0.045 0.224 2169 Planarity : 0.006 0.060 1342 Dihedral : 31.501 173.019 4212 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.81 % Allowed : 4.19 % 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: 1.01 (0.29), residues: 729 helix: 1.35 (0.21), residues: 535 sheet: None (None), residues: 0 loop : -1.21 (0.40), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 72 TYR 0.013 0.002 TYR F 72 PHE 0.022 0.003 PHE C 25 HIS 0.007 0.002 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.19 (13153) covalent geometry : angle 0.65067 / 0.39 (19088) hydrogen bonds : bond 0.06491 / 4.33 ( 771) hydrogen bonds : angle 2.88675 / 2.09 ( 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 68 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.287 Fit side-chains REVERT: C 88 ARG cc_start: 0.8726 (mpt180) cc_final: 0.8485 (mmt-90) REVERT: E 60 LEU cc_start: 0.8352 (mt) cc_final: 0.8017 (mt) REVERT: F 84 MET cc_start: 0.8179 (mmm) cc_final: 0.7936 (mmm) outliers start: 5 outliers final: 2 residues processed: 67 average time/residue: 0.2383 time to fit residues: 19.4653 Evaluate side-chains 62 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU 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: 0.7980 chunk 44 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 53 optimal weight: 0.2980 chunk 85 optimal weight: 4.9990 chunk 16 optimal weight: 0.0980 chunk 80 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 75 HIS D 81 ASN E 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.151036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.118844 restraints weight = 18220.990| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.36 r_work: 0.3330 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13153 Z= 0.188 Angle : 0.623 8.068 19088 Z= 0.365 Chirality : 0.044 0.227 2169 Planarity : 0.005 0.049 1342 Dihedral : 31.625 166.082 4210 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.81 % Allowed : 4.35 % Favored : 94.84 % 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: 1.71 (0.30), residues: 729 helix: 1.89 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -1.10 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 29 TYR 0.010 0.001 TYR G 57 PHE 0.013 0.001 PHE C 25 HIS 0.007 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.19 (13153) covalent geometry : angle 0.62341 / 0.37 (19088) hydrogen bonds : bond 0.05514 / 3.70 ( 771) hydrogen bonds : angle 2.65801 / 1.93 ( 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 80 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.286 Fit side-chains REVERT: A 72 ARG cc_start: 0.8247 (mtt-85) cc_final: 0.8020 (mtt90) REVERT: A 131 ARG cc_start: 0.8655 (mtt180) cc_final: 0.8409 (mtt180) REVERT: E 72 ARG cc_start: 0.8557 (mtt90) cc_final: 0.8139 (mtt90) REVERT: F 84 MET cc_start: 0.8129 (mmm) cc_final: 0.7881 (mmm) outliers start: 5 outliers final: 1 residues processed: 79 average time/residue: 0.3082 time to fit residues: 28.4931 Evaluate side-chains 75 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 60 optimal weight: 0.4980 chunk 43 optimal weight: 0.1980 chunk 95 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 44 optimal weight: 0.3980 chunk 2 optimal weight: 0.0050 chunk 21 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.151069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.119033 restraints weight = 18320.200| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.35 r_work: 0.3332 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13153 Z= 0.152 Angle : 0.582 7.732 19088 Z= 0.349 Chirality : 0.042 0.223 2169 Planarity : 0.004 0.053 1342 Dihedral : 31.487 166.922 4210 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.65 % Allowed : 4.84 % 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: 2.15 (0.30), residues: 729 helix: 2.24 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -1.03 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 35 TYR 0.007 0.001 TYR D 37 PHE 0.009 0.001 PHE C 25 HIS 0.003 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.15 (13153) covalent geometry : angle 0.58179 / 0.35 (19088) hydrogen bonds : bond 0.04987 / 3.36 ( 771) hydrogen bonds : angle 2.54453 / 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 77 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.435 Fit side-chains REVERT: A 131 ARG cc_start: 0.8661 (mtt180) cc_final: 0.8404 (mtt180) REVERT: E 60 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7993 (mt) REVERT: E 72 ARG cc_start: 0.8572 (mtt90) cc_final: 0.8077 (mtt90) REVERT: F 84 MET cc_start: 0.8105 (mmm) cc_final: 0.7883 (mmm) outliers start: 4 outliers final: 2 residues processed: 75 average time/residue: 0.2993 time to fit residues: 26.3086 Evaluate side-chains 73 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain E residue 60 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 59 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 83 optimal weight: 50.0000 chunk 28 optimal weight: 0.2980 chunk 52 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 19 optimal weight: 0.0070 overall best weight: 0.4798 ------------------------------------------------------------------------------- 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 = 0.3873 r_free = 0.3873 target = 0.148734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.116720 restraints weight = 18238.493| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.34 r_work: 0.3300 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13153 Z= 0.176 Angle : 0.609 7.686 19088 Z= 0.358 Chirality : 0.042 0.231 2169 Planarity : 0.005 0.057 1342 Dihedral : 31.566 162.629 4210 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.48 % Allowed : 5.48 % Favored : 94.03 % 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: 2.25 (0.30), residues: 729 helix: 2.32 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -1.03 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 99 TYR 0.008 0.001 TYR A 99 PHE 0.013 0.002 PHE A 84 HIS 0.006 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.18 (13153) covalent geometry : angle 0.60891 / 0.36 (19088) hydrogen bonds : bond 0.05258 / 3.55 ( 771) hydrogen bonds : angle 2.56116 / 1.86 ( 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 71 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.307 Fit side-chains REVERT: B 84 MET cc_start: 0.8319 (mmm) cc_final: 0.8116 (mmm) REVERT: D 59 MET cc_start: 0.8324 (mmm) cc_final: 0.7864 (mmm) REVERT: E 48 LEU cc_start: 0.8600 (mt) cc_final: 0.8343 (mp) REVERT: F 84 MET cc_start: 0.8131 (mmm) cc_final: 0.7850 (mmm) outliers start: 3 outliers final: 1 residues processed: 70 average time/residue: 0.2410 time to fit residues: 20.1293 Evaluate side-chains 68 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 45 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 chunk 77 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3842 r_free = 0.3842 target = 0.146285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.114506 restraints weight = 18032.526| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.37 r_work: 0.3261 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13153 Z= 0.203 Angle : 0.633 7.444 19088 Z= 0.368 Chirality : 0.044 0.248 2169 Planarity : 0.005 0.080 1342 Dihedral : 31.605 158.854 4210 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.16 % Allowed : 5.81 % Favored : 94.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.30), residues: 729 helix: 2.28 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -0.95 (0.40), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 32 TYR 0.009 0.001 TYR G 57 PHE 0.013 0.002 PHE A 84 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.20 (13153) covalent geometry : angle 0.63270 / 0.37 (19088) hydrogen bonds : bond 0.05399 / 3.62 ( 771) hydrogen bonds : angle 2.60149 / 1.88 ( 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 70 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 0.308 Fit side-chains REVERT: A 90 MET cc_start: 0.8043 (mmm) cc_final: 0.7699 (mmm) REVERT: D 59 MET cc_start: 0.8269 (mmm) cc_final: 0.7837 (mmm) REVERT: E 48 LEU cc_start: 0.8587 (mt) cc_final: 0.8356 (mp) REVERT: E 49 ARG cc_start: 0.8658 (ttm-80) cc_final: 0.8410 (ttp-110) REVERT: F 84 MET cc_start: 0.8150 (mmm) cc_final: 0.7939 (mmm) outliers start: 1 outliers final: 1 residues processed: 70 average time/residue: 0.2435 time to fit residues: 20.6599 Evaluate side-chains 68 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 52 optimal weight: 0.0970 chunk 80 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 48 optimal weight: 0.3980 chunk 87 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.3844 r_free = 0.3844 target = 0.146308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.113189 restraints weight = 17849.806| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.46 r_work: 0.3244 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.5037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13153 Z= 0.187 Angle : 0.610 7.495 19088 Z= 0.358 Chirality : 0.043 0.249 2169 Planarity : 0.004 0.054 1342 Dihedral : 31.626 156.392 4210 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.32 % Allowed : 5.65 % Favored : 94.03 % 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: 2.42 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -0.96 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 35 TYR 0.008 0.001 TYR A 99 PHE 0.008 0.001 PHE C 25 HIS 0.003 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.19 (13153) covalent geometry : angle 0.61022 / 0.36 (19088) hydrogen bonds : bond 0.05188 / 3.48 ( 771) hydrogen bonds : angle 2.54214 / 1.84 ( 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 67 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 0.186 Fit side-chains REVERT: A 90 MET cc_start: 0.8101 (mmm) cc_final: 0.7764 (mmm) REVERT: E 48 LEU cc_start: 0.8597 (mt) cc_final: 0.8343 (mp) REVERT: E 60 LEU cc_start: 0.8257 (mm) cc_final: 0.7962 (mt) REVERT: F 84 MET cc_start: 0.8155 (mmm) cc_final: 0.7893 (mmm) REVERT: H 56 MET cc_start: 0.8294 (tpp) cc_final: 0.7922 (tpp) outliers start: 2 outliers final: 2 residues processed: 66 average time/residue: 0.2633 time to fit residues: 20.5755 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 : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain E residue 129 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 37 optimal weight: 0.0870 chunk 73 optimal weight: 3.9990 chunk 43 optimal weight: 0.0770 chunk 46 optimal weight: 0.0980 chunk 57 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 30 optimal weight: 0.3980 chunk 62 optimal weight: 0.0980 chunk 31 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.1516 ------------------------------------------------------------------------------- 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 = 0.3896 r_free = 0.3896 target = 0.150260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.117396 restraints weight = 17840.527| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.42 r_work: 0.3299 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 13153 Z= 0.128 Angle : 0.561 7.450 19088 Z= 0.340 Chirality : 0.040 0.226 2169 Planarity : 0.004 0.053 1342 Dihedral : 31.429 155.412 4210 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.16 % Allowed : 6.29 % Favored : 93.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.75 (0.31), residues: 729 helix: 2.69 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.94 (0.41), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 35 TYR 0.010 0.001 TYR D 37 PHE 0.008 0.001 PHE E 67 HIS 0.002 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00190 / 0.13 (13153) covalent geometry : angle 0.56146 / 0.34 (19088) hydrogen bonds : bond 0.04556 / 3.06 ( 771) hydrogen bonds : angle 2.36312 / 1.70 ( 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 78 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 77 time to evaluate : 0.323 Fit side-chains REVERT: A 96 SER cc_start: 0.8441 (OUTLIER) cc_final: 0.8070 (m) REVERT: D 59 MET cc_start: 0.8239 (mmm) cc_final: 0.7776 (mmm) REVERT: E 48 LEU cc_start: 0.8513 (mt) cc_final: 0.8267 (mp) REVERT: F 84 MET cc_start: 0.8041 (mmm) cc_final: 0.7818 (mmm) outliers start: 1 outliers final: 0 residues processed: 78 average time/residue: 0.2748 time to fit residues: 25.0825 Evaluate side-chains 76 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 47 optimal weight: 0.4980 chunk 82 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 34 optimal weight: 0.1980 chunk 87 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3847 r_free = 0.3847 target = 0.146488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.113462 restraints weight = 17924.251| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.47 r_work: 0.3254 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13153 Z= 0.182 Angle : 0.602 7.370 19088 Z= 0.353 Chirality : 0.042 0.222 2169 Planarity : 0.004 0.054 1342 Dihedral : 31.567 157.054 4210 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.32 % Allowed : 6.45 % 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: 2.54 (0.30), residues: 729 helix: 2.53 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -0.89 (0.41), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 72 TYR 0.008 0.001 TYR A 99 PHE 0.008 0.001 PHE G 25 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.18 (13153) covalent geometry : angle 0.60157 / 0.35 (19088) hydrogen bonds : bond 0.05096 / 3.43 ( 771) hydrogen bonds : angle 2.50729 / 1.81 ( 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 69 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.311 Fit side-chains REVERT: A 96 SER cc_start: 0.8495 (OUTLIER) cc_final: 0.8185 (m) REVERT: D 59 MET cc_start: 0.8257 (mmm) cc_final: 0.7809 (mmm) REVERT: E 48 LEU cc_start: 0.8563 (mt) cc_final: 0.8318 (mp) REVERT: E 60 LEU cc_start: 0.8239 (mm) cc_final: 0.7936 (mt) REVERT: F 84 MET cc_start: 0.8157 (mmm) cc_final: 0.7882 (mmm) outliers start: 2 outliers final: 1 residues processed: 68 average time/residue: 0.2863 time to fit residues: 23.1455 Evaluate side-chains 69 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain E residue 129 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 36 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 68 optimal weight: 20.0000 chunk 90 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 39 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 4 optimal weight: 0.0470 chunk 42 optimal weight: 0.6980 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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 = 0.3823 r_free = 0.3823 target = 0.144605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.112958 restraints weight = 17846.901| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.28 r_work: 0.3246 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.5502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13153 Z= 0.182 Angle : 0.613 7.275 19088 Z= 0.359 Chirality : 0.043 0.240 2169 Planarity : 0.004 0.052 1342 Dihedral : 31.671 158.232 4210 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.16 % Allowed : 6.77 % 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: 2.36 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -0.93 (0.41), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 35 TYR 0.009 0.001 TYR A 99 PHE 0.007 0.001 PHE E 67 HIS 0.003 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.18 (13153) covalent geometry : angle 0.61255 / 0.36 (19088) hydrogen bonds : bond 0.05112 / 3.43 ( 771) hydrogen bonds : angle 2.54067 / 1.84 ( 1904) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3437.92 seconds wall clock time: 59 minutes 20.31 seconds (3560.31 seconds total)