Starting phenix.real_space_refine on Wed Mar 4 09:21:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e0r_47367/03_2026/9e0r_47367.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e0r_47367/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9e0r_47367/03_2026/9e0r_47367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e0r_47367/03_2026/9e0r_47367.map" model { file = "/net/cci-nas-00/data/ceres_data/9e0r_47367/03_2026/9e0r_47367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e0r_47367/03_2026/9e0r_47367.cif" } 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-dev-5986/lib/python3.9/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: 2.21, per 1000 atoms: 0.18 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: 0.95 Conformation dependent library (CDL) restraints added in 271.8 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: 1.87 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: 1.82 Time building geometry restraints manager: 1.34 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=" 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 bond pdb=" N VAL H 108 " pdb=" CA VAL H 108 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.20e-02 6.94e+03 8.19e+00 ... (remaining 13148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 17567 2.18 - 4.36: 1495 4.36 - 6.53: 20 6.53 - 8.71: 5 8.71 - 10.89: 1 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=" 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=" O3' DG J 148 " pdb=" C3' DG J 148 " pdb=" C2' DG J 148 " ideal model delta sigma weight residual 111.50 104.20 7.30 1.50e+00 4.44e-01 2.37e+01 angle pdb=" O3' DG J 147 " pdb=" C3' DG J 147 " pdb=" C2' DG J 147 " ideal model delta sigma weight residual 111.50 104.64 6.86 1.50e+00 4.44e-01 2.09e+01 angle pdb=" O3' DC I 74 " pdb=" C3' DC I 74 " pdb=" C2' DC I 74 " ideal model delta sigma weight residual 111.50 118.32 -6.82 1.50e+00 4.44e-01 2.07e+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 - 0.052: 1358 0.052 - 0.103: 669 0.103 - 0.155: 111 0.155 - 0.207: 26 0.207 - 0.258: 5 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 -2.66 -2.40 -0.26 2.00e-01 2.50e+01 1.67e+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 -2.66 -2.42 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA ILE C 79 " pdb=" N ILE C 79 " pdb=" C ILE C 79 " pdb=" CB ILE C 79 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.22e+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: 7.370 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.840 Find NCS groups from input model: 0.180 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 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= 0.599 Angle : 1.147 10.890 19088 Z= 0.848 Chirality : 0.058 0.258 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 covalent geometry : bond 0.00877 (13153) covalent geometry : angle 1.14729 (19088) hydrogen bonds : bond 0.15780 ( 771) hydrogen bonds : angle 5.37817 ( 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 : 0.285 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: 0.1453 time to fit residues: 14.9576 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 : 0.223 ------------------------------------------------------------------------------- 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: 1.9990 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... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 31 HIS E 68 GLN F 25 ASN G 31 HIS H 81 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.156324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.124259 restraints weight = 18142.833| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.48 r_work: 0.3391 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13153 Z= 0.208 Angle : 0.606 6.366 19088 Z= 0.361 Chirality : 0.036 0.152 2169 Planarity : 0.005 0.044 1342 Dihedral : 30.980 176.217 4212 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.32 % Allowed : 2.74 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.28), residues: 729 helix: 0.62 (0.20), residues: 533 sheet: None (None), residues: 0 loop : -1.26 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 45 TYR 0.013 0.002 TYR F 72 PHE 0.023 0.002 PHE C 25 HIS 0.006 0.002 HIS H 106 Details of bonding type rmsd covalent geometry : bond 0.00458 (13153) covalent geometry : angle 0.60642 (19088) hydrogen bonds : bond 0.04982 ( 771) hydrogen bonds : angle 2.87479 ( 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 76 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.229 Fit side-chains REVERT: C 33 LEU cc_start: 0.8525 (mt) cc_final: 0.8284 (mp) REVERT: D 98 LEU cc_start: 0.8293 (tp) cc_final: 0.8074 (tp) REVERT: E 53 ARG cc_start: 0.8430 (ttt180) cc_final: 0.8197 (ttp80) REVERT: E 60 LEU cc_start: 0.8307 (mt) cc_final: 0.8004 (mt) REVERT: E 129 ARG cc_start: 0.7827 (ttm170) cc_final: 0.7622 (ttm170) REVERT: H 117 LYS cc_start: 0.8186 (tptm) cc_final: 0.7909 (tptm) outliers start: 2 outliers final: 2 residues processed: 76 average time/residue: 0.2704 time to fit residues: 24.3840 Evaluate side-chains 70 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain D residue 97 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 37 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 39 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS E 68 GLN H 81 ASN H 106 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.147613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.114870 restraints weight = 18220.835| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.47 r_work: 0.3245 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 13153 Z= 0.260 Angle : 0.602 5.124 19088 Z= 0.364 Chirality : 0.038 0.153 2169 Planarity : 0.004 0.052 1342 Dihedral : 31.229 171.612 4210 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.32 % Allowed : 4.19 % Favored : 95.48 % 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: 1.00 (0.29), residues: 729 helix: 1.34 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -1.24 (0.40), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 35 TYR 0.012 0.001 TYR D 118 PHE 0.012 0.002 PHE G 25 HIS 0.003 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00584 (13153) covalent geometry : angle 0.60234 (19088) hydrogen bonds : bond 0.05352 ( 771) hydrogen bonds : angle 2.73752 ( 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 77 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 75 time to evaluate : 0.293 Fit side-chains REVERT: C 33 LEU cc_start: 0.8591 (mt) cc_final: 0.8278 (mp) REVERT: C 42 ARG cc_start: 0.8819 (mtm180) cc_final: 0.8588 (mtp180) REVERT: D 59 MET cc_start: 0.8203 (mmm) cc_final: 0.7845 (mmm) REVERT: E 48 LEU cc_start: 0.8556 (mt) cc_final: 0.8321 (mp) REVERT: E 53 ARG cc_start: 0.8445 (ttt180) cc_final: 0.8199 (ttp80) REVERT: E 60 LEU cc_start: 0.8394 (mt) cc_final: 0.8180 (mt) REVERT: E 116 ARG cc_start: 0.8808 (mtm110) cc_final: 0.8515 (mtm-85) REVERT: F 84 MET cc_start: 0.8237 (mmm) cc_final: 0.7896 (mmm) REVERT: G 32 ARG cc_start: 0.8579 (tmm-80) cc_final: 0.8343 (ttp80) REVERT: G 99 ARG cc_start: 0.7897 (mtt90) cc_final: 0.7682 (mtt90) outliers start: 2 outliers final: 1 residues processed: 76 average time/residue: 0.3018 time to fit residues: 26.7771 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 : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 109 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 47 optimal weight: 0.1980 chunk 44 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 51 optimal weight: 0.4980 chunk 11 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 53 optimal weight: 0.2980 chunk 85 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN H 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.147532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.115538 restraints weight = 18050.542| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.43 r_work: 0.3259 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13153 Z= 0.211 Angle : 0.554 5.162 19088 Z= 0.340 Chirality : 0.035 0.160 2169 Planarity : 0.004 0.055 1342 Dihedral : 31.005 169.975 4210 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.65 % Allowed : 4.19 % Favored : 95.16 % 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: 1.74 (0.30), residues: 729 helix: 1.93 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -1.11 (0.40), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 35 TYR 0.007 0.001 TYR G 50 PHE 0.012 0.001 PHE E 67 HIS 0.006 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00469 (13153) covalent geometry : angle 0.55394 (19088) hydrogen bonds : bond 0.04396 ( 771) hydrogen bonds : angle 2.45906 ( 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 65 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.305 Fit side-chains REVERT: D 59 MET cc_start: 0.8255 (mmm) cc_final: 0.7828 (mmm) REVERT: E 48 LEU cc_start: 0.8574 (mt) cc_final: 0.8343 (mp) REVERT: E 129 ARG cc_start: 0.7889 (ttm170) cc_final: 0.7684 (ttm170) REVERT: F 84 MET cc_start: 0.8219 (mmm) cc_final: 0.7903 (mmm) REVERT: G 32 ARG cc_start: 0.8686 (tmm-80) cc_final: 0.8414 (ttp80) outliers start: 4 outliers final: 0 residues processed: 64 average time/residue: 0.3125 time to fit residues: 23.1753 Evaluate side-chains 59 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 2 optimal weight: 0.3980 chunk 21 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 ASN H 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.143544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.112116 restraints weight = 18006.217| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.34 r_work: 0.3218 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.5565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 13153 Z= 0.266 Angle : 0.592 5.246 19088 Z= 0.360 Chirality : 0.038 0.167 2169 Planarity : 0.005 0.054 1342 Dihedral : 31.234 167.609 4210 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.16 % Allowed : 5.16 % Favored : 94.68 % 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: 1.89 (0.30), residues: 729 helix: 2.02 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -1.02 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 35 TYR 0.010 0.001 TYR D 118 PHE 0.011 0.002 PHE G 25 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00600 (13153) covalent geometry : angle 0.59193 (19088) hydrogen bonds : bond 0.04885 ( 771) hydrogen bonds : angle 2.58672 ( 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 63 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.241 Fit side-chains REVERT: A 90 MET cc_start: 0.7947 (mmm) cc_final: 0.7707 (mmm) REVERT: E 48 LEU cc_start: 0.8569 (mt) cc_final: 0.8346 (mp) REVERT: E 60 LEU cc_start: 0.8270 (mm) cc_final: 0.7987 (mt) REVERT: E 129 ARG cc_start: 0.7786 (ttm170) cc_final: 0.7581 (ttm170) REVERT: E 131 ARG cc_start: 0.8436 (mtt180) cc_final: 0.8204 (mtt180) REVERT: F 84 MET cc_start: 0.8210 (mmm) cc_final: 0.7818 (mmm) REVERT: G 32 ARG cc_start: 0.8767 (tmm-80) cc_final: 0.8467 (ttp80) outliers start: 1 outliers final: 1 residues processed: 62 average time/residue: 0.2953 time to fit residues: 21.5136 Evaluate side-chains 61 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 109 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: 10.0000 chunk 28 optimal weight: 0.4980 chunk 52 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 8 optimal weight: 0.1980 chunk 81 optimal weight: 0.9990 chunk 98 optimal weight: 8.9990 chunk 19 optimal weight: 0.0970 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.145842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.114497 restraints weight = 18016.410| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.33 r_work: 0.3256 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.5680 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= 0.196 Angle : 0.546 5.149 19088 Z= 0.336 Chirality : 0.034 0.164 2169 Planarity : 0.004 0.055 1342 Dihedral : 31.044 165.052 4210 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 6.13 % 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: 2.30 (0.30), residues: 729 helix: 2.34 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -0.97 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 35 TYR 0.007 0.001 TYR G 50 PHE 0.011 0.001 PHE E 67 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00435 (13153) covalent geometry : angle 0.54587 (19088) hydrogen bonds : bond 0.04244 ( 771) hydrogen bonds : angle 2.40353 ( 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 61 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.306 Fit side-chains REVERT: E 48 LEU cc_start: 0.8556 (mt) cc_final: 0.8331 (mp) REVERT: E 60 LEU cc_start: 0.8290 (mm) cc_final: 0.8015 (mt) REVERT: E 131 ARG cc_start: 0.8418 (mtt180) cc_final: 0.8167 (mtt180) REVERT: F 84 MET cc_start: 0.8162 (mmm) cc_final: 0.7831 (mmm) REVERT: G 32 ARG cc_start: 0.8735 (tmm-80) cc_final: 0.8457 (ttp80) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.2821 time to fit residues: 20.2488 Evaluate side-chains 59 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 45 optimal weight: 0.0470 chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.144339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.113323 restraints weight = 17868.228| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.31 r_work: 0.3229 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.5886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13153 Z= 0.217 Angle : 0.562 10.264 19088 Z= 0.343 Chirality : 0.035 0.166 2169 Planarity : 0.004 0.054 1342 Dihedral : 31.120 160.134 4210 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % 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: 2.34 (0.30), residues: 729 helix: 2.38 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -0.97 (0.41), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 35 TYR 0.008 0.001 TYR D 118 PHE 0.009 0.001 PHE E 67 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00485 (13153) covalent geometry : angle 0.56242 (19088) hydrogen bonds : bond 0.04456 ( 771) hydrogen bonds : angle 2.45863 ( 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 61 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.217 Fit side-chains REVERT: A 96 SER cc_start: 0.8555 (OUTLIER) cc_final: 0.8067 (m) REVERT: E 48 LEU cc_start: 0.8563 (mt) cc_final: 0.8344 (mp) REVERT: E 60 LEU cc_start: 0.8285 (mm) cc_final: 0.8002 (mt) REVERT: E 128 ARG cc_start: 0.8676 (mtp85) cc_final: 0.8436 (mtp85) REVERT: E 131 ARG cc_start: 0.8397 (mtt180) cc_final: 0.8153 (mtt180) REVERT: F 84 MET cc_start: 0.8160 (mmm) cc_final: 0.7915 (mmm) REVERT: G 32 ARG cc_start: 0.8726 (tmm-80) cc_final: 0.8466 (ttp80) outliers start: 1 outliers final: 0 residues processed: 61 average time/residue: 0.2849 time to fit residues: 20.4431 Evaluate side-chains 62 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 52 optimal weight: 0.0170 chunk 80 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 11 optimal weight: 0.0270 chunk 17 optimal weight: 0.4980 chunk 89 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.145158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.114060 restraints weight = 17857.076| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.29 r_work: 0.3256 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.5938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13153 Z= 0.197 Angle : 0.547 7.935 19088 Z= 0.335 Chirality : 0.034 0.162 2169 Planarity : 0.004 0.055 1342 Dihedral : 31.026 156.163 4210 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.32 % Allowed : 6.29 % Favored : 93.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.30), residues: 729 helix: 2.52 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -0.95 (0.41), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 35 TYR 0.007 0.001 TYR G 50 PHE 0.010 0.001 PHE E 67 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00437 (13153) covalent geometry : angle 0.54694 (19088) hydrogen bonds : bond 0.04228 ( 771) hydrogen bonds : angle 2.39295 ( 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 62 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.291 Fit side-chains REVERT: A 96 SER cc_start: 0.8515 (OUTLIER) cc_final: 0.8056 (m) REVERT: E 60 LEU cc_start: 0.8288 (mm) cc_final: 0.8002 (mt) REVERT: E 128 ARG cc_start: 0.8664 (mtp85) cc_final: 0.8423 (mtp85) REVERT: E 131 ARG cc_start: 0.8389 (mtt180) cc_final: 0.8122 (mtt180) REVERT: F 84 MET cc_start: 0.8135 (mmm) cc_final: 0.7897 (mmm) REVERT: G 32 ARG cc_start: 0.8717 (tmm-80) cc_final: 0.8457 (ttp80) outliers start: 2 outliers final: 1 residues processed: 61 average time/residue: 0.2804 time to fit residues: 20.1715 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 : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain E residue 129 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 37 optimal weight: 0.3980 chunk 73 optimal weight: 0.9990 chunk 43 optimal weight: 0.0970 chunk 46 optimal weight: 0.5980 chunk 57 optimal weight: 0.3980 chunk 97 optimal weight: 1.9990 chunk 30 optimal weight: 0.3980 chunk 62 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.146843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.115734 restraints weight = 17867.567| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.29 r_work: 0.3279 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.6063 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= 0.178 Angle : 0.529 6.570 19088 Z= 0.325 Chirality : 0.033 0.161 2169 Planarity : 0.004 0.056 1342 Dihedral : 30.870 150.432 4210 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.32 % Allowed : 6.13 % 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: 2.67 (0.30), residues: 729 helix: 2.62 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -0.88 (0.42), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 35 TYR 0.007 0.001 TYR G 50 PHE 0.010 0.001 PHE E 67 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00391 (13153) covalent geometry : angle 0.52937 (19088) hydrogen bonds : bond 0.04111 ( 771) hydrogen bonds : angle 2.31720 ( 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 73 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.324 Fit side-chains REVERT: A 96 SER cc_start: 0.8471 (OUTLIER) cc_final: 0.8026 (m) REVERT: E 60 LEU cc_start: 0.8271 (mm) cc_final: 0.7963 (mt) REVERT: E 128 ARG cc_start: 0.8658 (mtp85) cc_final: 0.8418 (mtp85) REVERT: E 131 ARG cc_start: 0.8381 (mtt180) cc_final: 0.8103 (mtt180) REVERT: F 84 MET cc_start: 0.8123 (mmm) cc_final: 0.7815 (mmm) REVERT: G 32 ARG cc_start: 0.8701 (tmm-80) cc_final: 0.8454 (ttp80) outliers start: 2 outliers final: 1 residues processed: 72 average time/residue: 0.3229 time to fit residues: 26.9837 Evaluate side-chains 71 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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 47 optimal weight: 0.3980 chunk 82 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 66 optimal weight: 0.2980 chunk 34 optimal weight: 0.0370 chunk 87 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 26 optimal weight: 0.0000 chunk 67 optimal weight: 0.3980 overall best weight: 0.2262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.146403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.115381 restraints weight = 18008.703| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.32 r_work: 0.3282 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.6070 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= 0.153 Angle : 0.526 8.924 19088 Z= 0.322 Chirality : 0.032 0.178 2169 Planarity : 0.004 0.070 1342 Dihedral : 30.868 150.326 4210 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.32 % Allowed : 6.29 % Favored : 93.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.83 (0.31), residues: 729 helix: 2.74 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -0.83 (0.42), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 35 TYR 0.008 0.001 TYR H 37 PHE 0.010 0.001 PHE E 67 HIS 0.002 0.000 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00329 (13153) covalent geometry : angle 0.52599 (19088) hydrogen bonds : bond 0.03956 ( 771) hydrogen bonds : angle 2.28971 ( 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 71 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.349 Fit side-chains REVERT: A 96 SER cc_start: 0.8482 (OUTLIER) cc_final: 0.8053 (m) REVERT: E 60 LEU cc_start: 0.8267 (mm) cc_final: 0.7967 (mt) REVERT: E 128 ARG cc_start: 0.8676 (mtp85) cc_final: 0.8434 (mtp85) REVERT: E 131 ARG cc_start: 0.8376 (mtt180) cc_final: 0.8104 (mtt180) REVERT: F 84 MET cc_start: 0.8117 (mmm) cc_final: 0.7835 (mmm) REVERT: G 32 ARG cc_start: 0.8700 (tmm-80) cc_final: 0.8451 (ttp80) REVERT: H 56 MET cc_start: 0.8041 (tpp) cc_final: 0.7814 (tpp) outliers start: 2 outliers final: 1 residues processed: 70 average time/residue: 0.3002 time to fit residues: 24.4695 Evaluate side-chains 70 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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: 1.9990 chunk 92 optimal weight: 0.9990 chunk 65 optimal weight: 0.3980 chunk 68 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 42 optimal weight: 0.2980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.143278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.112368 restraints weight = 17906.415| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.30 r_work: 0.3226 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.6221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 13153 Z= 0.260 Angle : 0.580 10.912 19088 Z= 0.350 Chirality : 0.037 0.169 2169 Planarity : 0.004 0.055 1342 Dihedral : 31.054 151.791 4210 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.32 % Allowed : 6.29 % Favored : 93.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.47 (0.30), residues: 729 helix: 2.47 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -0.93 (0.42), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 35 TYR 0.010 0.001 TYR A 99 PHE 0.008 0.001 PHE G 25 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00586 (13153) covalent geometry : angle 0.57992 (19088) hydrogen bonds : bond 0.04670 ( 771) hydrogen bonds : angle 2.50483 ( 1904) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3094.97 seconds wall clock time: 53 minutes 23.37 seconds (3203.37 seconds total)