Starting phenix.real_space_refine on Sun Sep 13 09:50:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v9c_31815/09_2026/7v9c_31815.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v9c_31815/09_2026/7v9c_31815.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v9c_31815/09_2026/7v9c_31815.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v9c_31815/09_2026/7v9c_31815.map" model { file = "/net/cci-nas-00/data/ceres_data/7v9c_31815/09_2026/7v9c_31815.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v9c_31815/09_2026/7v9c_31815.cif" } resolution = 4.5 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= 0.002 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 545 5.49 5 S 28 5.16 5 C 12898 2.51 5 N 4353 2.21 5 O 5404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23228 Number of models: 1 Model: "" Number of chains: 18 Chain: "I" Number of atoms: 5778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 5778 Classifications: {'DNA': 273} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 272} Chain: "J" Number of atoms: 5412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 5412 Classifications: {'DNA': 273} Link IDs: {'rna3p': 272} Chain: "A" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "K" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "L" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "M" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "N" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "O" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "P" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "Q" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "R" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Time building chain proxies: 4.87, per 1000 atoms: 0.21 Number of scatterers: 23228 At special positions: 0 Unit cell: (193.908, 126.984, 145.002, 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 28 16.00 P 545 15.00 O 5404 8.00 N 4353 7.00 C 12898 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: 1.79 Conformation dependent library (CDL) restraints added in 673.5 milliseconds 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2824 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 8 sheets defined 71.1% alpha, 1.6% beta 21 base pairs and 275 stacking pairs defined. Time for finding SS restraints: 2.55 Creating SS restraints... Processing helix chain 'A' and resid 46 through 57 removed outlier: 3.540A pdb=" N GLU A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 79 removed outlier: 3.750A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 removed outlier: 4.080A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 3.957A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 35 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.851A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 121 Processing helix chain 'E' and resid 46 through 57 removed outlier: 3.540A pdb=" N GLU E 50 " --> pdb=" O VAL E 46 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 79 removed outlier: 3.751A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 removed outlier: 4.080A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 17 through 22 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 3.957A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 35 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.852A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 121 Processing helix chain 'K' and resid 46 through 57 removed outlier: 3.539A pdb=" N GLU K 50 " --> pdb=" O VAL K 46 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER K 57 " --> pdb=" O ARG K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 79 removed outlier: 3.751A pdb=" N ASP K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE K 78 " --> pdb=" O ILE K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 114 Processing helix chain 'K' and resid 120 through 131 Processing helix chain 'L' and resid 25 through 29 removed outlier: 4.081A pdb=" N ILE L 29 " --> pdb=" O ILE L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 42 Processing helix chain 'L' and resid 49 through 76 Processing helix chain 'L' and resid 82 through 94 Processing helix chain 'M' and resid 17 through 22 Processing helix chain 'M' and resid 27 through 37 Processing helix chain 'M' and resid 45 through 73 removed outlier: 3.958A pdb=" N VAL M 49 " --> pdb=" O ALA M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 90 Processing helix chain 'M' and resid 90 through 97 Processing helix chain 'N' and resid 35 through 46 Processing helix chain 'N' and resid 52 through 81 Processing helix chain 'N' and resid 87 through 99 removed outlier: 3.852A pdb=" N ILE N 91 " --> pdb=" O THR N 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 101 through 121 Processing helix chain 'O' and resid 46 through 57 removed outlier: 3.539A pdb=" N GLU O 50 " --> pdb=" O VAL O 46 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER O 57 " --> pdb=" O ARG O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 64 through 79 removed outlier: 3.751A pdb=" N ASP O 77 " --> pdb=" O GLU O 73 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE O 78 " --> pdb=" O ILE O 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 86 through 114 Processing helix chain 'O' and resid 120 through 131 Processing helix chain 'P' and resid 25 through 29 removed outlier: 4.080A pdb=" N ILE P 29 " --> pdb=" O ILE P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 30 through 42 Processing helix chain 'P' and resid 49 through 76 Processing helix chain 'P' and resid 82 through 94 Processing helix chain 'Q' and resid 17 through 22 Processing helix chain 'Q' and resid 27 through 37 Processing helix chain 'Q' and resid 45 through 73 removed outlier: 3.957A pdb=" N VAL Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 90 Processing helix chain 'Q' and resid 90 through 97 Processing helix chain 'R' and resid 35 through 46 Processing helix chain 'R' and resid 52 through 81 Processing helix chain 'R' and resid 87 through 99 removed outlier: 3.852A pdb=" N ILE R 91 " --> pdb=" O THR R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 121 Processing sheet with id=AA1, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.257A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 100 through 102 removed outlier: 7.205A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.234A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'L' and resid 96 through 98 Processing sheet with id=AA6, first strand: chain 'M' and resid 42 through 43 removed outlier: 7.249A pdb=" N ARG M 42 " --> pdb=" O ILE N 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'M' and resid 100 through 102 removed outlier: 7.201A pdb=" N THR M 101 " --> pdb=" O TYR P 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'Q' and resid 42 through 43 removed outlier: 7.235A pdb=" N ARG Q 42 " --> pdb=" O ILE R 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 788 hydrogen bonds defined for protein. 2352 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 49 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 275 stacking parallelities Total time for adding SS restraints: 3.49 Time building geometry restraints manager: 2.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4231 1.33 - 1.45: 8176 1.45 - 1.57: 11203 1.57 - 1.69: 1089 1.69 - 1.81: 48 Bond restraints: 24747 Sorted by residual: bond pdb=" O3' DG I 69 " pdb=" P DT I 70 " ideal model delta sigma weight residual 1.607 1.648 -0.041 1.20e-02 6.94e+03 1.17e+01 bond pdb=" C3' DG I 224 " pdb=" C2' DG I 224 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 bond pdb=" C3' DC J 155 " pdb=" C2' DC J 155 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" C3' DC J 177 " pdb=" C2' DC J 177 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DA J 79 " pdb=" C2' DA J 79 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 ... (remaining 24742 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 33853 1.55 - 3.10: 1865 3.10 - 4.65: 20 4.65 - 6.21: 16 6.21 - 7.76: 1 Bond angle restraints: 35755 Sorted by residual: angle pdb=" C2' DT I 70 " pdb=" C1' DT I 70 " pdb=" N1 DT I 70 " ideal model delta sigma weight residual 114.30 122.06 -7.76 1.40e+00 5.10e-01 3.07e+01 angle pdb=" O4' DA I 84 " pdb=" C4' DA I 84 " pdb=" C3' DA I 84 " ideal model delta sigma weight residual 106.00 102.94 3.06 6.00e-01 2.78e+00 2.60e+01 angle pdb=" O4' DA I 204 " pdb=" C4' DA I 204 " pdb=" C3' DA I 204 " ideal model delta sigma weight residual 106.00 103.03 2.97 6.00e-01 2.78e+00 2.44e+01 angle pdb=" O4' DG I 87 " pdb=" C4' DG I 87 " pdb=" C3' DG I 87 " ideal model delta sigma weight residual 106.00 103.19 2.81 6.00e-01 2.78e+00 2.20e+01 angle pdb=" O4' DC J 135 " pdb=" C4' DC J 135 " pdb=" C3' DC J 135 " ideal model delta sigma weight residual 106.00 103.21 2.79 6.00e-01 2.78e+00 2.16e+01 ... (remaining 35750 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.57: 11026 35.57 - 71.15: 2374 71.15 - 106.72: 148 106.72 - 142.30: 3 142.30 - 177.87: 6 Dihedral angle restraints: 13557 sinusoidal: 9171 harmonic: 4386 Sorted by residual: dihedral pdb=" C4' DC J 177 " pdb=" C3' DC J 177 " pdb=" O3' DC J 177 " pdb=" P DC J 178 " ideal model delta sinusoidal sigma weight residual -140.00 37.87 -177.87 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT J 54 " pdb=" C3' DT J 54 " pdb=" O3' DT J 54 " pdb=" P DA J 55 " ideal model delta sinusoidal sigma weight residual -140.00 37.32 -177.32 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DA J 79 " pdb=" C3' DA J 79 " pdb=" O3' DA J 79 " pdb=" P DA J 80 " ideal model delta sinusoidal sigma weight residual -140.00 36.45 -176.45 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 13554 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3827 0.077 - 0.154: 234 0.154 - 0.231: 2 0.231 - 0.308: 1 0.308 - 0.385: 1 Chirality restraints: 4065 Sorted by residual: chirality pdb=" C3' DT I 70 " pdb=" C4' DT I 70 " pdb=" O3' DT I 70 " pdb=" C2' DT I 70 " both_signs ideal model delta sigma weight residual False -2.73 -2.35 -0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" C1' DT I 70 " pdb=" O4' DT I 70 " pdb=" C2' DT I 70 " pdb=" N1 DT I 70 " both_signs ideal model delta sigma weight residual False 2.43 2.19 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" C3' DT I 71 " pdb=" C4' DT I 71 " pdb=" O3' DT I 71 " pdb=" C2' DT I 71 " both_signs ideal model delta sigma weight residual False -2.73 -2.90 0.17 2.00e-01 2.50e+01 7.36e-01 ... (remaining 4062 not shown) Planarity restraints: 2638 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 9 " -0.028 2.00e-02 2.50e+03 1.16e-02 4.04e+00 pdb=" N9 DG I 9 " 0.024 2.00e-02 2.50e+03 pdb=" C8 DG I 9 " 0.012 2.00e-02 2.50e+03 pdb=" N7 DG I 9 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DG I 9 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DG I 9 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 9 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DG I 9 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 9 " 0.002 2.00e-02 2.50e+03 pdb=" N2 DG I 9 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DG I 9 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DG I 9 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA J 103 " 0.027 2.00e-02 2.50e+03 1.18e-02 3.81e+00 pdb=" N9 DA J 103 " -0.022 2.00e-02 2.50e+03 pdb=" C8 DA J 103 " 0.000 2.00e-02 2.50e+03 pdb=" N7 DA J 103 " -0.010 2.00e-02 2.50e+03 pdb=" C5 DA J 103 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DA J 103 " 0.005 2.00e-02 2.50e+03 pdb=" N6 DA J 103 " 0.011 2.00e-02 2.50e+03 pdb=" N1 DA J 103 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DA J 103 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DA J 103 " -0.007 2.00e-02 2.50e+03 pdb=" C4 DA J 103 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 70 " 0.017 2.00e-02 2.50e+03 1.02e-02 2.62e+00 pdb=" N1 DT I 70 " -0.015 2.00e-02 2.50e+03 pdb=" C2 DT I 70 " -0.000 2.00e-02 2.50e+03 pdb=" O2 DT I 70 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DT I 70 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DT I 70 " 0.002 2.00e-02 2.50e+03 pdb=" O4 DT I 70 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DT I 70 " -0.003 2.00e-02 2.50e+03 pdb=" C7 DT I 70 " 0.013 2.00e-02 2.50e+03 pdb=" C6 DT I 70 " -0.018 2.00e-02 2.50e+03 ... (remaining 2635 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3719 2.77 - 3.30: 20217 3.30 - 3.84: 42132 3.84 - 4.37: 45709 4.37 - 4.90: 70386 Nonbonded interactions: 182163 Sorted by model distance: nonbonded pdb=" OP1 DA J 110 " pdb=" N VAL C 43 " model vdw 2.240 3.120 nonbonded pdb=" OP2 DA J 19 " pdb=" OH TYR H 39 " model vdw 2.258 3.040 nonbonded pdb=" NH2 ARG A 63 " pdb=" O GLY B 28 " model vdw 2.259 3.120 nonbonded pdb=" NH2 ARG K 63 " pdb=" O GLY L 28 " model vdw 2.298 3.120 nonbonded pdb=" N2 DG I 194 " pdb=" N3 DC J 81 " model vdw 2.302 2.560 ... (remaining 182158 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 40 through 134) selection = chain 'K' selection = (chain 'O' and resid 40 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' selection = (chain 'L' and resid 25 through 102) selection = chain 'P' } ncs_group { reference = (chain 'C' and resid 16 through 118) selection = (chain 'G' and resid 16 through 118) selection = (chain 'M' and resid 16 through 118) selection = (chain 'Q' and resid 16 through 118) } ncs_group { reference = (chain 'D' and resid 28 through 121) selection = chain 'H' selection = (chain 'N' and resid 28 through 121) selection = chain 'R' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.200 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: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.230 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3769 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 : 0.005 0.041 24747 Z= 0.464 Angle : 0.646 7.757 35755 Z= 0.623 Chirality : 0.040 0.385 4065 Planarity : 0.003 0.024 2638 Dihedral : 28.916 177.874 10733 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.94 % Allowed : 4.98 % Favored : 94.08 % Rotamer: Outliers : 1.27 % Allowed : 16.56 % Favored : 82.17 % 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: -0.37 (0.19), residues: 1486 helix: 0.86 (0.14), residues: 1052 sheet: None (None), residues: 0 loop : -3.08 (0.20), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 40 TYR 0.002 0.000 TYR G 50 PHE 0.001 0.000 PHE R 62 HIS 0.001 0.000 HIS P 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.46 (24747) covalent geometry : angle 0.64614 / 0.62 (35755) hydrogen bonds : bond 0.12565 / 14.06 ( 837) hydrogen bonds : angle 5.21699 / 6.71 ( 2446) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 455 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.6247 (m-80) cc_final: 0.5543 (m-10) REVERT: A 58 THR cc_start: 0.7507 (p) cc_final: 0.7225 (t) REVERT: A 60 LEU cc_start: 0.5833 (mt) cc_final: 0.5540 (mp) REVERT: A 103 LEU cc_start: 0.6742 (tp) cc_final: 0.6467 (tp) REVERT: A 126 LEU cc_start: 0.7629 (tp) cc_final: 0.7016 (tp) REVERT: B 34 ILE cc_start: 0.7166 (mt) cc_final: 0.6933 (mm) REVERT: B 39 ARG cc_start: 0.6713 (mmt-90) cc_final: 0.6490 (mmt180) REVERT: B 60 VAL cc_start: 0.6556 (t) cc_final: 0.5716 (p) REVERT: B 81 VAL cc_start: 0.5830 (t) cc_final: 0.5478 (t) REVERT: C 41 GLU cc_start: 0.6830 (tm-30) cc_final: 0.6428 (tp30) REVERT: C 78 ILE cc_start: 0.5287 (mt) cc_final: 0.4966 (pt) REVERT: C 82 HIS cc_start: 0.6922 (m170) cc_final: 0.6547 (m170) REVERT: C 114 VAL cc_start: 0.6648 (t) cc_final: 0.5429 (t) REVERT: C 115 LEU cc_start: 0.6637 (mt) cc_final: 0.5986 (mt) REVERT: D 56 MET cc_start: 0.8096 (tmm) cc_final: 0.7639 (tpp) REVERT: D 70 ILE cc_start: 0.7090 (mm) cc_final: 0.6677 (pt) REVERT: D 91 ILE cc_start: 0.6142 (mt) cc_final: 0.5513 (mt) REVERT: E 62 ILE cc_start: 0.7592 (mt) cc_final: 0.7271 (mm) REVERT: E 106 ASP cc_start: 0.7059 (m-30) cc_final: 0.6657 (m-30) REVERT: H 58 ILE cc_start: 0.7244 (mt) cc_final: 0.6969 (mt) REVERT: H 65 ASP cc_start: 0.6381 (t70) cc_final: 0.5673 (t0) REVERT: H 70 ILE cc_start: 0.7876 (mm) cc_final: 0.7297 (mm) REVERT: M 17 ARG cc_start: 0.1572 (mtt90) cc_final: 0.0567 (mtm-85) REVERT: M 31 HIS cc_start: 0.2294 (t70) cc_final: 0.1738 (t70) REVERT: M 39 TYR cc_start: 0.0867 (m-80) cc_final: 0.0340 (m-80) REVERT: M 42 ARG cc_start: -0.0284 (mtp180) cc_final: -0.0741 (tmt170) REVERT: M 68 ASN cc_start: 0.6618 (m-40) cc_final: 0.5277 (t0) REVERT: M 87 ILE cc_start: 0.5032 (mm) cc_final: 0.4567 (tt) REVERT: M 110 ASN cc_start: 0.3290 (t0) cc_final: 0.2808 (t0) REVERT: N 97 LEU cc_start: 0.5946 (mt) cc_final: 0.4453 (mt) REVERT: O 67 PHE cc_start: 0.5080 (t80) cc_final: 0.4859 (t80) REVERT: Q 56 GLU cc_start: 0.3543 (tp30) cc_final: 0.3267 (tt0) REVERT: R 36 VAL cc_start: 0.1866 (OUTLIER) cc_final: 0.1469 (t) REVERT: R 64 ASN cc_start: 0.5278 (m-40) cc_final: 0.4908 (t0) REVERT: R 84 SER cc_start: 0.5716 (m) cc_final: 0.5231 (p) REVERT: R 103 LEU cc_start: 0.5101 (mp) cc_final: 0.4642 (mt) outliers start: 16 outliers final: 3 residues processed: 468 average time/residue: 0.2014 time to fit residues: 135.9621 Evaluate side-chains 180 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 176 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 50.0000 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN B 93 GLN C 31 HIS C 38 ASN C 84 GLN C 104 GLN D 44 GLN E 85 GLN E 113 HIS G 24 GLN G 31 HIS G 84 GLN H 79 HIS K 93 GLN M 31 HIS M 38 ASN M 104 GLN O 113 HIS ** P 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 31 HIS Q 104 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.104566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.086133 restraints weight = 205051.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.088113 restraints weight = 137394.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.089417 restraints weight = 100101.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.090571 restraints weight = 78260.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.091234 restraints weight = 64140.297| |-----------------------------------------------------------------------------| r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4930 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24747 Z= 0.161 Angle : 0.616 12.033 35755 Z= 0.356 Chirality : 0.040 0.305 4065 Planarity : 0.005 0.089 2638 Dihedral : 32.003 177.977 7733 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.89 % Favored : 96.57 % Rotamer: Outliers : 0.48 % Allowed : 2.69 % Favored : 96.83 % 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: 0.83 (0.20), residues: 1486 helix: 1.81 (0.15), residues: 1036 sheet: None (None), residues: 0 loop : -2.63 (0.22), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 35 TYR 0.034 0.002 TYR F 88 PHE 0.041 0.002 PHE P 61 HIS 0.015 0.001 HIS K 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.16 (24747) covalent geometry : angle 0.61587 / 0.36 (35755) hydrogen bonds : bond 0.05558 / 6.18 ( 837) hydrogen bonds : angle 3.63172 / 4.76 ( 2446) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 263 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.7466 (t0) cc_final: 0.7207 (m-30) REVERT: B 81 VAL cc_start: 0.5342 (t) cc_final: 0.4994 (t) REVERT: C 78 ILE cc_start: 0.5240 (mt) cc_final: 0.4838 (pt) REVERT: D 56 MET cc_start: 0.6976 (tmm) cc_final: 0.6424 (tpp) REVERT: F 78 ARG cc_start: 0.4948 (ttm110) cc_final: 0.4611 (mtm110) REVERT: H 102 GLU cc_start: 0.6987 (mp0) cc_final: 0.6502 (tp30) REVERT: K 74 ILE cc_start: 0.4890 (mt) cc_final: 0.4514 (mt) REVERT: K 125 GLN cc_start: 0.6462 (mt0) cc_final: 0.6189 (pp30) REVERT: M 33 LEU cc_start: 0.4709 (mt) cc_final: 0.4393 (mt) REVERT: N 91 ILE cc_start: 0.6886 (tt) cc_final: 0.6336 (pt) REVERT: O 113 HIS cc_start: 0.3634 (t-90) cc_final: 0.3247 (t-170) REVERT: P 34 ILE cc_start: 0.4423 (mp) cc_final: 0.4011 (mt) REVERT: R 64 ASN cc_start: 0.6118 (m-40) cc_final: 0.5579 (t0) outliers start: 6 outliers final: 4 residues processed: 268 average time/residue: 0.1685 time to fit residues: 68.3616 Evaluate side-chains 158 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 154 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 144 optimal weight: 5.9990 chunk 154 optimal weight: 40.0000 chunk 99 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 chunk 44 optimal weight: 50.0000 chunk 15 optimal weight: 40.0000 chunk 191 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 148 optimal weight: 30.0000 chunk 173 optimal weight: 6.9990 chunk 53 optimal weight: 50.0000 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS C 84 GLN E 68 GLN E 85 GLN H 46 HIS H 79 HIS K 68 GLN K 85 GLN M 31 HIS ** N 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 GLN O 85 GLN ** P 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.097945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.076131 restraints weight = 229632.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.077821 restraints weight = 165450.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.078933 restraints weight = 129711.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.079741 restraints weight = 108730.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.080169 restraints weight = 95323.999| |-----------------------------------------------------------------------------| r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5344 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 24747 Z= 0.200 Angle : 0.694 11.830 35755 Z= 0.393 Chirality : 0.042 0.265 4065 Planarity : 0.007 0.099 2638 Dihedral : 32.052 179.062 7733 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.30 % Favored : 96.30 % Rotamer: Outliers : 0.08 % Allowed : 5.94 % Favored : 93.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.21), residues: 1486 helix: 1.59 (0.15), residues: 1062 sheet: None (None), residues: 0 loop : -2.38 (0.24), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 69 TYR 0.044 0.003 TYR F 88 PHE 0.022 0.003 PHE N 62 HIS 0.010 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.20 (24747) covalent geometry : angle 0.69401 / 0.39 (35755) hydrogen bonds : bond 0.05517 / 6.42 ( 837) hydrogen bonds : angle 3.87194 / 5.08 ( 2446) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 211 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 LYS cc_start: 0.7079 (tmtt) cc_final: 0.6822 (tptp) REVERT: C 78 ILE cc_start: 0.5560 (mt) cc_final: 0.4889 (mm) REVERT: D 56 MET cc_start: 0.7412 (tmm) cc_final: 0.6832 (tpt) REVERT: G 39 TYR cc_start: 0.6546 (m-10) cc_final: 0.6282 (m-10) REVERT: H 102 GLU cc_start: 0.7040 (mp0) cc_final: 0.6449 (tp30) REVERT: K 125 GLN cc_start: 0.6469 (mt0) cc_final: 0.6158 (pp30) REVERT: O 113 HIS cc_start: 0.3687 (t-90) cc_final: 0.3329 (t-170) REVERT: R 64 ASN cc_start: 0.6159 (m-40) cc_final: 0.5859 (t0) REVERT: R 105 LYS cc_start: 0.2947 (mptt) cc_final: 0.2595 (mptt) outliers start: 1 outliers final: 1 residues processed: 212 average time/residue: 0.1655 time to fit residues: 53.7148 Evaluate side-chains 132 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 71 optimal weight: 8.9990 chunk 181 optimal weight: 7.9990 chunk 129 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 19 optimal weight: 40.0000 chunk 68 optimal weight: 0.9990 chunk 85 optimal weight: 9.9990 chunk 10 optimal weight: 50.0000 chunk 136 optimal weight: 3.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN E 85 GLN H 81 ASN K 108 ASN ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 ASN N 81 ASN ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.091070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.069808 restraints weight = 229803.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.071500 restraints weight = 161302.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.072404 restraints weight = 123852.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.073337 restraints weight = 103321.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.073964 restraints weight = 89206.237| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5186 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 24747 Z= 0.174 Angle : 0.631 9.223 35755 Z= 0.366 Chirality : 0.040 0.243 4065 Planarity : 0.006 0.068 2638 Dihedral : 32.150 177.890 7733 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.47 % Allowed : 2.83 % Favored : 96.70 % Rotamer: Outliers : 0.16 % Allowed : 3.25 % Favored : 96.59 % 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: 0.95 (0.21), residues: 1486 helix: 1.71 (0.15), residues: 1060 sheet: None (None), residues: 0 loop : -2.25 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 53 TYR 0.048 0.003 TYR E 54 PHE 0.022 0.002 PHE O 67 HIS 0.009 0.002 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.17 (24747) covalent geometry : angle 0.63127 / 0.37 (35755) hydrogen bonds : bond 0.04975 / 5.66 ( 837) hydrogen bonds : angle 3.82547 / 5.05 ( 2446) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 195 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 ILE cc_start: 0.6861 (mm) cc_final: 0.6598 (tp) REVERT: B 97 LEU cc_start: 0.7378 (tp) cc_final: 0.7099 (tt) REVERT: B 100 PHE cc_start: 0.2844 (m-80) cc_final: 0.1789 (m-10) REVERT: C 78 ILE cc_start: 0.4795 (mt) cc_final: 0.4344 (mm) REVERT: D 56 MET cc_start: 0.7350 (tmm) cc_final: 0.7084 (tpp) REVERT: D 85 THR cc_start: 0.5768 (m) cc_final: 0.5486 (p) REVERT: E 42 ARG cc_start: 0.3211 (mmm160) cc_final: 0.3002 (tpt90) REVERT: P 34 ILE cc_start: 0.4311 (mp) cc_final: 0.4055 (mt) outliers start: 2 outliers final: 2 residues processed: 197 average time/residue: 0.1722 time to fit residues: 51.7876 Evaluate side-chains 128 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 126 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 40 optimal weight: 30.0000 chunk 152 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 195 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 chunk 30 optimal weight: 20.0000 chunk 22 optimal weight: 40.0000 chunk 118 optimal weight: 7.9990 chunk 194 optimal weight: 6.9990 chunk 11 optimal weight: 50.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN E 85 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS K 85 GLN K 93 GLN M 38 ASN ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.087667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.066872 restraints weight = 237174.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.068403 restraints weight = 163579.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.069520 restraints weight = 124937.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.070184 restraints weight = 102381.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.070494 restraints weight = 89223.088| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5266 moved from start: 0.5617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.133 24747 Z= 0.205 Angle : 0.731 11.222 35755 Z= 0.414 Chirality : 0.043 0.227 4065 Planarity : 0.008 0.181 2638 Dihedral : 32.320 179.295 7733 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.31 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % 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: 0.36 (0.20), residues: 1486 helix: 1.23 (0.15), residues: 1052 sheet: None (None), residues: 0 loop : -2.27 (0.24), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 35 TYR 0.062 0.003 TYR F 88 PHE 0.044 0.003 PHE N 62 HIS 0.012 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.21 (24747) covalent geometry : angle 0.73068 / 0.41 (35755) hydrogen bonds : bond 0.05758 / 6.63 ( 837) hydrogen bonds : angle 4.19121 / 5.54 ( 2446) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 78 ILE cc_start: 0.4126 (mt) cc_final: 0.3573 (mm) REVERT: D 56 MET cc_start: 0.7322 (tmm) cc_final: 0.7066 (tpp) REVERT: G 92 GLU cc_start: 0.6653 (tt0) cc_final: 0.6437 (tt0) REVERT: N 68 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8604 (mm-30) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.1603 time to fit residues: 45.6007 Evaluate side-chains 126 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 126 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 61 optimal weight: 0.0470 chunk 133 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 33 optimal weight: 30.0000 chunk 167 optimal weight: 0.5980 chunk 35 optimal weight: 40.0000 chunk 194 optimal weight: 20.0000 chunk 13 optimal weight: 40.0000 chunk 87 optimal weight: 8.9990 overall best weight: 3.9284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN E 85 GLN E 108 ASN H 46 HIS K 85 GLN O 76 GLN ** P 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.086951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.065977 restraints weight = 239511.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.067488 restraints weight = 166657.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.068299 restraints weight = 127125.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.069381 restraints weight = 105425.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.069691 restraints weight = 91236.651| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5326 moved from start: 0.6149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24747 Z= 0.174 Angle : 0.645 10.243 35755 Z= 0.374 Chirality : 0.041 0.179 4065 Planarity : 0.006 0.137 2638 Dihedral : 32.387 179.379 7733 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.70 % Favored : 96.10 % Rotamer: Outliers : 0.08 % Allowed : 2.22 % Favored : 97.70 % 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: 0.63 (0.21), residues: 1486 helix: 1.42 (0.15), residues: 1056 sheet: None (None), residues: 0 loop : -2.18 (0.25), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 63 TYR 0.043 0.003 TYR F 88 PHE 0.055 0.003 PHE P 61 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.17 (24747) covalent geometry : angle 0.64469 / 0.37 (35755) hydrogen bonds : bond 0.05072 / 5.72 ( 837) hydrogen bonds : angle 4.10143 / 5.39 ( 2446) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 181 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 PHE cc_start: 0.3870 (m-80) cc_final: 0.3570 (m-80) REVERT: C 78 ILE cc_start: 0.4322 (mt) cc_final: 0.3783 (mm) REVERT: D 85 THR cc_start: 0.5205 (m) cc_final: 0.4933 (p) REVERT: D 102 GLU cc_start: 0.6003 (pm20) cc_final: 0.5684 (pm20) REVERT: E 42 ARG cc_start: 0.2865 (mmm160) cc_final: 0.2557 (tpt90) REVERT: K 119 ILE cc_start: 0.4838 (pt) cc_final: 0.4304 (mt) REVERT: N 40 LYS cc_start: 0.6344 (mmtt) cc_final: 0.6080 (tppt) REVERT: P 81 VAL cc_start: 0.1120 (t) cc_final: 0.0897 (t) outliers start: 1 outliers final: 0 residues processed: 182 average time/residue: 0.1725 time to fit residues: 47.8278 Evaluate side-chains 125 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 146 optimal weight: 10.0000 chunk 28 optimal weight: 40.0000 chunk 102 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 163 optimal weight: 0.2980 chunk 67 optimal weight: 0.9990 chunk 56 optimal weight: 0.4980 chunk 54 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 170 optimal weight: 0.3980 chunk 75 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN D 92 GLN E 85 GLN E 108 ASN K 85 GLN M 38 ASN ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.087316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.066556 restraints weight = 238905.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.068082 restraints weight = 168055.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.068832 restraints weight = 128076.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.069785 restraints weight = 106697.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.070531 restraints weight = 92611.107| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5442 moved from start: 0.6261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 24747 Z= 0.139 Angle : 0.575 10.915 35755 Z= 0.337 Chirality : 0.037 0.177 4065 Planarity : 0.004 0.073 2638 Dihedral : 32.289 177.195 7733 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.23 % Favored : 96.70 % Rotamer: Outliers : 0.16 % Allowed : 1.43 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.21), residues: 1486 helix: 1.89 (0.15), residues: 1056 sheet: None (None), residues: 0 loop : -1.95 (0.26), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 69 TYR 0.041 0.002 TYR M 50 PHE 0.012 0.001 PHE R 67 HIS 0.006 0.001 HIS P 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.14 (24747) covalent geometry : angle 0.57523 / 0.34 (35755) hydrogen bonds : bond 0.04371 / 5.04 ( 837) hydrogen bonds : angle 3.80661 / 5.02 ( 2446) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 173 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8069 (mpp) cc_final: 0.7667 (mmt) REVERT: C 78 ILE cc_start: 0.4301 (mt) cc_final: 0.4065 (mt) REVERT: D 56 MET cc_start: 0.7552 (mtm) cc_final: 0.7187 (tpp) REVERT: D 85 THR cc_start: 0.5366 (m) cc_final: 0.5098 (p) REVERT: E 123 ASP cc_start: 0.8228 (m-30) cc_final: 0.7853 (m-30) REVERT: H 56 MET cc_start: 0.7822 (tmm) cc_final: 0.7537 (mmt) REVERT: K 119 ILE cc_start: 0.5079 (pt) cc_final: 0.4600 (mt) REVERT: N 68 GLU cc_start: 0.8922 (tm-30) cc_final: 0.8612 (mm-30) REVERT: P 81 VAL cc_start: 0.0907 (t) cc_final: 0.0578 (t) outliers start: 2 outliers final: 0 residues processed: 175 average time/residue: 0.1627 time to fit residues: 44.4249 Evaluate side-chains 127 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 20.0000 chunk 174 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 chunk 152 optimal weight: 20.0000 chunk 168 optimal weight: 5.9990 chunk 44 optimal weight: 40.0000 chunk 135 optimal weight: 0.6980 chunk 190 optimal weight: 6.9990 chunk 170 optimal weight: 0.9990 chunk 172 optimal weight: 9.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN E 85 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN K 85 GLN L 27 GLN ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.086216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.065091 restraints weight = 236725.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.066593 restraints weight = 165851.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.067641 restraints weight = 127817.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.067965 restraints weight = 105919.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.068891 restraints weight = 95634.536| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5326 moved from start: 0.6635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 24747 Z= 0.151 Angle : 0.599 9.930 35755 Z= 0.350 Chirality : 0.038 0.164 4065 Planarity : 0.005 0.072 2638 Dihedral : 32.268 178.566 7733 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.21), residues: 1486 helix: 1.87 (0.15), residues: 1054 sheet: None (None), residues: 0 loop : -1.95 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 72 TYR 0.038 0.002 TYR M 50 PHE 0.047 0.002 PHE P 61 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.15 (24747) covalent geometry : angle 0.59876 / 0.35 (35755) hydrogen bonds : bond 0.04500 / 5.11 ( 837) hydrogen bonds : angle 3.87892 / 5.12 ( 2446) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.7967 (mpp) cc_final: 0.7702 (mmm) REVERT: C 78 ILE cc_start: 0.4220 (mt) cc_final: 0.4001 (mt) REVERT: E 42 ARG cc_start: 0.3303 (mmm160) cc_final: 0.3001 (tpt90) REVERT: H 56 MET cc_start: 0.7791 (tmm) cc_final: 0.7477 (mmt) REVERT: K 119 ILE cc_start: 0.4744 (pt) cc_final: 0.4242 (mt) REVERT: N 68 GLU cc_start: 0.8926 (tm-30) cc_final: 0.8643 (mm-30) REVERT: P 81 VAL cc_start: 0.0969 (t) cc_final: 0.0665 (t) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.1452 time to fit residues: 39.2663 Evaluate side-chains 129 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 52 optimal weight: 50.0000 chunk 159 optimal weight: 20.0000 chunk 177 optimal weight: 2.9990 chunk 2 optimal weight: 50.0000 chunk 172 optimal weight: 6.9990 chunk 10 optimal weight: 50.0000 chunk 29 optimal weight: 30.0000 chunk 188 optimal weight: 5.9990 chunk 37 optimal weight: 30.0000 chunk 143 optimal weight: 8.9990 chunk 18 optimal weight: 40.0000 overall best weight: 8.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN E 108 ASN F 25 ASN G 38 ASN G 68 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN H 79 HIS K 85 GLN M 38 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.081232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.060616 restraints weight = 240736.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.061969 restraints weight = 170832.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.062787 restraints weight = 132592.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.063520 restraints weight = 111164.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.064135 restraints weight = 96184.010| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5587 moved from start: 0.8257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.267 24747 Z= 0.306 Angle : 1.005 23.268 35755 Z= 0.545 Chirality : 0.056 0.463 4065 Planarity : 0.011 0.083 2638 Dihedral : 32.704 179.384 7733 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 24.52 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.26 % Favored : 93.47 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Cbeta Deviations : 0.07 % 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: -1.13 (0.20), residues: 1486 helix: -0.01 (0.14), residues: 1052 sheet: None (None), residues: 0 loop : -2.48 (0.26), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.002 ARG O 69 TYR 0.064 0.005 TYR F 88 PHE 0.030 0.004 PHE O 67 HIS 0.051 0.005 HIS P 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00620 / 0.31 (24747) covalent geometry : angle 1.00480 / 0.54 (35755) hydrogen bonds : bond 0.07405 / 8.26 ( 837) hydrogen bonds : angle 5.18043 / 7.01 ( 2446) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 78 ILE cc_start: 0.4218 (mt) cc_final: 0.3889 (mt) REVERT: K 119 ILE cc_start: 0.5532 (pt) cc_final: 0.5290 (pt) REVERT: P 34 ILE cc_start: 0.2811 (mp) cc_final: 0.2589 (mp) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.1707 time to fit residues: 42.5204 Evaluate side-chains 116 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 82 optimal weight: 20.0000 chunk 123 optimal weight: 0.7980 chunk 161 optimal weight: 6.9990 chunk 174 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 158 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 9 optimal weight: 50.0000 chunk 57 optimal weight: 3.9990 chunk 24 optimal weight: 40.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN F 25 ASN H 46 HIS K 85 GLN ** M 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 GLN ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.082507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.061647 restraints weight = 239077.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.063108 restraints weight = 167638.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.064093 restraints weight = 129417.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.064787 restraints weight = 107298.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.065091 restraints weight = 93291.444| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5542 moved from start: 0.8152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24747 Z= 0.160 Angle : 0.678 14.177 35755 Z= 0.389 Chirality : 0.043 0.284 4065 Planarity : 0.005 0.072 2638 Dihedral : 32.606 179.099 7733 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % 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: 0.06 (0.21), residues: 1486 helix: 0.96 (0.15), residues: 1058 sheet: None (None), residues: 0 loop : -2.32 (0.26), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG Q 29 TYR 0.039 0.002 TYR F 88 PHE 0.017 0.002 PHE N 62 HIS 0.010 0.001 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.16 (24747) covalent geometry : angle 0.67827 / 0.39 (35755) hydrogen bonds : bond 0.04955 / 5.54 ( 837) hydrogen bonds : angle 4.31870 / 5.82 ( 2446) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.7984 (mpp) cc_final: 0.7605 (mmm) REVERT: C 78 ILE cc_start: 0.3928 (mt) cc_final: 0.3678 (mt) REVERT: D 99 LEU cc_start: 0.6108 (mm) cc_final: 0.5863 (mp) REVERT: E 42 ARG cc_start: 0.3521 (mmm160) cc_final: 0.3229 (tpt90) REVERT: H 56 MET cc_start: 0.7992 (tmm) cc_final: 0.7764 (mmt) REVERT: L 49 LEU cc_start: 0.4683 (mt) cc_final: 0.4471 (tp) REVERT: N 34 TYR cc_start: 0.5291 (m-80) cc_final: 0.5082 (m-80) REVERT: N 68 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8692 (mm-30) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.1602 time to fit residues: 40.6667 Evaluate side-chains 123 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 22 optimal weight: 40.0000 chunk 106 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 11 optimal weight: 50.0000 chunk 18 optimal weight: 40.0000 chunk 117 optimal weight: 0.7980 chunk 182 optimal weight: 0.6980 chunk 145 optimal weight: 4.9990 chunk 47 optimal weight: 50.0000 chunk 100 optimal weight: 6.9990 chunk 155 optimal weight: 0.9980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 GLN K 93 GLN L 93 GLN O 93 GLN ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.082307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.061693 restraints weight = 236595.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.063044 restraints weight = 163545.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.064020 restraints weight = 125381.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.064616 restraints weight = 103358.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.065253 restraints weight = 90046.303| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5526 moved from start: 0.8270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24747 Z= 0.156 Angle : 0.649 12.536 35755 Z= 0.373 Chirality : 0.041 0.197 4065 Planarity : 0.005 0.067 2638 Dihedral : 32.490 179.338 7733 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.16 % Allowed : 0.48 % Favored : 99.37 % 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: 0.40 (0.21), residues: 1486 helix: 1.22 (0.15), residues: 1060 sheet: None (None), residues: 0 loop : -2.22 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG O 69 TYR 0.037 0.002 TYR M 50 PHE 0.014 0.002 PHE N 62 HIS 0.006 0.001 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.16 (24747) covalent geometry : angle 0.64930 / 0.37 (35755) hydrogen bonds : bond 0.04721 / 5.28 ( 837) hydrogen bonds : angle 4.16772 / 5.61 ( 2446) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5226.47 seconds wall clock time: 90 minutes 40.27 seconds (5440.27 seconds total)