Starting phenix.real_space_refine on Thu Mar 5 12:50:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v9c_31815/03_2026/7v9c_31815.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v9c_31815/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7v9c_31815/03_2026/7v9c_31815.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v9c_31815/03_2026/7v9c_31815.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v9c_31815/03_2026/7v9c_31815.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v9c_31815/03_2026/7v9c_31815.map" } 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-dev-5986/lib/python3.9/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: 4.69, per 1000 atoms: 0.20 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: 1.34 Conformation dependent library (CDL) restraints added in 759.4 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: 2.68 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: 3.13 Time building geometry restraints manager: 1.99 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 1.50e-02 4.44e+03 7.48e+00 bond pdb=" O3' DA I 72 " pdb=" P DG I 73 " ideal model delta sigma weight residual 1.607 1.637 -0.030 1.50e-02 4.44e+03 3.92e+00 bond pdb=" C3' DT J 54 " pdb=" O3' DT J 54 " ideal model delta sigma weight residual 1.422 1.455 -0.033 3.00e-02 1.11e+03 1.24e+00 bond pdb=" C3' DA I 18 " pdb=" O3' DA I 18 " ideal model delta sigma weight residual 1.422 1.454 -0.032 3.00e-02 1.11e+03 1.12e+00 bond pdb=" C3' DA J 223 " pdb=" O3' DA J 223 " ideal model delta sigma weight residual 1.422 1.450 -0.028 3.00e-02 1.11e+03 8.93e-01 ... (remaining 24742 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 35212 1.71 - 3.42: 518 3.42 - 5.13: 22 5.13 - 6.85: 2 6.85 - 8.56: 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 113.50 122.06 -8.56 1.50e+00 4.44e-01 3.25e+01 angle pdb=" O3' DT I 71 " pdb=" C3' DT I 71 " pdb=" C2' DT I 71 " ideal model delta sigma weight residual 111.50 105.48 6.02 1.50e+00 4.44e-01 1.61e+01 angle pdb=" C4' DT I 70 " pdb=" C3' DT I 70 " pdb=" O3' DT I 70 " ideal model delta sigma weight residual 110.00 115.61 -5.61 1.50e+00 4.44e-01 1.40e+01 angle pdb=" C4' DT I 71 " pdb=" C3' DT I 71 " pdb=" O3' DT I 71 " ideal model delta sigma weight residual 110.00 105.53 4.47 1.50e+00 4.44e-01 8.88e+00 angle pdb=" C1' DT I 70 " pdb=" N1 DT I 70 " pdb=" C2 DT I 70 " ideal model delta sigma weight residual 119.35 123.51 -4.16 1.50e+00 4.44e-01 7.67e+00 ... (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 - 0.063: 3895 0.063 - 0.126: 166 0.126 - 0.189: 1 0.189 - 0.251: 1 0.251 - 0.314: 2 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 -2.66 -2.35 -0.31 2.00e-01 2.50e+01 2.47e+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 2.47 2.19 0.28 2.00e-01 2.50e+01 2.02e+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 -2.66 -2.90 0.24 2.00e-01 2.50e+01 1.46e+00 ... (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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.780 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: 0.430 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 18.660 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3920 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 : 0.002 0.041 24747 Z= 0.116 Angle : 0.435 8.557 35755 Z= 0.264 Chirality : 0.030 0.314 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 covalent geometry : bond 0.00240 (24747) covalent geometry : angle 0.43512 (35755) hydrogen bonds : bond 0.12565 ( 837) hydrogen bonds : angle 5.21699 ( 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 : 0.626 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: A 54 TYR cc_start: 0.6247 (m-80) cc_final: 0.5540 (m-10) REVERT: A 58 THR cc_start: 0.7507 (p) cc_final: 0.7221 (t) REVERT: A 60 LEU cc_start: 0.5833 (mt) cc_final: 0.5552 (mp) REVERT: A 103 LEU cc_start: 0.6742 (tp) cc_final: 0.6461 (tp) REVERT: A 126 LEU cc_start: 0.7629 (tp) cc_final: 0.7023 (tp) REVERT: B 34 ILE cc_start: 0.7166 (mt) cc_final: 0.6936 (mm) REVERT: B 39 ARG cc_start: 0.6713 (mmt-90) cc_final: 0.6499 (mmt180) REVERT: B 60 VAL cc_start: 0.6556 (t) cc_final: 0.5718 (p) REVERT: B 81 VAL cc_start: 0.5830 (t) cc_final: 0.5484 (t) REVERT: C 41 GLU cc_start: 0.6830 (tm-30) cc_final: 0.6418 (tp30) REVERT: C 78 ILE cc_start: 0.5287 (mt) cc_final: 0.4977 (pt) REVERT: C 82 HIS cc_start: 0.6922 (m170) cc_final: 0.6546 (m170) REVERT: C 114 VAL cc_start: 0.6648 (t) cc_final: 0.5424 (t) REVERT: C 115 LEU cc_start: 0.6637 (mt) cc_final: 0.5989 (mt) REVERT: D 56 MET cc_start: 0.8096 (tmm) cc_final: 0.7643 (tpp) REVERT: D 70 ILE cc_start: 0.7090 (mm) cc_final: 0.6668 (pt) REVERT: D 91 ILE cc_start: 0.6142 (mt) cc_final: 0.5591 (mt) REVERT: E 62 ILE cc_start: 0.7592 (mt) cc_final: 0.7261 (mm) REVERT: E 106 ASP cc_start: 0.7059 (m-30) cc_final: 0.6650 (m-30) REVERT: H 58 ILE cc_start: 0.7244 (mt) cc_final: 0.6970 (mt) REVERT: H 65 ASP cc_start: 0.6381 (t70) cc_final: 0.5676 (t0) REVERT: H 70 ILE cc_start: 0.7876 (mm) cc_final: 0.7295 (mm) REVERT: M 17 ARG cc_start: 0.1572 (mtt90) cc_final: 0.0447 (mtt90) REVERT: M 31 HIS cc_start: 0.2294 (t70) cc_final: 0.1757 (t70) REVERT: M 39 TYR cc_start: 0.0867 (m-80) cc_final: 0.0341 (m-80) REVERT: M 42 ARG cc_start: -0.0284 (mtp180) cc_final: -0.0591 (tmt170) REVERT: M 68 ASN cc_start: 0.6618 (m-40) cc_final: 0.5283 (t0) REVERT: M 87 ILE cc_start: 0.5032 (mm) cc_final: 0.4561 (tt) REVERT: M 110 ASN cc_start: 0.3290 (t0) cc_final: 0.2805 (t0) REVERT: N 97 LEU cc_start: 0.5946 (mt) cc_final: 0.4454 (mt) REVERT: O 67 PHE cc_start: 0.5080 (t80) cc_final: 0.4860 (t80) REVERT: Q 56 GLU cc_start: 0.3543 (tp30) cc_final: 0.3265 (tt0) REVERT: R 36 VAL cc_start: 0.1866 (OUTLIER) cc_final: 0.1465 (t) REVERT: R 64 ASN cc_start: 0.5278 (m-40) cc_final: 0.4909 (t0) REVERT: R 84 SER cc_start: 0.5716 (m) cc_final: 0.5274 (p) REVERT: R 103 LEU cc_start: 0.5101 (mp) cc_final: 0.4641 (mt) outliers start: 16 outliers final: 3 residues processed: 468 average time/residue: 0.1914 time to fit residues: 127.9023 Evaluate side-chains 176 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 172 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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: 10.0000 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 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: 8.9990 chunk 91 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN B 25 ASN C 38 ASN C 104 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN E 113 HIS G 24 GLN G 31 HIS H 79 HIS K 68 GLN K 85 GLN K 108 ASN M 31 HIS M 38 ASN M 104 GLN O 113 HIS Q 31 HIS Q 104 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.095368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.078890 restraints weight = 232121.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.079814 restraints weight = 151712.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.080392 restraints weight = 103272.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.080430 restraints weight = 93144.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.080660 restraints weight = 87314.090| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5538 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 24747 Z= 0.172 Angle : 0.611 10.936 35755 Z= 0.346 Chirality : 0.034 0.152 4065 Planarity : 0.005 0.083 2638 Dihedral : 31.940 178.777 7733 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.40 % Allowed : 2.62 % Favored : 96.97 % Rotamer: Outliers : 0.16 % Allowed : 4.36 % 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: 0.89 (0.21), residues: 1486 helix: 1.78 (0.15), residues: 1060 sheet: None (None), residues: 0 loop : -2.64 (0.23), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 35 TYR 0.032 0.003 TYR F 88 PHE 0.033 0.003 PHE P 61 HIS 0.007 0.002 HIS K 113 Details of bonding type rmsd covalent geometry : bond 0.00371 (24747) covalent geometry : angle 0.61127 (35755) hydrogen bonds : bond 0.04727 ( 837) hydrogen bonds : angle 3.58880 ( 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 264 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 262 time to evaluate : 0.512 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: A 54 TYR cc_start: 0.6634 (m-10) cc_final: 0.6425 (m-10) REVERT: A 58 THR cc_start: 0.7106 (p) cc_final: 0.6896 (t) REVERT: A 77 ASP cc_start: 0.7267 (t0) cc_final: 0.6949 (m-30) REVERT: B 39 ARG cc_start: 0.6698 (mmt-90) cc_final: 0.6451 (mmt180) REVERT: B 58 LEU cc_start: 0.8726 (tt) cc_final: 0.8453 (pp) REVERT: B 66 ILE cc_start: 0.8482 (mt) cc_final: 0.8071 (tt) REVERT: C 78 ILE cc_start: 0.5371 (mt) cc_final: 0.4952 (mm) REVERT: C 82 HIS cc_start: 0.6779 (m170) cc_final: 0.6456 (m170) REVERT: E 59 GLU cc_start: 0.7064 (pt0) cc_final: 0.6843 (pt0) REVERT: E 101 VAL cc_start: 0.8286 (t) cc_final: 0.8026 (m) REVERT: E 123 ASP cc_start: 0.7832 (m-30) cc_final: 0.7297 (t0) REVERT: G 64 GLU cc_start: 0.7855 (tp30) cc_final: 0.7319 (tp30) REVERT: H 39 TYR cc_start: 0.6937 (t80) cc_final: 0.6556 (t80) REVERT: K 74 ILE cc_start: 0.4703 (mt) cc_final: 0.4414 (mt) REVERT: O 105 GLU cc_start: 0.7102 (tt0) cc_final: 0.6628 (tp30) REVERT: R 40 LYS cc_start: 0.2855 (mmtm) cc_final: 0.2648 (mttm) REVERT: R 64 ASN cc_start: 0.6183 (m-40) cc_final: 0.5668 (t0) REVERT: R 84 SER cc_start: 0.6444 (m) cc_final: 0.6132 (p) outliers start: 2 outliers final: 1 residues processed: 264 average time/residue: 0.1576 time to fit residues: 63.3043 Evaluate side-chains 149 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 0.676 ------------------------------------------------------------------------------- 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: 0.8980 chunk 154 optimal weight: 40.0000 chunk 99 optimal weight: 7.9990 chunk 109 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 191 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 148 optimal weight: 10.0000 chunk 173 optimal weight: 30.0000 chunk 53 optimal weight: 20.0000 overall best weight: 4.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS E 85 GLN E 108 ASN G 68 ASN H 81 ASN ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 64 ASN ** P 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 68 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.084548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.063721 restraints weight = 236593.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.065242 restraints weight = 163231.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.066204 restraints weight = 124815.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.067081 restraints weight = 102568.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.067687 restraints weight = 88110.392| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5652 moved from start: 0.7052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 24747 Z= 0.256 Angle : 0.775 9.890 35755 Z= 0.439 Chirality : 0.042 0.257 4065 Planarity : 0.008 0.138 2638 Dihedral : 32.483 179.731 7733 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.44 % Favored : 95.22 % Rotamer: Outliers : 0.55 % Allowed : 5.55 % Favored : 93.90 % 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: -0.29 (0.20), residues: 1486 helix: 0.73 (0.15), residues: 1056 sheet: None (None), residues: 0 loop : -2.55 (0.24), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG G 42 TYR 0.041 0.004 TYR F 88 PHE 0.030 0.003 PHE B 61 HIS 0.014 0.003 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00542 (24747) covalent geometry : angle 0.77489 (35755) hydrogen bonds : bond 0.06136 ( 837) hydrogen bonds : angle 4.55423 ( 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 215 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 208 time to evaluate : 0.590 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: B 39 ARG cc_start: 0.5315 (mmt-90) cc_final: 0.5009 (mmp80) REVERT: B 63 GLU cc_start: 0.7344 (pt0) cc_final: 0.7137 (pp20) REVERT: D 56 MET cc_start: 0.7484 (tmm) cc_final: 0.7255 (tpp) REVERT: G 50 TYR cc_start: 0.6517 (t80) cc_final: 0.5863 (t80) REVERT: H 56 MET cc_start: 0.7773 (tmm) cc_final: 0.7406 (tpp) REVERT: H 92 GLN cc_start: 0.8148 (tt0) cc_final: 0.7818 (tp40) REVERT: H 108 VAL cc_start: 0.7407 (t) cc_final: 0.7177 (t) REVERT: M 35 ARG cc_start: 0.4225 (mtt90) cc_final: 0.3842 (mtt180) REVERT: O 69 ARG cc_start: 0.4170 (mtt-85) cc_final: 0.3344 (tpp-160) REVERT: O 105 GLU cc_start: 0.6822 (tt0) cc_final: 0.6558 (tp30) REVERT: R 103 LEU cc_start: 0.3750 (mp) cc_final: 0.3352 (mp) outliers start: 7 outliers final: 2 residues processed: 215 average time/residue: 0.1749 time to fit residues: 55.5252 Evaluate side-chains 134 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 132 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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: 0.2980 chunk 181 optimal weight: 20.0000 chunk 129 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 10 optimal weight: 20.0000 chunk 136 optimal weight: 5.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN E 85 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN G 73 ASN K 85 GLN M 38 ASN N 44 GLN ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 68 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 = 0.4040 r_free = 0.4040 target = 0.083414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.062693 restraints weight = 238801.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.064058 restraints weight = 167930.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.064977 restraints weight = 128629.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.065865 restraints weight = 106055.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.066142 restraints weight = 91141.029| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5758 moved from start: 0.7774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 24747 Z= 0.182 Angle : 0.637 8.243 35755 Z= 0.363 Chirality : 0.035 0.235 4065 Planarity : 0.005 0.069 2638 Dihedral : 32.373 179.568 7733 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.23 % Favored : 96.70 % Rotamer: Outliers : 0.08 % Allowed : 3.33 % 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: 0.38 (0.21), residues: 1486 helix: 1.26 (0.15), residues: 1060 sheet: None (None), residues: 0 loop : -2.40 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 129 TYR 0.026 0.002 TYR M 50 PHE 0.026 0.002 PHE K 78 HIS 0.011 0.002 HIS M 31 Details of bonding type rmsd covalent geometry : bond 0.00392 (24747) covalent geometry : angle 0.63656 (35755) hydrogen bonds : bond 0.04805 ( 837) hydrogen bonds : angle 4.07448 ( 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 186 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 185 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ARG cc_start: 0.5722 (ttt180) cc_final: 0.5505 (ttt-90) REVERT: B 39 ARG cc_start: 0.5239 (mmt-90) cc_final: 0.5022 (mmt-90) REVERT: B 100 PHE cc_start: 0.5201 (m-80) cc_final: 0.4996 (m-80) REVERT: C 78 ILE cc_start: 0.4078 (mt) cc_final: 0.3804 (mt) REVERT: D 56 MET cc_start: 0.7432 (tmm) cc_final: 0.7154 (tpp) REVERT: H 56 MET cc_start: 0.7886 (tmm) cc_final: 0.7602 (mmm) REVERT: K 119 ILE cc_start: 0.5599 (pt) cc_final: 0.5042 (mt) REVERT: L 49 LEU cc_start: 0.4612 (mt) cc_final: 0.4400 (tp) outliers start: 1 outliers final: 1 residues processed: 186 average time/residue: 0.1639 time to fit residues: 45.8260 Evaluate side-chains 118 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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: 10.0000 chunk 152 optimal weight: 30.0000 chunk 58 optimal weight: 8.9990 chunk 99 optimal weight: 4.9990 chunk 195 optimal weight: 9.9990 chunk 123 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 194 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 85 GLN E 108 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 HIS H 81 ASN K 85 GLN L 27 GLN L 93 GLN O 76 GLN ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 68 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.076387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.056138 restraints weight = 252136.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.057432 restraints weight = 181898.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.058130 restraints weight = 143032.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.058901 restraints weight = 120335.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.059188 restraints weight = 105384.596| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6057 moved from start: 1.0653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 24747 Z= 0.314 Angle : 0.930 14.164 35755 Z= 0.521 Chirality : 0.050 0.264 4065 Planarity : 0.009 0.080 2638 Dihedral : 33.323 175.516 7733 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 25.35 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.45 % Favored : 94.35 % Rotamer: Outliers : 0.40 % Allowed : 5.07 % Favored : 94.53 % 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: -1.34 (0.19), residues: 1486 helix: -0.16 (0.14), residues: 1062 sheet: None (None), residues: 0 loop : -2.63 (0.25), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 53 TYR 0.038 0.004 TYR B 51 PHE 0.030 0.004 PHE O 67 HIS 0.011 0.003 HIS R 46 Details of bonding type rmsd covalent geometry : bond 0.00685 (24747) covalent geometry : angle 0.93028 (35755) hydrogen bonds : bond 0.07453 ( 837) hydrogen bonds : angle 5.36007 ( 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 165 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 160 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 LEU cc_start: 0.5712 (mp) cc_final: 0.4993 (mt) REVERT: C 78 ILE cc_start: 0.4183 (mt) cc_final: 0.3938 (mt) REVERT: D 56 MET cc_start: 0.7676 (tmm) cc_final: 0.7298 (tpp) REVERT: G 118 LYS cc_start: 0.5719 (tmtt) cc_final: 0.5415 (ptmt) REVERT: H 56 MET cc_start: 0.8173 (tmm) cc_final: 0.7905 (tpp) REVERT: M 84 GLN cc_start: 0.6287 (tp-100) cc_final: 0.6013 (tm-30) outliers start: 5 outliers final: 3 residues processed: 163 average time/residue: 0.1423 time to fit residues: 36.4073 Evaluate side-chains 105 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 102 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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: 6.9990 chunk 78 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 133 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 167 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 194 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN D 79 HIS E 85 GLN E 108 ASN K 85 GLN L 93 GLN M 104 GLN ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 106 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.075957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.055737 restraints weight = 251730.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.057047 restraints weight = 179865.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.057855 restraints weight = 139849.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.058590 restraints weight = 116960.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.058864 restraints weight = 101995.394| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6100 moved from start: 1.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 24747 Z= 0.243 Angle : 0.769 10.924 35755 Z= 0.433 Chirality : 0.041 0.183 4065 Planarity : 0.007 0.065 2638 Dihedral : 33.270 178.998 7733 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.24 % Favored : 95.56 % Rotamer: Outliers : 0.24 % Allowed : 3.57 % Favored : 96.20 % 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 (0.20), residues: 1486 helix: 0.32 (0.15), residues: 1056 sheet: None (None), residues: 0 loop : -2.57 (0.25), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 32 TYR 0.032 0.003 TYR M 50 PHE 0.026 0.003 PHE R 67 HIS 0.009 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00528 (24747) covalent geometry : angle 0.76890 (35755) hydrogen bonds : bond 0.05869 ( 837) hydrogen bonds : angle 4.77886 ( 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 159 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 156 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 78 ILE cc_start: 0.3901 (mt) cc_final: 0.3647 (mt) REVERT: D 56 MET cc_start: 0.7668 (tmm) cc_final: 0.7394 (mtt) REVERT: E 52 ARG cc_start: 0.6008 (mtt90) cc_final: 0.5807 (tpt90) REVERT: H 92 GLN cc_start: 0.8220 (tt0) cc_final: 0.8005 (tm-30) REVERT: H 96 ARG cc_start: 0.7022 (mtt180) cc_final: 0.6782 (mtp-110) REVERT: K 119 ILE cc_start: 0.5655 (pt) cc_final: 0.5084 (pt) REVERT: N 34 TYR cc_start: 0.5690 (m-80) cc_final: 0.5383 (m-80) REVERT: Q 35 ARG cc_start: 0.4799 (mtm110) cc_final: 0.4583 (mpt90) outliers start: 3 outliers final: 1 residues processed: 157 average time/residue: 0.1730 time to fit residues: 40.8455 Evaluate side-chains 111 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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: 0.7980 chunk 28 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 163 optimal weight: 0.0030 chunk 67 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 170 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 overall best weight: 2.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS E 85 GLN E 108 ASN H 79 HIS H 81 ASN H 92 GLN K 85 GLN L 93 GLN ** 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 = 0.4002 r_free = 0.4002 target = 0.077550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.060098 restraints weight = 230507.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.061623 restraints weight = 142375.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.062683 restraints weight = 99838.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.063367 restraints weight = 77647.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.063969 restraints weight = 65236.603| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5853 moved from start: 1.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 24747 Z= 0.175 Angle : 0.647 9.724 35755 Z= 0.372 Chirality : 0.036 0.175 4065 Planarity : 0.005 0.053 2638 Dihedral : 32.908 179.335 7733 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.58 % Favored : 95.29 % Rotamer: Outliers : 0.24 % Allowed : 1.74 % Favored : 98.02 % 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: 0.16 (0.21), residues: 1486 helix: 1.05 (0.15), residues: 1062 sheet: None (None), residues: 0 loop : -2.34 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 116 TYR 0.021 0.002 TYR H 34 PHE 0.013 0.002 PHE R 67 HIS 0.013 0.001 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00375 (24747) covalent geometry : angle 0.64659 (35755) hydrogen bonds : bond 0.04670 ( 837) hydrogen bonds : angle 4.22169 ( 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 156 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 153 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 ARG cc_start: 0.6406 (ttt180) cc_final: 0.6164 (ttt-90) REVERT: B 81 VAL cc_start: 0.5118 (t) cc_final: 0.4743 (t) REVERT: C 78 ILE cc_start: 0.3906 (mt) cc_final: 0.3699 (mt) REVERT: D 53 SER cc_start: 0.7599 (p) cc_final: 0.6947 (m) REVERT: H 115 VAL cc_start: 0.8050 (p) cc_final: 0.7847 (p) REVERT: L 34 ILE cc_start: 0.3303 (mt) cc_final: 0.3008 (mm) REVERT: L 49 LEU cc_start: 0.5454 (tp) cc_final: 0.5252 (tp) REVERT: L 52 GLU cc_start: 0.6875 (mp0) cc_final: 0.6460 (pp20) REVERT: Q 35 ARG cc_start: 0.4698 (mtm110) cc_final: 0.4464 (mpt90) outliers start: 3 outliers final: 1 residues processed: 154 average time/residue: 0.1573 time to fit residues: 37.5945 Evaluate side-chains 113 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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: 5.9990 chunk 174 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 152 optimal weight: 20.0000 chunk 168 optimal weight: 5.9990 chunk 44 optimal weight: 20.0000 chunk 135 optimal weight: 4.9990 chunk 190 optimal weight: 0.9990 chunk 170 optimal weight: 6.9990 chunk 172 optimal weight: 0.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN E 108 ASN G 38 ASN H 81 ASN K 85 GLN K 93 GLN L 64 ASN L 93 GLN Q 68 ASN ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.077977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.060372 restraints weight = 229078.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.061945 restraints weight = 142375.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.062994 restraints weight = 100067.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.063595 restraints weight = 77887.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.064260 restraints weight = 65791.124| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5857 moved from start: 1.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 24747 Z= 0.162 Angle : 0.618 10.743 35755 Z= 0.354 Chirality : 0.035 0.181 4065 Planarity : 0.005 0.152 2638 Dihedral : 32.609 179.870 7733 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.51 % Favored : 95.42 % Rotamer: Outliers : 0.24 % Allowed : 1.43 % Favored : 98.34 % 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: 0.72 (0.21), residues: 1486 helix: 1.48 (0.15), residues: 1062 sheet: None (None), residues: 0 loop : -2.19 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG L 40 TYR 0.019 0.002 TYR H 34 PHE 0.014 0.002 PHE R 67 HIS 0.004 0.001 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00347 (24747) covalent geometry : angle 0.61787 (35755) hydrogen bonds : bond 0.04371 ( 837) hydrogen bonds : angle 4.03976 ( 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 154 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 151 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 23 LEU cc_start: 0.4324 (mm) cc_final: 0.3195 (mt) REVERT: C 56 GLU cc_start: 0.8079 (tp30) cc_final: 0.7806 (tt0) REVERT: C 78 ILE cc_start: 0.3686 (mt) cc_final: 0.3472 (mt) REVERT: K 119 ILE cc_start: 0.5199 (pt) cc_final: 0.4736 (mp) REVERT: N 80 TYR cc_start: 0.6191 (m-10) cc_final: 0.5951 (m-10) REVERT: Q 35 ARG cc_start: 0.4768 (mtm110) cc_final: 0.4504 (mpt90) outliers start: 3 outliers final: 0 residues processed: 152 average time/residue: 0.1434 time to fit residues: 34.9855 Evaluate side-chains 111 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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: 20.0000 chunk 159 optimal weight: 7.9990 chunk 177 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 172 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 188 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 143 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS E 85 GLN E 108 ASN H 64 ASN H 81 ASN K 85 GLN ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 GLN O 93 GLN ** P 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 68 ASN ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 64 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.074281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.055854 restraints weight = 250103.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.057333 restraints weight = 159302.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.058270 restraints weight = 116461.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.059047 restraints weight = 93162.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.059526 restraints weight = 78466.059| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6081 moved from start: 1.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 24747 Z= 0.278 Angle : 0.837 10.577 35755 Z= 0.467 Chirality : 0.046 0.272 4065 Planarity : 0.007 0.078 2638 Dihedral : 33.013 179.847 7733 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 23.28 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.45 % Favored : 94.28 % Rotamer: Outliers : 0.24 % Allowed : 1.90 % Favored : 97.86 % 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: -0.56 (0.20), residues: 1486 helix: 0.48 (0.15), residues: 1054 sheet: None (None), residues: 0 loop : -2.47 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 36 TYR 0.031 0.003 TYR D 80 PHE 0.022 0.003 PHE K 104 HIS 0.014 0.002 HIS M 31 Details of bonding type rmsd covalent geometry : bond 0.00613 (24747) covalent geometry : angle 0.83739 (35755) hydrogen bonds : bond 0.06793 ( 837) hydrogen bonds : angle 5.00153 ( 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 131 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 128 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 56 MET cc_start: 0.7516 (ttt) cc_final: 0.7210 (tpp) REVERT: N 56 MET cc_start: 0.3477 (ttt) cc_final: 0.3243 (mmm) outliers start: 3 outliers final: 1 residues processed: 130 average time/residue: 0.1426 time to fit residues: 29.2385 Evaluate side-chains 93 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.640 ------------------------------------------------------------------------------- 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: 2.9990 chunk 123 optimal weight: 0.7980 chunk 161 optimal weight: 3.9990 chunk 174 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 158 optimal weight: 8.9990 chunk 111 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN E 108 ASN G 38 ASN K 85 GLN L 93 GLN Q 68 ASN ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 92 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.076636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.057512 restraints weight = 245503.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.059011 restraints weight = 156635.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.059925 restraints weight = 114715.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.060764 restraints weight = 92052.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.061170 restraints weight = 77884.044| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5982 moved from start: 1.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 24747 Z= 0.185 Angle : 0.678 9.239 35755 Z= 0.386 Chirality : 0.037 0.201 4065 Planarity : 0.005 0.056 2638 Dihedral : 32.827 179.198 7733 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % 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: 0.04 (0.21), residues: 1486 helix: 0.95 (0.15), residues: 1054 sheet: None (None), residues: 0 loop : -2.31 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 116 TYR 0.023 0.002 TYR E 54 PHE 0.032 0.002 PHE P 61 HIS 0.021 0.002 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00399 (24747) covalent geometry : angle 0.67810 (35755) hydrogen bonds : bond 0.05090 ( 837) hydrogen bonds : angle 4.39597 ( 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 144 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 142 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 23 LEU cc_start: 0.4918 (mt) cc_final: 0.4664 (mp) REVERT: C 56 GLU cc_start: 0.8105 (tp30) cc_final: 0.7834 (tt0) REVERT: C 78 ILE cc_start: 0.3645 (mt) cc_final: 0.3372 (mt) REVERT: D 56 MET cc_start: 0.7245 (ttt) cc_final: 0.6951 (tpp) REVERT: K 119 ILE cc_start: 0.5399 (pt) cc_final: 0.5025 (mp) REVERT: N 56 MET cc_start: 0.3493 (ttt) cc_final: 0.3233 (mmm) outliers start: 2 outliers final: 0 residues processed: 144 average time/residue: 0.1478 time to fit residues: 33.3659 Evaluate side-chains 107 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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: 10.0000 chunk 106 optimal weight: 7.9990 chunk 119 optimal weight: 0.9980 chunk 11 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 chunk 182 optimal weight: 8.9990 chunk 145 optimal weight: 0.6980 chunk 47 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN E 108 ASN H 81 ASN K 85 GLN L 93 GLN ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 92 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.075080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.057288 restraints weight = 236528.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.058945 restraints weight = 147907.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.059992 restraints weight = 105000.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.060727 restraints weight = 82040.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.061139 restraints weight = 68744.841| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5937 moved from start: 1.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 24747 Z= 0.202 Angle : 0.708 8.827 35755 Z= 0.401 Chirality : 0.039 0.168 4065 Planarity : 0.006 0.059 2638 Dihedral : 32.811 179.320 7733 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.24 % Allowed : 1.03 % Favored : 98.73 % 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 (0.21), residues: 1486 helix: 0.81 (0.15), residues: 1058 sheet: None (None), residues: 0 loop : -2.31 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 116 TYR 0.028 0.003 TYR M 50 PHE 0.017 0.002 PHE K 78 HIS 0.008 0.002 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00438 (24747) covalent geometry : angle 0.70791 (35755) hydrogen bonds : bond 0.05503 ( 837) hydrogen bonds : angle 4.52680 ( 2446) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4615.57 seconds wall clock time: 79 minutes 49.35 seconds (4789.35 seconds total)