Starting phenix.real_space_refine on Sat Jul 4 17:53:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v9c_31815/07_2026/7v9c_31815.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v9c_31815/07_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_31815/07_2026/7v9c_31815.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v9c_31815/07_2026/7v9c_31815.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v9c_31815/07_2026/7v9c_31815.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v9c_31815/07_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-6108/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: 4.75, 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: 2.43 Conformation dependent library (CDL) restraints added in 573.4 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: 2.66 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: 3.79 Time building geometry restraints manager: 2.52 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=" 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 bond pdb=" C3' DG I 236 " pdb=" C2' DG I 236 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 ... (remaining 24742 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 33862 1.55 - 3.10: 1859 3.10 - 4.65: 17 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: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 21.390 Find NCS groups from input model: 0.290 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.610 ------------------------------------------------------------------------------- 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= 0.463 Angle : 0.640 7.757 35755 Z= 0.618 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 0.64038 / 0.62 (35755) hydrogen bonds : bond 0.12565 / 14.05 ( 837) hydrogen bonds : angle 5.21699 / 6.72 ( 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 : 0.599 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: 0.2121 time to fit residues: 142.2080 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 : 0.630 ------------------------------------------------------------------------------- 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: 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: 8.9990 chunk 91 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 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 = 0.4420 r_free = 0.4420 target = 0.103998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.085501 restraints weight = 205283.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.087459 restraints weight = 135605.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.088800 restraints weight = 98216.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.089879 restraints weight = 76660.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.090552 restraints weight = 62901.242| |-----------------------------------------------------------------------------| r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4943 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 24747 Z= 0.175 Angle : 0.642 11.866 35755 Z= 0.368 Chirality : 0.041 0.304 4065 Planarity : 0.005 0.095 2638 Dihedral : 32.031 177.233 7733 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.69 % Favored : 96.77 % Rotamer: Outliers : 0.48 % Allowed : 3.33 % 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: 0.84 (0.20), residues: 1486 helix: 1.80 (0.15), residues: 1036 sheet: None (None), residues: 0 loop : -2.59 (0.22), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 76 TYR 0.037 0.003 TYR F 88 PHE 0.047 0.003 PHE P 61 HIS 0.017 0.002 HIS K 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.17 (24747) covalent geometry : angle 0.64221 / 0.37 (35755) hydrogen bonds : bond 0.05574 / 6.17 ( 837) hydrogen bonds : angle 3.70149 / 4.85 ( 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 258 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 252 time to evaluate : 0.796 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: A 77 ASP cc_start: 0.7491 (t0) cc_final: 0.7253 (m-30) REVERT: C 78 ILE cc_start: 0.5271 (mt) cc_final: 0.4877 (pt) REVERT: D 56 MET cc_start: 0.7040 (tmm) cc_final: 0.6539 (tpp) REVERT: H 102 GLU cc_start: 0.7061 (mp0) cc_final: 0.6552 (tp30) REVERT: K 74 ILE cc_start: 0.5006 (mt) cc_final: 0.4663 (mt) REVERT: K 125 GLN cc_start: 0.6501 (mt0) cc_final: 0.6226 (pp30) REVERT: M 33 LEU cc_start: 0.4764 (mt) cc_final: 0.4424 (mt) REVERT: N 91 ILE cc_start: 0.6934 (tt) cc_final: 0.6396 (pt) REVERT: O 67 PHE cc_start: 0.5517 (t80) cc_final: 0.5022 (t80) REVERT: O 113 HIS cc_start: 0.3632 (t-90) cc_final: 0.3240 (t-170) REVERT: P 34 ILE cc_start: 0.4382 (mp) cc_final: 0.3990 (mt) REVERT: R 64 ASN cc_start: 0.6171 (m-40) cc_final: 0.5804 (t0) outliers start: 6 outliers final: 4 residues processed: 256 average time/residue: 0.1810 time to fit residues: 70.2854 Evaluate side-chains 155 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 151 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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: 6.9990 chunk 154 optimal weight: 20.0000 chunk 99 optimal weight: 7.9990 chunk 109 optimal weight: 0.9990 chunk 44 optimal weight: 50.0000 chunk 15 optimal weight: 30.0000 chunk 191 optimal weight: 0.6980 chunk 58 optimal weight: 10.0000 chunk 148 optimal weight: 9.9990 chunk 173 optimal weight: 20.0000 chunk 53 optimal weight: 50.0000 overall best weight: 5.3388 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN H 46 HIS H 79 HIS H 81 ASN H 92 GLN K 68 GLN K 85 GLN K 108 ASN L 27 GLN O 85 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.093200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.071701 restraints weight = 233035.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.073297 restraints weight = 165655.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.074463 restraints weight = 128861.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 71)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.075320 restraints weight = 107587.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.075622 restraints weight = 93772.228| |-----------------------------------------------------------------------------| r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5395 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.153 24747 Z= 0.236 Angle : 0.787 12.972 35755 Z= 0.442 Chirality : 0.045 0.236 4065 Planarity : 0.008 0.078 2638 Dihedral : 32.182 178.808 7733 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.77 % Favored : 95.76 % Rotamer: Outliers : 0.55 % Allowed : 6.74 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.20), residues: 1486 helix: 1.12 (0.15), residues: 1058 sheet: None (None), residues: 0 loop : -2.45 (0.23), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG G 42 TYR 0.055 0.004 TYR B 88 PHE 0.044 0.004 PHE N 62 HIS 0.009 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.24 (24747) covalent geometry : angle 0.78718 / 0.44 (35755) hydrogen bonds : bond 0.06175 / 7.19 ( 837) hydrogen bonds : angle 4.29145 / 5.64 ( 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 210 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 203 time to evaluate : 0.648 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: 0.7257 (OUTLIER) cc_final: 0.6924 (tt) REVERT: B 75 HIS cc_start: 0.6575 (t70) cc_final: 0.6255 (t-170) REVERT: C 78 ILE cc_start: 0.5246 (mt) cc_final: 0.4741 (mm) REVERT: G 39 TYR cc_start: 0.6712 (m-10) cc_final: 0.6471 (m-10) REVERT: H 102 GLU cc_start: 0.6981 (mp0) cc_final: 0.6378 (tp30) REVERT: K 68 GLN cc_start: 0.4871 (OUTLIER) cc_final: 0.4355 (mt0) REVERT: L 25 ASN cc_start: 0.2675 (m-40) cc_final: 0.2341 (m-40) REVERT: R 105 LYS cc_start: 0.2995 (mptt) cc_final: 0.2650 (mptt) outliers start: 7 outliers final: 4 residues processed: 208 average time/residue: 0.1885 time to fit residues: 58.6451 Evaluate side-chains 127 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 121 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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: 7.9990 chunk 181 optimal weight: 20.0000 chunk 129 optimal weight: 8.9990 chunk 56 optimal weight: 8.9990 chunk 88 optimal weight: 8.9990 chunk 93 optimal weight: 0.4980 chunk 19 optimal weight: 40.0000 chunk 68 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 10 optimal weight: 50.0000 chunk 136 optimal weight: 0.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS H 79 HIS H 92 GLN K 85 GLN K 93 GLN L 25 ASN ** N 81 ASN ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.091417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.070126 restraints weight = 236081.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.071719 restraints weight = 165837.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.072848 restraints weight = 129114.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.073706 restraints weight = 106813.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.074214 restraints weight = 92689.664| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5425 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 24747 Z= 0.190 Angle : 0.662 10.670 35755 Z= 0.382 Chirality : 0.042 0.205 4065 Planarity : 0.006 0.067 2638 Dihedral : 32.306 178.173 7733 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.40 % Allowed : 2.89 % Favored : 96.70 % Rotamer: Outliers : 0.08 % Allowed : 4.28 % Favored : 95.64 % 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: 0.58 (0.20), residues: 1486 helix: 1.41 (0.15), residues: 1058 sheet: None (None), residues: 0 loop : -2.31 (0.24), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 129 TYR 0.047 0.003 TYR E 54 PHE 0.017 0.002 PHE D 62 HIS 0.020 0.002 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.19 (24747) covalent geometry : angle 0.66172 / 0.38 (35755) hydrogen bonds : bond 0.05260 / 5.91 ( 837) hydrogen bonds : angle 4.03672 / 5.33 ( 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 181 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 0.641 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 97 LEU cc_start: 0.7797 (tt) cc_final: 0.7463 (tt) REVERT: B 100 PHE cc_start: 0.4042 (m-80) cc_final: 0.3378 (m-80) REVERT: C 78 ILE cc_start: 0.4889 (mt) cc_final: 0.4569 (mm) outliers start: 1 outliers final: 1 residues processed: 181 average time/residue: 0.1769 time to fit residues: 49.3751 Evaluate side-chains 125 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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: 6.9990 chunk 58 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 195 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 30 optimal weight: 30.0000 chunk 22 optimal weight: 30.0000 chunk 118 optimal weight: 7.9990 chunk 194 optimal weight: 1.9990 chunk 11 optimal weight: 50.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS H 79 HIS K 85 GLN L 25 ASN ** 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 = 0.4109 r_free = 0.4109 target = 0.087445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.066531 restraints weight = 238734.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.068215 restraints weight = 165315.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.069345 restraints weight = 125862.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.070164 restraints weight = 102876.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.070544 restraints weight = 88687.906| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5253 moved from start: 0.5757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.127 24747 Z= 0.181 Angle : 0.662 11.279 35755 Z= 0.380 Chirality : 0.040 0.237 4065 Planarity : 0.006 0.092 2638 Dihedral : 32.392 178.265 7733 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.90 % Favored : 95.90 % Rotamer: Outliers : 0.08 % Allowed : 4.04 % Favored : 95.88 % 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: 0.66 (0.21), residues: 1486 helix: 1.47 (0.15), residues: 1058 sheet: None (None), residues: 0 loop : -2.28 (0.25), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 129 TYR 0.049 0.003 TYR F 88 PHE 0.042 0.003 PHE P 61 HIS 0.011 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.18 (24747) covalent geometry : angle 0.66161 / 0.38 (35755) hydrogen bonds : bond 0.05136 / 5.94 ( 837) hydrogen bonds : angle 4.04623 / 5.37 ( 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 185 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 0.685 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: C 78 ILE cc_start: 0.4387 (mt) cc_final: 0.3854 (mm) REVERT: F 53 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7565 (mt-10) REVERT: H 56 MET cc_start: 0.7621 (tmm) cc_final: 0.7196 (mmm) REVERT: K 119 ILE cc_start: 0.4905 (pt) cc_final: 0.4367 (mt) outliers start: 1 outliers final: 0 residues processed: 184 average time/residue: 0.1787 time to fit residues: 50.3952 Evaluate side-chains 130 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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: 0.0770 chunk 78 optimal weight: 3.9990 chunk 61 optimal weight: 20.0000 chunk 133 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 33 optimal weight: 30.0000 chunk 167 optimal weight: 9.9990 chunk 35 optimal weight: 30.0000 chunk 194 optimal weight: 8.9990 chunk 13 optimal weight: 40.0000 chunk 87 optimal weight: 8.9990 overall best weight: 4.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 HIS K 85 GLN ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 GLN ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.085959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.065310 restraints weight = 236868.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.066630 restraints weight = 163284.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.067798 restraints weight = 124048.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.068395 restraints weight = 101433.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.069090 restraints weight = 88634.826| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5305 moved from start: 0.6452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 24747 Z= 0.183 Angle : 0.661 10.536 35755 Z= 0.382 Chirality : 0.041 0.286 4065 Planarity : 0.006 0.066 2638 Dihedral : 32.459 179.375 7733 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.37 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % 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: 0.50 (0.21), residues: 1486 helix: 1.31 (0.15), residues: 1060 sheet: None (None), residues: 0 loop : -2.24 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 129 TYR 0.040 0.003 TYR M 50 PHE 0.032 0.003 PHE P 61 HIS 0.024 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.18 (24747) covalent geometry : angle 0.66111 / 0.38 (35755) hydrogen bonds : bond 0.05233 / 5.86 ( 837) hydrogen bonds : angle 4.17505 / 5.53 ( 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 174 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.641 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 84 MET cc_start: 0.7854 (mpp) cc_final: 0.7384 (mmm) REVERT: C 78 ILE cc_start: 0.4173 (mt) cc_final: 0.3658 (mm) REVERT: F 53 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7680 (mt-10) REVERT: H 56 MET cc_start: 0.7667 (tmm) cc_final: 0.7290 (mmm) REVERT: K 119 ILE cc_start: 0.4913 (pt) cc_final: 0.4378 (mt) REVERT: N 59 MET cc_start: 0.8664 (mmp) cc_final: 0.8417 (mmt) REVERT: P 81 VAL cc_start: 0.1070 (t) cc_final: 0.0817 (t) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1776 time to fit residues: 47.6863 Evaluate side-chains 128 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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: 6.9990 chunk 28 optimal weight: 40.0000 chunk 102 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 54 optimal weight: 0.1980 chunk 59 optimal weight: 5.9990 chunk 170 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN E 108 ASN H 79 HIS H 81 ASN H 92 GLN K 85 GLN L 25 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 = 0.4062 r_free = 0.4062 target = 0.084606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.063869 restraints weight = 238478.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.065182 restraints weight = 167121.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.066430 restraints weight = 129007.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.066730 restraints weight = 106683.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.067429 restraints weight = 96574.980| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5528 moved from start: 0.7068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 24747 Z= 0.182 Angle : 0.666 9.915 35755 Z= 0.382 Chirality : 0.041 0.199 4065 Planarity : 0.006 0.049 2638 Dihedral : 32.516 179.320 7733 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.31 % Favored : 95.63 % Rotamer: Outliers : 0.08 % Allowed : 2.54 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.21), residues: 1486 helix: 1.28 (0.15), residues: 1056 sheet: None (None), residues: 0 loop : -2.11 (0.26), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 32 TYR 0.041 0.003 TYR F 88 PHE 0.018 0.002 PHE N 62 HIS 0.010 0.002 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.18 (24747) covalent geometry : angle 0.66571 / 0.38 (35755) hydrogen bonds : bond 0.05219 / 5.98 ( 837) hydrogen bonds : angle 4.22265 / 5.60 ( 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 171 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 170 time to evaluate : 0.635 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: A 49 ARG cc_start: 0.5336 (ttt180) cc_final: 0.5115 (ttt180) REVERT: C 78 ILE cc_start: 0.4254 (mt) cc_final: 0.3772 (mm) REVERT: F 53 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7783 (mm-30) REVERT: H 56 MET cc_start: 0.7753 (tmm) cc_final: 0.7387 (mmm) REVERT: K 119 ILE cc_start: 0.5174 (pt) cc_final: 0.4964 (pt) REVERT: N 36 VAL cc_start: 0.7138 (m) cc_final: 0.6930 (p) REVERT: P 81 VAL cc_start: 0.1095 (t) cc_final: 0.0807 (t) outliers start: 1 outliers final: 1 residues processed: 171 average time/residue: 0.1856 time to fit residues: 48.1614 Evaluate side-chains 126 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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: 0.3980 chunk 174 optimal weight: 20.0000 chunk 78 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 152 optimal weight: 0.9980 chunk 168 optimal weight: 7.9990 chunk 44 optimal weight: 50.0000 chunk 135 optimal weight: 0.0070 chunk 190 optimal weight: 20.0000 chunk 170 optimal weight: 10.0000 chunk 172 optimal weight: 8.9990 overall best weight: 2.0802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS E 85 GLN H 79 HIS K 85 GLN ** M 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 ASN ** 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 = 0.4067 r_free = 0.4067 target = 0.084718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.063760 restraints weight = 238220.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.065215 restraints weight = 166143.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.065989 restraints weight = 127411.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.066992 restraints weight = 106006.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.067485 restraints weight = 91755.557| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5469 moved from start: 0.7231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24747 Z= 0.150 Angle : 0.605 10.010 35755 Z= 0.353 Chirality : 0.038 0.164 4065 Planarity : 0.004 0.041 2638 Dihedral : 32.456 178.726 7733 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.08 % Allowed : 1.11 % Favored : 98.81 % 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: 0.87 (0.21), residues: 1486 helix: 1.57 (0.15), residues: 1062 sheet: None (None), residues: 0 loop : -2.07 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 40 TYR 0.039 0.002 TYR M 50 PHE 0.015 0.002 PHE P 100 HIS 0.004 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.15 (24747) covalent geometry : angle 0.60539 / 0.35 (35755) hydrogen bonds : bond 0.04609 / 5.23 ( 837) hydrogen bonds : angle 3.98434 / 5.29 ( 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 166 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 0.689 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: A 49 ARG cc_start: 0.5344 (ttt180) cc_final: 0.5107 (ttt180) REVERT: B 84 MET cc_start: 0.7851 (mpp) cc_final: 0.7440 (mmm) REVERT: F 53 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7713 (mm-30) REVERT: H 56 MET cc_start: 0.7780 (tmm) cc_final: 0.7377 (mmm) REVERT: K 119 ILE cc_start: 0.4953 (pt) cc_final: 0.4089 (mt) REVERT: L 44 LYS cc_start: 0.6093 (tptt) cc_final: 0.5811 (tppt) REVERT: L 72 TYR cc_start: 0.5288 (m-10) cc_final: 0.5073 (m-80) REVERT: P 81 VAL cc_start: 0.0812 (t) cc_final: 0.0535 (t) outliers start: 1 outliers final: 0 residues processed: 165 average time/residue: 0.1813 time to fit residues: 45.8980 Evaluate side-chains 124 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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: 0.2980 chunk 177 optimal weight: 1.9990 chunk 2 optimal weight: 50.0000 chunk 172 optimal weight: 8.9990 chunk 10 optimal weight: 50.0000 chunk 29 optimal weight: 30.0000 chunk 188 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 143 optimal weight: 30.0000 chunk 18 optimal weight: 40.0000 overall best weight: 10.2592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN G 68 ASN H 79 HIS H 81 ASN K 85 GLN L 25 ASN L 93 GLN ** M 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 ASN O 76 GLN ** P 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.079764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.059016 restraints weight = 247706.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.060412 restraints weight = 176062.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.061279 restraints weight = 136932.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.062096 restraints weight = 113765.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 69)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.062592 restraints weight = 98840.069| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5603 moved from start: 0.8907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 24747 Z= 0.332 Angle : 1.050 28.608 35755 Z= 0.565 Chirality : 0.060 0.671 4065 Planarity : 0.011 0.104 2638 Dihedral : 32.989 178.589 7733 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 25.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.00 % Favored : 92.87 % Rotamer: Outliers : 0.16 % Allowed : 2.30 % Favored : 97.54 % 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: -1.55 (0.19), residues: 1486 helix: -0.34 (0.14), residues: 1056 sheet: None (None), residues: 0 loop : -2.61 (0.26), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.081 0.002 ARG A 42 TYR 0.058 0.005 TYR F 88 PHE 0.048 0.005 PHE O 67 HIS 0.017 0.004 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00669 / 0.33 (24747) covalent geometry : angle 1.05037 / 0.57 (35755) hydrogen bonds : bond 0.07745 / 8.59 ( 837) hydrogen bonds : angle 5.25056 / 7.04 ( 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 156 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 154 time to evaluate : 0.642 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: B 62 LEU cc_start: 0.7010 (mm) cc_final: 0.6783 (mm) REVERT: B 84 MET cc_start: 0.7640 (mpp) cc_final: 0.7420 (mpp) REVERT: C 78 ILE cc_start: 0.3935 (mt) cc_final: 0.3712 (mt) REVERT: G 92 GLU cc_start: 0.6565 (tt0) cc_final: 0.6347 (tt0) REVERT: H 56 MET cc_start: 0.8017 (tmm) cc_final: 0.7687 (tpp) REVERT: K 119 ILE cc_start: 0.4918 (pt) cc_final: 0.4658 (pt) REVERT: L 44 LYS cc_start: 0.6370 (tptt) cc_final: 0.5947 (mmmm) outliers start: 2 outliers final: 1 residues processed: 155 average time/residue: 0.1756 time to fit residues: 42.0665 Evaluate side-chains 114 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.642 ------------------------------------------------------------------------------- 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: 6.9990 chunk 123 optimal weight: 4.9990 chunk 161 optimal weight: 7.9990 chunk 174 optimal weight: 0.9980 chunk 131 optimal weight: 6.9990 chunk 158 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 9 optimal weight: 50.0000 chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 40.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN H 79 HIS K 85 GLN L 93 GLN ** M 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.080790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.059932 restraints weight = 240674.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.061391 restraints weight = 167979.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.062356 restraints weight = 129363.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.063120 restraints weight = 106892.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.063648 restraints weight = 92290.700| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5531 moved from start: 0.8845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 24747 Z= 0.172 Angle : 0.717 28.191 35755 Z= 0.404 Chirality : 0.044 0.208 4065 Planarity : 0.005 0.061 2638 Dihedral : 32.909 179.467 7733 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.16 % Allowed : 0.79 % Favored : 99.05 % 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: -0.32 (0.20), residues: 1486 helix: 0.68 (0.15), residues: 1062 sheet: None (None), residues: 0 loop : -2.51 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 42 TYR 0.039 0.003 TYR F 88 PHE 0.031 0.003 PHE K 67 HIS 0.007 0.001 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.17 (24747) covalent geometry : angle 0.71669 / 0.40 (35755) hydrogen bonds : bond 0.05329 / 5.94 ( 837) hydrogen bonds : angle 4.47287 / 5.94 ( 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 157 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 155 time to evaluate : 0.634 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 49 ARG cc_start: 0.5689 (ttt180) cc_final: 0.5465 (ttt180) REVERT: A 125 GLN cc_start: 0.6964 (mt0) cc_final: 0.6732 (pp30) REVERT: B 62 LEU cc_start: 0.7207 (mm) cc_final: 0.6970 (mm) REVERT: B 84 MET cc_start: 0.7835 (mpp) cc_final: 0.7603 (mmt) REVERT: C 78 ILE cc_start: 0.3728 (mt) cc_final: 0.3470 (mt) REVERT: D 80 TYR cc_start: 0.7255 (m-80) cc_final: 0.6833 (m-10) REVERT: D 99 LEU cc_start: 0.6080 (mm) cc_final: 0.5860 (mp) REVERT: H 56 MET cc_start: 0.8038 (tmm) cc_final: 0.7746 (mmm) REVERT: L 52 GLU cc_start: 0.6305 (mp0) cc_final: 0.5816 (tp30) REVERT: L 72 TYR cc_start: 0.5519 (m-10) cc_final: 0.5286 (m-80) outliers start: 2 outliers final: 0 residues processed: 155 average time/residue: 0.1711 time to fit residues: 41.5495 Evaluate side-chains 120 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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: 10.0000 chunk 119 optimal weight: 20.0000 chunk 11 optimal weight: 50.0000 chunk 18 optimal weight: 40.0000 chunk 117 optimal weight: 9.9990 chunk 182 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 47 optimal weight: 50.0000 chunk 100 optimal weight: 2.9990 chunk 155 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 HIS H 81 ASN K 85 GLN K 93 GLN ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 GLN ** M 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 79 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.079023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.058491 restraints weight = 244630.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.059840 restraints weight = 172488.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.060827 restraints weight = 133218.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.061514 restraints weight = 109546.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.061944 restraints weight = 95185.775| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5608 moved from start: 0.9380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 24747 Z= 0.235 Angle : 0.849 27.034 35755 Z= 0.469 Chirality : 0.049 0.417 4065 Planarity : 0.008 0.078 2638 Dihedral : 32.961 179.964 7733 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.19 % Favored : 93.74 % Rotamer: Outliers : 0.16 % Allowed : 0.87 % Favored : 98.97 % 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: -0.71 (0.20), residues: 1486 helix: 0.36 (0.15), residues: 1058 sheet: None (None), residues: 0 loop : -2.52 (0.26), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 55 TYR 0.089 0.004 TYR F 88 PHE 0.026 0.004 PHE P 61 HIS 0.016 0.003 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.24 (24747) covalent geometry : angle 0.84929 / 0.47 (35755) hydrogen bonds : bond 0.06266 / 6.95 ( 837) hydrogen bonds : angle 4.79619 / 6.40 ( 2446) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5694.38 seconds wall clock time: 98 minutes 29.35 seconds (5909.35 seconds total)