Starting phenix.real_space_refine (version: dev) on Fri Feb 24 12:54:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9c_31815/02_2023/7v9c_31815.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9c_31815/02_2023/7v9c_31815.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9c_31815/02_2023/7v9c_31815.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9c_31815/02_2023/7v9c_31815.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9c_31815/02_2023/7v9c_31815.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9c_31815/02_2023/7v9c_31815.pdb" } 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 ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/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: 12.31, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 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: 11.70 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 6.06 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: 6.52 Time building geometry restraints manager: 12.43 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: 99.60 - 106.19: 3397 106.19 - 112.77: 13178 112.77 - 119.36: 6807 119.36 - 125.94: 10558 125.94 - 132.53: 1815 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: 10564 35.57 - 71.15: 2296 71.15 - 106.72: 148 106.72 - 142.30: 3 142.30 - 177.87: 6 Dihedral angle restraints: 13017 sinusoidal: 8631 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 13014 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 2.520 nonbonded pdb=" OP2 DA J 19 " pdb=" OH TYR H 39 " model vdw 2.258 2.440 nonbonded pdb=" NH2 ARG A 63 " pdb=" O GLY B 28 " model vdw 2.259 2.520 nonbonded pdb=" NH2 ARG K 63 " pdb=" O GLY L 28 " model vdw 2.298 2.520 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 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 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. 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: 2.190 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: 9.410 Check model and map are aligned: 0.340 Process input model: 60.300 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.200 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.090 ------------------------------------------------------------------------------- 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 : 0.002 0.041 24747 Z= 0.123 Angle : 0.435 8.557 35755 Z= 0.264 Chirality : 0.030 0.314 4065 Planarity : 0.003 0.024 2638 Dihedral : 28.950 177.874 10193 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 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 *********************** 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 fitting. rotamer outliers: 16 poor density : 455 time to evaluate : 1.684 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 outliers start: 16 outliers final: 3 residues processed: 468 average time/residue: 0.4453 time to fit residues: 294.2209 Evaluate side-chains 158 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 155 time to evaluate : 1.980 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2053 time to fit residues: 3.6235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 20.0000 chunk 150 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 51 optimal weight: 20.0000 chunk 101 optimal weight: 3.9990 chunk 80 optimal weight: 0.0020 chunk 155 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 115 optimal weight: 8.9990 chunk 179 optimal weight: 0.0370 overall best weight: 1.6072 ------------------------------------------------------------------------------- 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 B 93 GLN C 31 HIS C 38 ASN C 84 GLN C 104 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN E 113 HIS G 24 GLN G 31 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN H 44 GLN 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 68 ASN Q 104 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3945 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 24747 Z= 0.174 Angle : 0.559 10.789 35755 Z= 0.319 Chirality : 0.032 0.141 4065 Planarity : 0.004 0.071 2638 Dihedral : 32.294 178.200 7193 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.47 % Allowed : 2.49 % Favored : 97.04 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.21), residues: 1486 helix: 1.94 (0.15), residues: 1048 sheet: None (None), residues: 0 loop : -2.52 (0.23), residues: 438 *********************** 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 266 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 261 time to evaluate : 1.920 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 outliers start: 5 outliers final: 3 residues processed: 264 average time/residue: 0.3651 time to fit residues: 145.6297 Evaluate side-chains 144 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 141 time to evaluate : 1.831 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2356 time to fit residues: 3.3929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 7.9990 chunk 55 optimal weight: 0.9980 chunk 149 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 180 optimal weight: 7.9990 chunk 194 optimal weight: 10.0000 chunk 160 optimal weight: 5.9990 chunk 178 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN C 31 HIS C 68 ASN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS H 81 ASN K 85 GLN L 25 ASN ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 ASN P 64 ASN ** P 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4211 moved from start: 0.5903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 24747 Z= 0.253 Angle : 0.670 9.585 35755 Z= 0.381 Chirality : 0.037 0.161 4065 Planarity : 0.006 0.098 2638 Dihedral : 32.631 178.086 7193 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.90 % Favored : 95.90 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.20), residues: 1486 helix: 1.42 (0.15), residues: 1060 sheet: None (None), residues: 0 loop : -2.46 (0.24), residues: 426 *********************** 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 208 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 203 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 208 average time/residue: 0.3887 time to fit residues: 120.4124 Evaluate side-chains 119 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 117 time to evaluate : 1.782 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1957 time to fit residues: 2.9409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 0.9990 chunk 135 optimal weight: 0.7980 chunk 93 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 120 optimal weight: 6.9990 chunk 180 optimal weight: 7.9990 chunk 191 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 171 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN H 92 GLN K 85 GLN N 44 GLN ** O 76 GLN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4244 moved from start: 0.6917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 24747 Z= 0.207 Angle : 0.603 8.801 35755 Z= 0.345 Chirality : 0.033 0.135 4065 Planarity : 0.005 0.063 2638 Dihedral : 32.700 179.526 7193 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.43 % Favored : 96.43 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.21), residues: 1486 helix: 1.68 (0.15), residues: 1056 sheet: None (None), residues: 0 loop : -2.20 (0.25), residues: 430 *********************** 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 173 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.887 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 outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.4198 time to fit residues: 105.9453 Evaluate side-chains 107 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.456 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 2 optimal weight: 20.0000 chunk 142 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 163 optimal weight: 0.0060 chunk 132 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 97 optimal weight: 1.9990 chunk 171 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 overall best weight: 2.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN H 44 GLN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 GLN ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 GLN M 24 GLN ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4311 moved from start: 0.8066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 24747 Z= 0.208 Angle : 0.612 8.560 35755 Z= 0.349 Chirality : 0.034 0.184 4065 Planarity : 0.005 0.062 2638 Dihedral : 32.818 178.939 7193 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.04 % Favored : 95.83 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.21), residues: 1486 helix: 1.73 (0.15), residues: 1058 sheet: None (None), residues: 0 loop : -2.10 (0.25), residues: 428 *********************** 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 168 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 166 time to evaluate : 1.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 166 average time/residue: 0.3841 time to fit residues: 96.0028 Evaluate side-chains 113 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.816 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 5.9990 chunk 172 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 191 optimal weight: 0.5980 chunk 159 optimal weight: 0.0270 chunk 88 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 overall best weight: 1.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN E 55 GLN E 85 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 GLN K 93 GLN ** L 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 64 ASN ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4291 moved from start: 0.8385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 24747 Z= 0.170 Angle : 0.561 11.277 35755 Z= 0.322 Chirality : 0.032 0.144 4065 Planarity : 0.004 0.046 2638 Dihedral : 32.774 179.925 7193 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.23 % Favored : 96.64 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.22), residues: 1486 helix: 2.06 (0.16), residues: 1058 sheet: None (None), residues: 0 loop : -1.88 (0.27), residues: 428 *********************** 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 165 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 164 time to evaluate : 1.632 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 outliers start: 1 outliers final: 0 residues processed: 165 average time/residue: 0.3414 time to fit residues: 88.5350 Evaluate side-chains 116 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.911 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 109 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 161 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS C 84 GLN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN H 81 ASN K 85 GLN L 64 ASN L 93 GLN M 84 GLN ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4312 moved from start: 0.8903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 24747 Z= 0.174 Angle : 0.570 10.532 35755 Z= 0.326 Chirality : 0.033 0.156 4065 Planarity : 0.004 0.045 2638 Dihedral : 32.680 179.500 7193 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.50 % Favored : 96.37 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.22), residues: 1486 helix: 1.99 (0.15), residues: 1062 sheet: None (None), residues: 0 loop : -1.86 (0.27), residues: 424 *********************** 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 169 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 166 time to evaluate : 2.128 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 outliers start: 3 outliers final: 2 residues processed: 168 average time/residue: 0.3754 time to fit residues: 96.9557 Evaluate side-chains 114 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 112 time to evaluate : 1.849 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2189 time to fit residues: 3.0407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 121 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 150 optimal weight: 5.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN E 108 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN K 85 GLN L 93 GLN M 84 GLN ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 108 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4429 moved from start: 1.0080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 24747 Z= 0.252 Angle : 0.688 9.966 35755 Z= 0.388 Chirality : 0.038 0.215 4065 Planarity : 0.006 0.056 2638 Dihedral : 32.966 179.878 7193 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.85 % Favored : 94.95 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.21), residues: 1486 helix: 1.34 (0.15), residues: 1062 sheet: None (None), residues: 0 loop : -2.03 (0.27), residues: 424 *********************** 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 155 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 153 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 153 average time/residue: 0.3440 time to fit residues: 82.3123 Evaluate side-chains 107 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 106 time to evaluate : 1.765 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2300 time to fit residues: 2.5722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 2.9990 chunk 182 optimal weight: 8.9990 chunk 166 optimal weight: 9.9990 chunk 177 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 139 optimal weight: 5.9990 chunk 54 optimal weight: 20.0000 chunk 160 optimal weight: 5.9990 chunk 168 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 GLN K 93 GLN L 27 GLN L 93 GLN ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 108 ASN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4476 moved from start: 1.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.078 24747 Z= 0.248 Angle : 0.690 11.942 35755 Z= 0.390 Chirality : 0.037 0.236 4065 Planarity : 0.005 0.051 2638 Dihedral : 33.165 179.315 7193 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 19.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.51 % Favored : 95.36 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.21), residues: 1486 helix: 1.26 (0.15), residues: 1052 sheet: None (None), residues: 0 loop : -2.10 (0.26), residues: 434 *********************** 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 165 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 164 time to evaluate : 1.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 164 average time/residue: 0.3657 time to fit residues: 92.9890 Evaluate side-chains 115 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.801 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 0.0870 chunk 114 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 130 optimal weight: 20.0000 chunk 197 optimal weight: 0.9990 chunk 181 optimal weight: 10.0000 chunk 157 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 124 optimal weight: 0.1980 overall best weight: 0.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 GLN K 93 GLN ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 108 ASN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4396 moved from start: 1.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 24747 Z= 0.175 Angle : 0.591 10.241 35755 Z= 0.336 Chirality : 0.033 0.222 4065 Planarity : 0.004 0.062 2638 Dihedral : 32.928 179.099 7193 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.63 % Favored : 96.23 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.21), residues: 1486 helix: 1.82 (0.15), residues: 1058 sheet: None (None), residues: 0 loop : -1.84 (0.28), residues: 428 ********************** 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 164 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 time to evaluate : 1.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 163 average time/residue: 0.3523 time to fit residues: 91.4396 Evaluate side-chains 114 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.814 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 20.0000 chunk 48 optimal weight: 10.0000 chunk 144 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 157 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 161 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 138 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN E 108 ASN G 38 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 HIS ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 GLN L 93 GLN ** M 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 HIS ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 GLN ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.074092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.053768 restraints weight = 253542.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.055032 restraints weight = 183351.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.055813 restraints weight = 143115.627| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5827 moved from start: 1.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.074 24747 Z= 0.337 Angle : 0.828 10.597 35755 Z= 0.460 Chirality : 0.044 0.266 4065 Planarity : 0.007 0.077 2638 Dihedral : 33.376 176.352 7193 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 26.21 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.79 % Favored : 93.88 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.20), residues: 1486 helix: 0.73 (0.15), residues: 1038 sheet: None (None), residues: 0 loop : -2.08 (0.26), residues: 448 =============================================================================== Job complete usr+sys time: 3609.08 seconds wall clock time: 66 minutes 38.53 seconds (3998.53 seconds total)