Starting phenix.real_space_refine on Tue Mar 19 03:49:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9c_31815/03_2024/7v9c_31815.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9c_31815/03_2024/7v9c_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_31815/03_2024/7v9c_31815.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9c_31815/03_2024/7v9c_31815.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9c_31815/03_2024/7v9c_31815.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9c_31815/03_2024/7v9c_31815.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 11.66, per 1000 atoms: 0.50 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: 11.05 Conformation dependent library (CDL) restraints added in 2.2 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: 7.86 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: 6.57 Time building geometry restraints manager: 11.76 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: 11026 35.57 - 71.15: 2374 71.15 - 106.72: 148 106.72 - 142.30: 3 142.30 - 177.87: 6 Dihedral angle restraints: 13557 sinusoidal: 9171 harmonic: 4386 Sorted by residual: dihedral pdb=" C4' DC J 177 " pdb=" C3' DC J 177 " pdb=" O3' DC J 177 " pdb=" P DC J 178 " ideal model delta sinusoidal sigma weight residual -140.00 37.87 -177.87 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT J 54 " pdb=" C3' DT J 54 " pdb=" O3' DT J 54 " pdb=" P DA J 55 " ideal model delta sinusoidal sigma weight residual -140.00 37.32 -177.32 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DA J 79 " pdb=" C3' DA J 79 " pdb=" O3' DA J 79 " pdb=" P DA J 80 " ideal model delta sinusoidal sigma weight residual -140.00 36.45 -176.45 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 13554 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3895 0.063 - 0.126: 166 0.126 - 0.189: 1 0.189 - 0.251: 1 0.251 - 0.314: 2 Chirality restraints: 4065 Sorted by residual: chirality pdb=" C3' DT I 70 " pdb=" C4' DT I 70 " pdb=" O3' DT I 70 " pdb=" C2' DT I 70 " both_signs ideal model delta sigma weight residual False -2.66 -2.35 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" C1' DT I 70 " pdb=" O4' DT I 70 " pdb=" C2' DT I 70 " pdb=" N1 DT I 70 " both_signs ideal model delta sigma weight residual False 2.47 2.19 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C3' DT I 71 " pdb=" C4' DT I 71 " pdb=" O3' DT I 71 " pdb=" C2' DT I 71 " both_signs ideal model delta sigma weight residual False -2.66 -2.90 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 4062 not shown) Planarity restraints: 2638 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 9 " -0.028 2.00e-02 2.50e+03 1.16e-02 4.04e+00 pdb=" N9 DG I 9 " 0.024 2.00e-02 2.50e+03 pdb=" C8 DG I 9 " 0.012 2.00e-02 2.50e+03 pdb=" N7 DG I 9 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DG I 9 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DG I 9 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 9 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DG I 9 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 9 " 0.002 2.00e-02 2.50e+03 pdb=" N2 DG I 9 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DG I 9 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DG I 9 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA J 103 " 0.027 2.00e-02 2.50e+03 1.18e-02 3.81e+00 pdb=" N9 DA J 103 " -0.022 2.00e-02 2.50e+03 pdb=" C8 DA J 103 " 0.000 2.00e-02 2.50e+03 pdb=" N7 DA J 103 " -0.010 2.00e-02 2.50e+03 pdb=" C5 DA J 103 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DA J 103 " 0.005 2.00e-02 2.50e+03 pdb=" N6 DA J 103 " 0.011 2.00e-02 2.50e+03 pdb=" N1 DA J 103 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DA J 103 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DA J 103 " -0.007 2.00e-02 2.50e+03 pdb=" C4 DA J 103 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 70 " 0.017 2.00e-02 2.50e+03 1.02e-02 2.62e+00 pdb=" N1 DT I 70 " -0.015 2.00e-02 2.50e+03 pdb=" C2 DT I 70 " -0.000 2.00e-02 2.50e+03 pdb=" O2 DT I 70 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DT I 70 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DT I 70 " 0.002 2.00e-02 2.50e+03 pdb=" O4 DT I 70 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DT I 70 " -0.003 2.00e-02 2.50e+03 pdb=" C7 DT I 70 " 0.013 2.00e-02 2.50e+03 pdb=" C6 DT I 70 " -0.018 2.00e-02 2.50e+03 ... (remaining 2635 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3719 2.77 - 3.30: 20217 3.30 - 3.84: 42132 3.84 - 4.37: 45709 4.37 - 4.90: 70386 Nonbonded interactions: 182163 Sorted by model distance: nonbonded pdb=" OP1 DA J 110 " pdb=" N VAL C 43 " model vdw 2.240 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 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: 3.010 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: 8.430 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 60.810 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3920 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24747 Z= 0.123 Angle : 0.435 8.557 35755 Z= 0.264 Chirality : 0.030 0.314 4065 Planarity : 0.003 0.024 2638 Dihedral : 28.916 177.874 10733 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.94 % Allowed : 4.98 % Favored : 94.08 % Rotamer: Outliers : 1.27 % Allowed : 16.56 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS P 75 PHE 0.001 0.000 PHE R 62 TYR 0.002 0.000 TYR G 50 ARG 0.001 0.000 ARG E 40 *********************** 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 : 1.716 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: 0.7508 (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: 0.6741 (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: 0.6417 (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: 0.2293 (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: 0.4254 time to fit residues: 281.5077 Evaluate side-chains 176 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 172 time to evaluate : 1.692 ------------------------------------------------------------------------------- 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: 4.9990 chunk 83 optimal weight: 0.9990 chunk 51 optimal weight: 20.0000 chunk 101 optimal weight: 0.5980 chunk 80 optimal weight: 0.1980 chunk 155 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 115 optimal weight: 8.9990 chunk 179 optimal weight: 0.0370 overall best weight: 1.3662 ------------------------------------------------------------------------------- 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 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: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4075 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 24747 Z= 0.173 Angle : 0.552 9.398 35755 Z= 0.317 Chirality : 0.032 0.138 4065 Planarity : 0.004 0.071 2638 Dihedral : 31.860 178.840 7733 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.62 % Favored : 97.04 % Rotamer: Outliers : 0.40 % Allowed : 3.80 % Favored : 95.80 % 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: 1.16 (0.21), residues: 1486 helix: 2.02 (0.15), residues: 1048 sheet: None (None), residues: 0 loop : -2.51 (0.23), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 113 PHE 0.038 0.002 PHE P 61 TYR 0.027 0.002 TYR F 88 ARG 0.005 0.001 ARG E 128 *********************** 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 276 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 271 time to evaluate : 1.861 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: B 39 ARG cc_start: 0.6691 (mmt-90) cc_final: 0.6429 (mmt180) REVERT: B 43 VAL cc_start: 0.6240 (t) cc_final: 0.5969 (t) REVERT: B 66 ILE cc_start: 0.8438 (mt) cc_final: 0.8011 (tt) REVERT: C 78 ILE cc_start: 0.5572 (mt) cc_final: 0.5116 (pt) REVERT: D 117 LYS cc_start: 0.6889 (tttm) cc_final: 0.6595 (mttt) REVERT: E 101 VAL cc_start: 0.8070 (t) cc_final: 0.7745 (m) REVERT: E 123 ASP cc_start: 0.7734 (m-30) cc_final: 0.7454 (t0) REVERT: G 64 GLU cc_start: 0.8233 (tp30) cc_final: 0.7827 (tp30) REVERT: H 70 ILE cc_start: 0.7811 (mm) cc_final: 0.7429 (mm) REVERT: H 119 THR cc_start: 0.7584 (m) cc_final: 0.7339 (t) REVERT: K 74 ILE cc_start: 0.3710 (mt) cc_final: 0.2920 (mt) REVERT: L 25 ASN cc_start: 0.3713 (m-40) cc_final: 0.3061 (m-40) REVERT: L 72 TYR cc_start: 0.4301 (m-10) cc_final: 0.3584 (m-80) REVERT: M 31 HIS cc_start: 0.1841 (t-90) cc_final: 0.1545 (t-170) REVERT: M 65 LEU cc_start: 0.6212 (mm) cc_final: 0.5797 (mm) REVERT: M 89 ASN cc_start: 0.4877 (m-40) cc_final: 0.3911 (t0) REVERT: O 67 PHE cc_start: 0.4980 (t80) cc_final: 0.4599 (t80) REVERT: O 109 LEU cc_start: 0.5709 (tt) cc_final: 0.5467 (tt) REVERT: P 34 ILE cc_start: 0.2240 (mp) cc_final: 0.1418 (mt) REVERT: R 64 ASN cc_start: 0.5359 (m-40) cc_final: 0.4775 (t0) REVERT: R 84 SER cc_start: 0.5738 (m) cc_final: 0.5386 (p) outliers start: 5 outliers final: 2 residues processed: 274 average time/residue: 0.3591 time to fit residues: 149.5003 Evaluate side-chains 150 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 148 time to evaluate : 1.790 ------------------------------------------------------------------------------- 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: 0.0670 chunk 55 optimal weight: 9.9990 chunk 149 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 180 optimal weight: 7.9990 chunk 194 optimal weight: 3.9990 chunk 160 optimal weight: 6.9990 chunk 178 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 chunk 144 optimal weight: 4.9990 overall best weight: 1.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 31 HIS C 38 ASN C 68 ASN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS H 79 HIS K 68 GLN K 85 GLN ** O 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 85 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4203 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24747 Z= 0.172 Angle : 0.550 8.193 35755 Z= 0.315 Chirality : 0.032 0.135 4065 Planarity : 0.005 0.112 2638 Dihedral : 31.863 177.125 7733 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.50 % Favored : 96.37 % Rotamer: Outliers : 0.16 % Allowed : 3.88 % Favored : 95.96 % 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: 1.46 (0.21), residues: 1486 helix: 2.13 (0.15), residues: 1050 sheet: None (None), residues: 0 loop : -2.11 (0.24), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS H 46 PHE 0.027 0.002 PHE N 62 TYR 0.044 0.002 TYR F 88 ARG 0.022 0.001 ARG K 129 *********************** 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 229 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 227 time to evaluate : 1.533 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: B 39 ARG cc_start: 0.6682 (mmt-90) cc_final: 0.6247 (mmt-90) REVERT: B 66 ILE cc_start: 0.8582 (mt) cc_final: 0.8011 (tt) REVERT: B 70 VAL cc_start: 0.6957 (t) cc_final: 0.6535 (p) REVERT: C 78 ILE cc_start: 0.5214 (mt) cc_final: 0.4887 (mm) REVERT: D 81 ASN cc_start: 0.6217 (p0) cc_final: 0.5858 (p0) REVERT: E 101 VAL cc_start: 0.8230 (t) cc_final: 0.7994 (m) REVERT: K 74 ILE cc_start: 0.3668 (mt) cc_final: 0.3002 (mt) REVERT: L 72 TYR cc_start: 0.4119 (m-10) cc_final: 0.3796 (m-80) REVERT: M 17 ARG cc_start: 0.1591 (mtt90) cc_final: 0.0638 (mtm-85) REVERT: O 105 GLU cc_start: 0.7087 (tt0) cc_final: 0.6721 (tp30) REVERT: P 87 VAL cc_start: 0.5899 (m) cc_final: 0.5384 (t) REVERT: R 64 ASN cc_start: 0.5457 (m-40) cc_final: 0.4788 (t0) REVERT: R 84 SER cc_start: 0.5967 (m) cc_final: 0.5532 (p) REVERT: R 90 GLU cc_start: 0.5251 (mp0) cc_final: 0.4927 (mt-10) REVERT: R 105 LYS cc_start: 0.3242 (mptt) cc_final: 0.2952 (mmmt) outliers start: 2 outliers final: 0 residues processed: 227 average time/residue: 0.3786 time to fit residues: 127.2850 Evaluate side-chains 153 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.385 ------------------------------------------------------------------------------- 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: 9.9990 chunk 135 optimal weight: 0.1980 chunk 93 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 120 optimal weight: 0.9990 chunk 180 optimal weight: 10.0000 chunk 191 optimal weight: 8.9990 chunk 94 optimal weight: 7.9990 chunk 171 optimal weight: 2.9990 chunk 51 optimal weight: 10.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 38 ASN E 85 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN H 46 HIS H 81 ASN H 92 GLN K 85 GLN N 44 GLN ** O 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 64 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4464 moved from start: 0.7188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 24747 Z= 0.267 Angle : 0.705 8.558 35755 Z= 0.400 Chirality : 0.038 0.185 4065 Planarity : 0.007 0.064 2638 Dihedral : 32.168 178.044 7733 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 19.69 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.10 % Favored : 95.69 % Rotamer: Outliers : 0.16 % Allowed : 5.47 % Favored : 94.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.35 (0.20), residues: 1486 helix: 1.22 (0.15), residues: 1060 sheet: None (None), residues: 0 loop : -2.34 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS B 75 PHE 0.023 0.003 PHE P 100 TYR 0.041 0.003 TYR E 54 ARG 0.014 0.001 ARG N 96 *********************** 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 200 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 198 time to evaluate : 1.557 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: 0.7363 (ttp-170) cc_final: 0.6233 (ptm-80) REVERT: B 59 LYS cc_start: 0.7072 (tttt) cc_final: 0.6783 (tttm) REVERT: B 63 GLU cc_start: 0.7361 (pt0) cc_final: 0.7064 (pp20) REVERT: B 70 VAL cc_start: 0.7335 (t) cc_final: 0.6942 (p) REVERT: D 53 SER cc_start: 0.6506 (p) cc_final: 0.5969 (m) REVERT: E 101 VAL cc_start: 0.8478 (t) cc_final: 0.8204 (m) REVERT: G 50 TYR cc_start: 0.6639 (t80) cc_final: 0.6354 (t80) REVERT: G 64 GLU cc_start: 0.8186 (pt0) cc_final: 0.7909 (tt0) REVERT: G 73 ASN cc_start: 0.5261 (t0) cc_final: 0.5011 (t0) REVERT: H 68 GLU cc_start: 0.6507 (mt-10) cc_final: 0.6260 (mt-10) REVERT: M 17 ARG cc_start: 0.1719 (mtt90) cc_final: -0.0496 (ptp-110) REVERT: O 105 GLU cc_start: 0.7161 (tt0) cc_final: 0.6795 (tp30) REVERT: O 120 MET cc_start: -0.0999 (mmt) cc_final: -0.1311 (mmt) REVERT: R 90 GLU cc_start: 0.4972 (mp0) cc_final: 0.4631 (mt-10) REVERT: R 105 LYS cc_start: 0.3336 (mptt) cc_final: 0.2257 (mmtp) outliers start: 2 outliers final: 2 residues processed: 200 average time/residue: 0.3972 time to fit residues: 118.1464 Evaluate side-chains 130 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 128 time to evaluate : 1.707 ------------------------------------------------------------------------------- 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: 3.9990 chunk 108 optimal weight: 3.9990 chunk 2 optimal weight: 20.0000 chunk 142 optimal weight: 9.9990 chunk 78 optimal weight: 0.0980 chunk 163 optimal weight: 0.6980 chunk 132 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 97 optimal weight: 1.9990 chunk 171 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN K 85 GLN ** O 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 93 GLN 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: 0.4433 moved from start: 0.7553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24747 Z= 0.183 Angle : 0.581 9.904 35755 Z= 0.332 Chirality : 0.033 0.176 4065 Planarity : 0.004 0.050 2638 Dihedral : 32.101 178.645 7733 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.43 % Favored : 96.43 % Rotamer: Outliers : 0.08 % Allowed : 1.82 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.20 (0.21), residues: 1486 helix: 1.86 (0.15), residues: 1056 sheet: None (None), residues: 0 loop : -2.01 (0.25), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 75 PHE 0.014 0.002 PHE B 61 TYR 0.020 0.002 TYR M 50 ARG 0.005 0.001 ARG C 77 *********************** 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 191 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 190 time to evaluate : 1.727 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 49 ARG cc_start: 0.7287 (ttp-170) cc_final: 0.6615 (ttt180) REVERT: B 59 LYS cc_start: 0.6967 (tttt) cc_final: 0.6681 (tttm) REVERT: B 62 LEU cc_start: 0.7245 (mm) cc_final: 0.6906 (mm) REVERT: C 78 ILE cc_start: 0.5285 (mt) cc_final: 0.4416 (mm) REVERT: E 59 GLU cc_start: 0.6167 (pt0) cc_final: 0.5918 (pt0) REVERT: E 101 VAL cc_start: 0.8380 (t) cc_final: 0.8112 (m) REVERT: F 70 VAL cc_start: 0.7411 (m) cc_final: 0.7126 (p) REVERT: H 42 LEU cc_start: 0.7639 (pp) cc_final: 0.7329 (tp) REVERT: H 82 LYS cc_start: 0.6900 (mppt) cc_final: 0.6691 (mtmt) REVERT: L 72 TYR cc_start: 0.3964 (m-10) cc_final: 0.3714 (m-80) REVERT: M 96 LEU cc_start: 0.0991 (tp) cc_final: 0.0787 (tt) REVERT: O 69 ARG cc_start: 0.3644 (mtt-85) cc_final: 0.2761 (tpp-160) REVERT: O 105 GLU cc_start: 0.7048 (tt0) cc_final: 0.6838 (tp30) REVERT: P 84 MET cc_start: 0.3990 (tpp) cc_final: 0.3774 (tpp) REVERT: R 40 LYS cc_start: 0.3238 (mmtm) cc_final: 0.2771 (mmtt) REVERT: R 64 ASN cc_start: 0.5279 (m-40) cc_final: 0.4691 (t0) REVERT: R 90 GLU cc_start: 0.4968 (mp0) cc_final: 0.4759 (mt-10) REVERT: R 105 LYS cc_start: 0.3356 (mptt) cc_final: 0.2581 (mmtp) outliers start: 1 outliers final: 1 residues processed: 191 average time/residue: 0.3714 time to fit residues: 106.0554 Evaluate side-chains 125 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 1.522 ------------------------------------------------------------------------------- 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: 7.9990 chunk 37 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 191 optimal weight: 0.7980 chunk 159 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 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** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN H 81 ASN K 85 GLN ** L 25 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4546 moved from start: 0.8731 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= 0.225 Angle : 0.658 9.431 35755 Z= 0.372 Chirality : 0.036 0.162 4065 Planarity : 0.006 0.070 2638 Dihedral : 32.239 179.886 7733 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.77 % Favored : 96.10 % Rotamer: Outliers : 0.16 % Allowed : 2.61 % Favored : 97.23 % 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: 0.79 (0.21), residues: 1486 helix: 1.51 (0.15), residues: 1060 sheet: None (None), residues: 0 loop : -2.06 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS F 75 PHE 0.032 0.002 PHE O 67 TYR 0.025 0.002 TYR N 37 ARG 0.009 0.001 ARG H 30 *********************** 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 168 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 166 time to evaluate : 1.697 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: A 49 ARG cc_start: 0.7375 (ttp-170) cc_final: 0.6331 (ptm-80) REVERT: A 104 PHE cc_start: 0.6830 (m-10) cc_final: 0.6611 (m-10) REVERT: B 59 LYS cc_start: 0.7031 (tttt) cc_final: 0.6723 (tttm) REVERT: B 63 GLU cc_start: 0.7481 (pt0) cc_final: 0.6993 (pp20) REVERT: C 23 LEU cc_start: 0.6897 (mt) cc_final: 0.6592 (mp) REVERT: C 78 ILE cc_start: 0.5185 (mt) cc_final: 0.4413 (mm) REVERT: E 101 VAL cc_start: 0.8421 (t) cc_final: 0.8155 (m) REVERT: H 42 LEU cc_start: 0.7757 (pp) cc_final: 0.7313 (tp) REVERT: L 49 LEU cc_start: 0.4979 (mt) cc_final: 0.4595 (tp) REVERT: O 69 ARG cc_start: 0.4428 (mtt-85) cc_final: 0.3196 (tpp-160) REVERT: R 67 PHE cc_start: 0.3581 (t80) cc_final: 0.2909 (t80) REVERT: R 90 GLU cc_start: 0.4898 (mp0) cc_final: 0.4433 (mt-10) REVERT: R 103 LEU cc_start: 0.5113 (mm) cc_final: 0.4862 (mt) REVERT: R 105 LYS cc_start: 0.3369 (mptt) cc_final: 0.2475 (mmtp) REVERT: R 115 VAL cc_start: 0.3812 (p) cc_final: 0.3430 (m) outliers start: 2 outliers final: 0 residues processed: 168 average time/residue: 0.3456 time to fit residues: 90.2824 Evaluate side-chains 118 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.859 ------------------------------------------------------------------------------- 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: 20.0000 chunk 21 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 chunk 139 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 161 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 chunk 190 optimal weight: 7.9990 chunk 119 optimal weight: 7.9990 chunk 116 optimal weight: 20.0000 chunk 88 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS C 24 GLN D 44 GLN E 85 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN K 85 GLN K 108 ASN L 27 GLN L 93 GLN ** M 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4684 moved from start: 1.0614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 24747 Z= 0.302 Angle : 0.793 12.491 35755 Z= 0.446 Chirality : 0.043 0.265 4065 Planarity : 0.007 0.064 2638 Dihedral : 32.798 178.305 7733 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 24.21 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.11 % Favored : 94.68 % Rotamer: Outliers : 0.24 % Allowed : 3.88 % 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 (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: -0.28 (0.20), residues: 1486 helix: 0.68 (0.15), residues: 1056 sheet: None (None), residues: 0 loop : -2.34 (0.25), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS F 75 PHE 0.040 0.003 PHE O 104 TYR 0.020 0.003 TYR C 50 ARG 0.021 0.001 ARG M 35 *********************** 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 161 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 158 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ARG cc_start: 0.7504 (ttp-170) cc_final: 0.6538 (ptm-80) REVERT: B 59 LYS cc_start: 0.7046 (tttt) cc_final: 0.6581 (tttm) REVERT: B 63 GLU cc_start: 0.7282 (pt0) cc_final: 0.6939 (pp20) REVERT: B 68 ASP cc_start: 0.6645 (m-30) cc_final: 0.5884 (m-30) REVERT: C 87 ILE cc_start: 0.7842 (mm) cc_final: 0.7626 (mt) REVERT: C 111 ILE cc_start: 0.6192 (mm) cc_final: 0.5943 (mm) REVERT: E 101 VAL cc_start: 0.8405 (t) cc_final: 0.8160 (m) REVERT: G 50 TYR cc_start: 0.6677 (t80) cc_final: 0.6431 (t80) REVERT: G 118 LYS cc_start: 0.7622 (tmtt) cc_final: 0.7337 (ptmt) REVERT: H 42 LEU cc_start: 0.7358 (pp) cc_final: 0.7072 (tp) REVERT: M 20 ARG cc_start: 0.2176 (mpt180) cc_final: 0.1754 (mmt90) REVERT: Q 29 ARG cc_start: 0.2409 (mpt90) cc_final: 0.1757 (mtt90) REVERT: Q 99 ARG cc_start: 0.2253 (mpt-90) cc_final: -0.0673 (mmt180) REVERT: R 56 MET cc_start: 0.5809 (ppp) cc_final: 0.5564 (ppp) REVERT: R 105 LYS cc_start: 0.3904 (mptt) cc_final: 0.3174 (tppt) outliers start: 3 outliers final: 2 residues processed: 159 average time/residue: 0.3513 time to fit residues: 85.1085 Evaluate side-chains 113 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 1.727 ------------------------------------------------------------------------------- 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: 6.9990 chunk 76 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 121 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN E 108 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 GLN K 108 ASN M 31 HIS ** O 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4648 moved from start: 1.0767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 24747 Z= 0.216 Angle : 0.666 20.121 35755 Z= 0.377 Chirality : 0.036 0.188 4065 Planarity : 0.005 0.060 2638 Dihedral : 32.618 179.399 7733 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.90 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.40 (0.21), residues: 1486 helix: 1.24 (0.15), residues: 1054 sheet: None (None), residues: 0 loop : -2.24 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS F 75 PHE 0.012 0.002 PHE R 67 TYR 0.023 0.002 TYR M 50 ARG 0.013 0.001 ARG R 89 *********************** 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 163 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.599 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: A 49 ARG cc_start: 0.7416 (ttp-170) cc_final: 0.6909 (ttt180) REVERT: B 59 LYS cc_start: 0.7073 (tttt) cc_final: 0.6551 (tttm) REVERT: B 62 LEU cc_start: 0.7415 (mm) cc_final: 0.7164 (mm) REVERT: B 63 GLU cc_start: 0.7239 (pt0) cc_final: 0.6960 (pp20) REVERT: B 100 PHE cc_start: 0.6728 (m-80) cc_final: 0.6216 (m-10) REVERT: C 87 ILE cc_start: 0.7941 (mm) cc_final: 0.7692 (mt) REVERT: C 111 ILE cc_start: 0.6015 (mm) cc_final: 0.5738 (mm) REVERT: E 59 GLU cc_start: 0.6221 (pt0) cc_final: 0.5885 (pm20) REVERT: E 101 VAL cc_start: 0.8332 (t) cc_final: 0.8050 (m) REVERT: G 118 LYS cc_start: 0.7656 (tmtt) cc_final: 0.7416 (ptpp) REVERT: H 42 LEU cc_start: 0.7452 (pp) cc_final: 0.7225 (tp) REVERT: H 82 LYS cc_start: 0.7038 (mppt) cc_final: 0.6512 (mtmt) REVERT: P 84 MET cc_start: 0.3677 (tpp) cc_final: 0.3277 (tpp) REVERT: Q 29 ARG cc_start: 0.2510 (mpt90) cc_final: 0.1682 (mtt90) REVERT: Q 99 ARG cc_start: 0.2217 (mpt-90) cc_final: -0.0690 (mmt180) REVERT: R 105 LYS cc_start: 0.4039 (mptt) cc_final: 0.3447 (mmtp) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.3601 time to fit residues: 88.9814 Evaluate side-chains 118 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.699 ------------------------------------------------------------------------------- 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: 4.9990 chunk 182 optimal weight: 20.0000 chunk 166 optimal weight: 0.7980 chunk 177 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 139 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 160 optimal weight: 0.8980 chunk 168 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** 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 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN G 38 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN K 85 GLN L 93 GLN ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4606 moved from start: 1.0865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24747 Z= 0.184 Angle : 0.617 15.105 35755 Z= 0.350 Chirality : 0.034 0.196 4065 Planarity : 0.005 0.059 2638 Dihedral : 32.398 179.901 7733 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.63 % Favored : 96.23 % Rotamer: Outliers : 0.32 % Allowed : 0.48 % Favored : 99.21 % 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: 1.03 (0.22), residues: 1486 helix: 1.69 (0.16), residues: 1058 sheet: None (None), residues: 0 loop : -1.97 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS L 75 PHE 0.026 0.002 PHE P 61 TYR 0.019 0.002 TYR N 34 ARG 0.015 0.001 ARG M 32 *********************** 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 171 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 167 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.7045 (tttt) cc_final: 0.6655 (tttm) REVERT: C 87 ILE cc_start: 0.7921 (mm) cc_final: 0.7718 (mt) REVERT: C 104 GLN cc_start: 0.6689 (tp-100) cc_final: 0.6441 (mm-40) REVERT: C 111 ILE cc_start: 0.6123 (mm) cc_final: 0.5713 (mm) REVERT: E 101 VAL cc_start: 0.8422 (t) cc_final: 0.8092 (m) REVERT: G 64 GLU cc_start: 0.8140 (pt0) cc_final: 0.7887 (tp30) REVERT: G 73 ASN cc_start: 0.5351 (t0) cc_final: 0.5015 (t0) REVERT: G 118 LYS cc_start: 0.7616 (tmtt) cc_final: 0.7309 (ptmt) REVERT: H 42 LEU cc_start: 0.7650 (pp) cc_final: 0.7334 (tp) REVERT: H 82 LYS cc_start: 0.6876 (mppt) cc_final: 0.6484 (mtmt) REVERT: L 49 LEU cc_start: 0.4892 (tp) cc_final: 0.4614 (mt) REVERT: P 84 MET cc_start: 0.3652 (tpp) cc_final: 0.3270 (tpp) REVERT: Q 29 ARG cc_start: 0.2715 (mpt90) cc_final: 0.1857 (mtt90) REVERT: Q 99 ARG cc_start: 0.2153 (mpt-90) cc_final: -0.0742 (mmt180) REVERT: R 105 LYS cc_start: 0.3914 (mptt) cc_final: 0.3388 (mmtp) outliers start: 4 outliers final: 0 residues processed: 169 average time/residue: 0.3554 time to fit residues: 91.7641 Evaluate side-chains 126 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.650 ------------------------------------------------------------------------------- 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: 0.0670 chunk 114 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 197 optimal weight: 20.0000 chunk 181 optimal weight: 10.0000 chunk 157 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 overall best weight: 1.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** 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 ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN K 85 GLN K 108 ASN L 93 GLN ** O 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 24 GLN ** 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: 0.4604 moved from start: 1.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24747 Z= 0.177 Angle : 0.601 15.706 35755 Z= 0.341 Chirality : 0.034 0.168 4065 Planarity : 0.004 0.059 2638 Dihedral : 32.292 179.486 7733 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.57 % Favored : 96.30 % Rotamer: Outliers : 0.16 % Allowed : 0.24 % Favored : 99.60 % 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: 1.20 (0.22), residues: 1486 helix: 1.84 (0.16), residues: 1058 sheet: None (None), residues: 0 loop : -1.99 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS H 106 PHE 0.025 0.002 PHE P 61 TYR 0.026 0.002 TYR E 54 ARG 0.010 0.000 ARG E 49 ********************** 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 158 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 156 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.7077 (tttt) cc_final: 0.6661 (tttm) REVERT: B 63 GLU cc_start: 0.7273 (pt0) cc_final: 0.6905 (pp20) REVERT: C 78 ILE cc_start: 0.5526 (mt) cc_final: 0.5110 (mt) REVERT: C 87 ILE cc_start: 0.7936 (mm) cc_final: 0.7727 (mt) REVERT: C 111 ILE cc_start: 0.6088 (mm) cc_final: 0.5628 (mm) REVERT: E 59 GLU cc_start: 0.6175 (pt0) cc_final: 0.5964 (pm20) REVERT: E 101 VAL cc_start: 0.8407 (t) cc_final: 0.8086 (m) REVERT: G 64 GLU cc_start: 0.8150 (pt0) cc_final: 0.7881 (tp30) REVERT: H 42 LEU cc_start: 0.7506 (pp) cc_final: 0.7254 (tp) REVERT: H 82 LYS cc_start: 0.6888 (mppt) cc_final: 0.6513 (mtmt) REVERT: L 52 GLU cc_start: 0.5908 (mp0) cc_final: 0.5241 (pp20) REVERT: L 72 TYR cc_start: 0.3895 (m-80) cc_final: 0.3432 (m-80) REVERT: P 84 MET cc_start: 0.3441 (tpp) cc_final: 0.3097 (tpp) REVERT: Q 29 ARG cc_start: 0.2715 (mpt90) cc_final: 0.1836 (mtt90) REVERT: R 105 LYS cc_start: 0.3890 (mptt) cc_final: 0.3332 (mmtp) outliers start: 2 outliers final: 0 residues processed: 157 average time/residue: 0.3450 time to fit residues: 85.4604 Evaluate side-chains 118 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.841 ------------------------------------------------------------------------------- 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: 6.9990 chunk 48 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 28 optimal weight: 10.9990 chunk 138 optimal weight: 5.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN E 108 ASN G 38 ASN H 64 ASN H 79 HIS H 81 ASN K 85 GLN L 93 GLN ** O 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3941 r_free = 0.3941 target = 0.079024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.057277 restraints weight = 248751.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.058326 restraints weight = 189635.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.059277 restraints weight = 155270.139| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6182 moved from start: 1.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 24747 Z= 0.269 Angle : 0.734 16.725 35755 Z= 0.412 Chirality : 0.040 0.223 4065 Planarity : 0.006 0.054 2638 Dihedral : 32.607 177.720 7733 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 23.07 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.11 % Favored : 94.62 % Rotamer: Outliers : 0.32 % Allowed : 0.71 % 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 (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: 0.35 (0.21), residues: 1486 helix: 1.15 (0.15), residues: 1050 sheet: None (None), residues: 0 loop : -2.07 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS P 75 PHE 0.016 0.003 PHE D 62 TYR 0.029 0.003 TYR C 50 ARG 0.009 0.001 ARG K 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3874.26 seconds wall clock time: 70 minutes 47.91 seconds (4247.91 seconds total)