Starting phenix.real_space_refine on Sun Sep 29 13:22:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9c_31815/09_2024/7v9c_31815.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9c_31815/09_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_31815/09_2024/7v9c_31815.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9c_31815/09_2024/7v9c_31815.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9c_31815/09_2024/7v9c_31815.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9c_31815/09_2024/7v9c_31815.cif" } 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 12.93, per 1000 atoms: 0.56 Number of scatterers: 23228 At special positions: 0 Unit cell: (193.908, 126.984, 145.002, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 545 15.00 O 5404 8.00 N 4353 7.00 C 12898 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.27 Conformation dependent library (CDL) restraints added in 1.8 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: 7.57 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: 6.51 Time building geometry restraints manager: 6.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4231 1.33 - 1.45: 8176 1.45 - 1.57: 11203 1.57 - 1.69: 1089 1.69 - 1.81: 48 Bond restraints: 24747 Sorted by residual: bond pdb=" O3' DG I 69 " pdb=" P DT I 70 " ideal model delta sigma weight residual 1.607 1.648 -0.041 1.50e-02 4.44e+03 7.48e+00 bond pdb=" O3' DA I 72 " pdb=" P DG I 73 " ideal model delta sigma weight residual 1.607 1.637 -0.030 1.50e-02 4.44e+03 3.92e+00 bond pdb=" C3' DT J 54 " pdb=" O3' DT J 54 " ideal model delta sigma weight residual 1.422 1.455 -0.033 3.00e-02 1.11e+03 1.24e+00 bond pdb=" C3' DA I 18 " pdb=" O3' DA I 18 " ideal model delta sigma weight residual 1.422 1.454 -0.032 3.00e-02 1.11e+03 1.12e+00 bond pdb=" C3' DA J 223 " pdb=" O3' DA J 223 " ideal model delta sigma weight residual 1.422 1.450 -0.028 3.00e-02 1.11e+03 8.93e-01 ... (remaining 24742 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 35212 1.71 - 3.42: 518 3.42 - 5.13: 22 5.13 - 6.85: 2 6.85 - 8.56: 1 Bond angle restraints: 35755 Sorted by residual: angle pdb=" C2' DT I 70 " pdb=" C1' DT I 70 " pdb=" N1 DT I 70 " ideal model delta sigma weight residual 113.50 122.06 -8.56 1.50e+00 4.44e-01 3.25e+01 angle pdb=" O3' DT I 71 " pdb=" C3' DT I 71 " pdb=" C2' DT I 71 " ideal model delta sigma weight residual 111.50 105.48 6.02 1.50e+00 4.44e-01 1.61e+01 angle pdb=" C4' DT I 70 " pdb=" C3' DT I 70 " pdb=" O3' DT I 70 " ideal model delta sigma weight residual 110.00 115.61 -5.61 1.50e+00 4.44e-01 1.40e+01 angle pdb=" C4' DT I 71 " pdb=" C3' DT I 71 " pdb=" O3' DT I 71 " ideal model delta sigma weight residual 110.00 105.53 4.47 1.50e+00 4.44e-01 8.88e+00 angle pdb=" C1' DT I 70 " pdb=" N1 DT I 70 " pdb=" C2 DT I 70 " ideal model delta sigma weight residual 119.35 123.51 -4.16 1.50e+00 4.44e-01 7.67e+00 ... (remaining 35750 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.57: 11026 35.57 - 71.15: 2374 71.15 - 106.72: 148 106.72 - 142.30: 3 142.30 - 177.87: 6 Dihedral angle restraints: 13557 sinusoidal: 9171 harmonic: 4386 Sorted by residual: dihedral pdb=" C4' DC J 177 " pdb=" C3' DC J 177 " pdb=" O3' DC J 177 " pdb=" P DC J 178 " ideal model delta sinusoidal sigma weight residual -140.00 37.87 -177.87 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT J 54 " pdb=" C3' DT J 54 " pdb=" O3' DT J 54 " pdb=" P DA J 55 " ideal model delta sinusoidal sigma weight residual -140.00 37.32 -177.32 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DA J 79 " pdb=" C3' DA J 79 " pdb=" O3' DA J 79 " pdb=" P DA J 80 " ideal model delta sinusoidal sigma weight residual -140.00 36.45 -176.45 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 13554 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3895 0.063 - 0.126: 166 0.126 - 0.189: 1 0.189 - 0.251: 1 0.251 - 0.314: 2 Chirality restraints: 4065 Sorted by residual: chirality pdb=" C3' DT I 70 " pdb=" C4' DT I 70 " pdb=" O3' DT I 70 " pdb=" C2' DT I 70 " both_signs ideal model delta sigma weight residual False -2.66 -2.35 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" C1' DT I 70 " pdb=" O4' DT I 70 " pdb=" C2' DT I 70 " pdb=" N1 DT I 70 " both_signs ideal model delta sigma weight residual False 2.47 2.19 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C3' DT I 71 " pdb=" C4' DT I 71 " pdb=" O3' DT I 71 " pdb=" C2' DT I 71 " both_signs ideal model delta sigma weight residual False -2.66 -2.90 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 4062 not shown) Planarity restraints: 2638 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 9 " -0.028 2.00e-02 2.50e+03 1.16e-02 4.04e+00 pdb=" N9 DG I 9 " 0.024 2.00e-02 2.50e+03 pdb=" C8 DG I 9 " 0.012 2.00e-02 2.50e+03 pdb=" N7 DG I 9 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DG I 9 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DG I 9 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 9 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DG I 9 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 9 " 0.002 2.00e-02 2.50e+03 pdb=" N2 DG I 9 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DG I 9 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DG I 9 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA J 103 " 0.027 2.00e-02 2.50e+03 1.18e-02 3.81e+00 pdb=" N9 DA J 103 " -0.022 2.00e-02 2.50e+03 pdb=" C8 DA J 103 " 0.000 2.00e-02 2.50e+03 pdb=" N7 DA J 103 " -0.010 2.00e-02 2.50e+03 pdb=" C5 DA J 103 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DA J 103 " 0.005 2.00e-02 2.50e+03 pdb=" N6 DA J 103 " 0.011 2.00e-02 2.50e+03 pdb=" N1 DA J 103 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DA J 103 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DA J 103 " -0.007 2.00e-02 2.50e+03 pdb=" C4 DA J 103 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 70 " 0.017 2.00e-02 2.50e+03 1.02e-02 2.62e+00 pdb=" N1 DT I 70 " -0.015 2.00e-02 2.50e+03 pdb=" C2 DT I 70 " -0.000 2.00e-02 2.50e+03 pdb=" O2 DT I 70 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DT I 70 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DT I 70 " 0.002 2.00e-02 2.50e+03 pdb=" O4 DT I 70 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DT I 70 " -0.003 2.00e-02 2.50e+03 pdb=" C7 DT I 70 " 0.013 2.00e-02 2.50e+03 pdb=" C6 DT I 70 " -0.018 2.00e-02 2.50e+03 ... (remaining 2635 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3719 2.77 - 3.30: 20217 3.30 - 3.84: 42132 3.84 - 4.37: 45709 4.37 - 4.90: 70386 Nonbonded interactions: 182163 Sorted by model distance: nonbonded pdb=" OP1 DA J 110 " pdb=" N VAL C 43 " model vdw 2.240 3.120 nonbonded pdb=" OP2 DA J 19 " pdb=" OH TYR H 39 " model vdw 2.258 3.040 nonbonded pdb=" NH2 ARG A 63 " pdb=" O GLY B 28 " model vdw 2.259 3.120 nonbonded pdb=" NH2 ARG K 63 " pdb=" O GLY L 28 " model vdw 2.298 3.120 nonbonded pdb=" N2 DG I 194 " pdb=" N3 DC J 81 " model vdw 2.302 2.560 ... (remaining 182158 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 40 through 134) selection = chain 'K' selection = (chain 'O' and resid 40 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' selection = (chain 'L' and resid 25 through 102) selection = chain 'P' } ncs_group { reference = (chain 'C' and resid 16 through 118) selection = (chain 'G' and resid 16 through 118) selection = (chain 'M' and resid 16 through 118) selection = (chain 'Q' and resid 16 through 118) } ncs_group { reference = (chain 'D' and resid 28 through 121) selection = chain 'H' selection = (chain 'N' and resid 28 through 121) selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.930 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 50.090 Find NCS groups from input model: 0.670 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.490 ------------------------------------------------------------------------------- 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 : 1.707 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: 0.4289 time to fit residues: 284.0562 Evaluate side-chains 176 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 172 time to evaluate : 1.714 ------------------------------------------------------------------------------- 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: 7.9990 chunk 83 optimal weight: 0.8980 chunk 51 optimal weight: 20.0000 chunk 101 optimal weight: 2.9990 chunk 80 optimal weight: 20.0000 chunk 155 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 chunk 179 optimal weight: 7.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- 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 38 ASN C 104 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN E 113 HIS F 75 HIS G 31 HIS K 85 GLN K 108 ASN ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 ASN M 104 GLN ** O 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 64 ASN ** P 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 31 HIS ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 104 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4400 moved from start: 0.5691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 24747 Z= 0.327 Angle : 0.833 12.186 35755 Z= 0.469 Chirality : 0.044 0.219 4065 Planarity : 0.008 0.118 2638 Dihedral : 32.361 178.251 7733 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.23 % Favored : 96.57 % Rotamer: Outliers : 0.71 % Allowed : 6.58 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.13 (0.20), residues: 1486 helix: 0.98 (0.15), residues: 1048 sheet: None (None), residues: 0 loop : -2.77 (0.22), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS B 75 PHE 0.036 0.004 PHE D 62 TYR 0.036 0.003 TYR F 88 ARG 0.012 0.001 ARG B 67 *********************** 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 224 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 215 time to evaluate : 1.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ARG cc_start: 0.6380 (mmm-85) cc_final: 0.5440 (tpt-90) REVERT: B 34 ILE cc_start: 0.7646 (mt) cc_final: 0.7357 (mm) REVERT: B 39 ARG cc_start: 0.6832 (mmt-90) cc_final: 0.5928 (mmt-90) REVERT: B 59 LYS cc_start: 0.7007 (tttt) cc_final: 0.6749 (mtpp) REVERT: B 70 VAL cc_start: 0.7358 (t) cc_final: 0.7123 (t) REVERT: C 78 ILE cc_start: 0.5623 (mt) cc_final: 0.5209 (mm) REVERT: D 81 ASN cc_start: 0.6690 (m-40) cc_final: 0.6458 (m-40) REVERT: E 41 TYR cc_start: 0.4722 (OUTLIER) cc_final: 0.3853 (m-80) REVERT: E 59 GLU cc_start: 0.6311 (pt0) cc_final: 0.6092 (pt0) REVERT: G 50 TYR cc_start: 0.6689 (t80) cc_final: 0.6294 (t80) REVERT: G 108 LEU cc_start: 0.6056 (OUTLIER) cc_final: 0.5855 (tt) REVERT: H 68 GLU cc_start: 0.6677 (mt-10) cc_final: 0.6439 (mt-10) REVERT: H 92 GLN cc_start: 0.6472 (tt0) cc_final: 0.6220 (tt0) REVERT: K 74 ILE cc_start: 0.4256 (mt) cc_final: 0.3625 (mt) REVERT: L 25 ASN cc_start: 0.4202 (m-40) cc_final: 0.3985 (m-40) REVERT: M 71 ARG cc_start: 0.5892 (mtm180) cc_final: 0.5219 (mmp80) REVERT: O 105 GLU cc_start: 0.7345 (tt0) cc_final: 0.6714 (tp30) REVERT: O 109 LEU cc_start: 0.5691 (tt) cc_final: 0.5111 (tt) REVERT: R 44 GLN cc_start: 0.2867 (mt0) cc_final: 0.2639 (mt0) outliers start: 9 outliers final: 3 residues processed: 224 average time/residue: 0.3902 time to fit residues: 129.1131 Evaluate side-chains 138 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 133 time to evaluate : 1.671 ------------------------------------------------------------------------------- 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: 0.7980 chunk 55 optimal weight: 6.9990 chunk 149 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 180 optimal weight: 20.0000 chunk 194 optimal weight: 6.9990 chunk 160 optimal weight: 5.9990 chunk 178 optimal weight: 8.9990 chunk 61 optimal weight: 7.9990 chunk 144 optimal weight: 2.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- 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 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN F 27 GLN H 92 GLN ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 HIS ** O 113 HIS ** 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 79 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4492 moved from start: 0.7297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 24747 Z= 0.270 Angle : 0.689 8.486 35755 Z= 0.392 Chirality : 0.038 0.397 4065 Planarity : 0.007 0.141 2638 Dihedral : 32.554 178.797 7733 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.97 % Favored : 95.69 % Rotamer: Outliers : 0.32 % Allowed : 5.47 % Favored : 94.22 % 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: 0.18 (0.20), residues: 1486 helix: 1.18 (0.15), residues: 1050 sheet: None (None), residues: 0 loop : -2.60 (0.23), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS M 31 PHE 0.033 0.004 PHE K 78 TYR 0.032 0.003 TYR D 80 ARG 0.018 0.001 ARG G 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 206 time to evaluate : 2.410 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 34 ILE cc_start: 0.7793 (mt) cc_final: 0.7451 (mm) REVERT: B 39 ARG cc_start: 0.6788 (mmt-90) cc_final: 0.6353 (mmt-90) REVERT: B 59 LYS cc_start: 0.7000 (tttt) cc_final: 0.6492 (mtpp) REVERT: G 73 ASN cc_start: 0.5728 (t0) cc_final: 0.5484 (t0) REVERT: H 42 LEU cc_start: 0.7424 (pp) cc_final: 0.7212 (tp) REVERT: P 87 VAL cc_start: 0.5760 (m) cc_final: 0.4713 (t) REVERT: R 40 LYS cc_start: 0.3569 (mmtm) cc_final: 0.2403 (mttm) REVERT: R 44 GLN cc_start: 0.2869 (mt0) cc_final: 0.2560 (mt0) outliers start: 4 outliers final: 3 residues processed: 209 average time/residue: 0.3729 time to fit residues: 117.3949 Evaluate side-chains 131 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 128 time to evaluate : 1.776 ------------------------------------------------------------------------------- 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: 10.0000 chunk 135 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 19 optimal weight: 10.9990 chunk 85 optimal weight: 9.9990 chunk 120 optimal weight: 0.6980 chunk 180 optimal weight: 10.0000 chunk 191 optimal weight: 8.9990 chunk 94 optimal weight: 7.9990 chunk 171 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 overall best weight: 6.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN D 81 ASN E 85 GLN G 84 GLN H 81 ASN H 106 HIS ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 ASN L 27 GLN M 31 HIS N 44 GLN O 76 GLN ** O 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 31 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4681 moved from start: 0.9837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 24747 Z= 0.347 Angle : 0.856 17.251 35755 Z= 0.478 Chirality : 0.045 0.219 4065 Planarity : 0.008 0.112 2638 Dihedral : 33.019 176.965 7733 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 21.57 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.98 % Favored : 94.75 % Rotamer: Outliers : 0.32 % Allowed : 6.97 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.94 (0.20), residues: 1486 helix: 0.19 (0.14), residues: 1066 sheet: None (None), residues: 0 loop : -2.66 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS R 46 PHE 0.025 0.004 PHE D 62 TYR 0.040 0.003 TYR Q 57 ARG 0.021 0.001 ARG A 42 *********************** 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 163 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 159 time to evaluate : 1.675 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 34 ILE cc_start: 0.7847 (mt) cc_final: 0.7542 (mm) REVERT: D 35 SER cc_start: 0.6275 (p) cc_final: 0.6072 (t) REVERT: G 50 TYR cc_start: 0.6787 (t80) cc_final: 0.6379 (t80) REVERT: H 28 ARG cc_start: 0.2664 (mpt-90) cc_final: 0.2279 (mmt90) REVERT: N 44 GLN cc_start: 0.4958 (mm110) cc_final: 0.4457 (mt0) REVERT: O 61 LEU cc_start: 0.3998 (tt) cc_final: 0.3754 (tp) REVERT: O 92 LEU cc_start: 0.7123 (mt) cc_final: 0.6910 (mt) REVERT: O 120 MET cc_start: -0.0421 (mmt) cc_final: -0.0721 (mmt) REVERT: Q 99 ARG cc_start: 0.1681 (mpt-90) cc_final: -0.0636 (mmt180) REVERT: R 105 LYS cc_start: 0.3493 (mptt) cc_final: 0.2974 (tppt) outliers start: 4 outliers final: 3 residues processed: 162 average time/residue: 0.3644 time to fit residues: 90.9068 Evaluate side-chains 112 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 109 time to evaluate : 1.745 ------------------------------------------------------------------------------- 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: 7.9990 chunk 108 optimal weight: 7.9990 chunk 2 optimal weight: 20.0000 chunk 142 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 163 optimal weight: 0.1980 chunk 132 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 97 optimal weight: 5.9990 chunk 171 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 overall best weight: 4.2388 ------------------------------------------------------------------------------- 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** E 85 GLN G 38 ASN H 106 HIS K 85 GLN L 25 ASN ** O 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4652 moved from start: 1.0157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 24747 Z= 0.250 Angle : 0.705 21.596 35755 Z= 0.396 Chirality : 0.038 0.186 4065 Planarity : 0.006 0.076 2638 Dihedral : 32.886 178.917 7733 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.10 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % 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: -0.09 (0.20), residues: 1486 helix: 0.87 (0.15), residues: 1056 sheet: None (None), residues: 0 loop : -2.42 (0.25), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 75 PHE 0.018 0.002 PHE R 67 TYR 0.025 0.002 TYR H 34 ARG 0.008 0.001 ARG K 63 *********************** 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 169 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 PHE cc_start: 0.6729 (m-10) cc_final: 0.6529 (m-10) REVERT: B 34 ILE cc_start: 0.7830 (mt) cc_final: 0.7458 (mm) REVERT: B 39 ARG cc_start: 0.6816 (mmt-90) cc_final: 0.6528 (mmt-90) REVERT: B 52 GLU cc_start: 0.7570 (mp0) cc_final: 0.7368 (mm-30) REVERT: B 70 VAL cc_start: 0.7444 (t) cc_final: 0.7199 (p) REVERT: C 78 ILE cc_start: 0.5769 (mt) cc_final: 0.5564 (mt) REVERT: C 104 GLN cc_start: 0.6860 (tp-100) cc_final: 0.6524 (mm-40) REVERT: G 50 TYR cc_start: 0.6688 (t80) cc_final: 0.6297 (t80) REVERT: H 82 LYS cc_start: 0.7019 (mppt) cc_final: 0.6733 (mtmt) REVERT: N 44 GLN cc_start: 0.4705 (mm110) cc_final: 0.4349 (mt0) REVERT: P 84 MET cc_start: 0.3733 (tpp) cc_final: 0.3470 (tpp) REVERT: Q 35 ARG cc_start: 0.5323 (mtm110) cc_final: 0.4783 (mpt90) REVERT: Q 99 ARG cc_start: 0.2255 (mpt-90) cc_final: -0.0705 (mmt180) REVERT: R 105 LYS cc_start: 0.3375 (mptt) cc_final: 0.2502 (tppt) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.3773 time to fit residues: 95.7415 Evaluate side-chains 110 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.827 ------------------------------------------------------------------------------- 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: 1.9990 chunk 172 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 191 optimal weight: 9.9990 chunk 159 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 chunk 100 optimal weight: 8.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 HIS K 85 GLN ** K 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 GLN ** O 113 HIS ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4691 moved from start: 1.0916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 24747 Z= 0.251 Angle : 0.712 17.108 35755 Z= 0.400 Chirality : 0.038 0.159 4065 Planarity : 0.006 0.061 2638 Dihedral : 32.839 177.592 7733 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.85 % Favored : 95.02 % Rotamer: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % 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: -0.03 (0.21), residues: 1486 helix: 0.96 (0.15), residues: 1048 sheet: None (None), residues: 0 loop : -2.48 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS O 113 PHE 0.016 0.002 PHE R 67 TYR 0.025 0.002 TYR D 80 ARG 0.006 0.001 ARG A 129 *********************** 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 154 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 ILE cc_start: 0.7851 (mt) cc_final: 0.7435 (mm) REVERT: B 70 VAL cc_start: 0.7452 (t) cc_final: 0.7195 (p) REVERT: C 23 LEU cc_start: 0.7147 (mt) cc_final: 0.6846 (mp) REVERT: G 50 TYR cc_start: 0.6699 (t80) cc_final: 0.6283 (t80) REVERT: G 118 LYS cc_start: 0.7404 (tmtt) cc_final: 0.7060 (ptmt) REVERT: H 82 LYS cc_start: 0.7072 (mppt) cc_final: 0.6628 (mtmt) REVERT: H 92 GLN cc_start: 0.6179 (tt0) cc_final: 0.5915 (tt0) REVERT: Q 29 ARG cc_start: 0.2910 (mpt90) cc_final: 0.1851 (mtt90) REVERT: Q 35 ARG cc_start: 0.5380 (mtm110) cc_final: 0.4772 (mpt90) REVERT: Q 99 ARG cc_start: 0.2140 (mpt-90) cc_final: -0.0692 (mmt180) REVERT: R 103 LEU cc_start: 0.4502 (mm) cc_final: 0.4298 (mt) REVERT: R 105 LYS cc_start: 0.3567 (mptt) cc_final: 0.2583 (tppt) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.3182 time to fit residues: 76.9997 Evaluate side-chains 111 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.626 ------------------------------------------------------------------------------- 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: 10.0000 chunk 21 optimal weight: 10.0000 chunk 109 optimal weight: 0.9990 chunk 139 optimal weight: 8.9990 chunk 108 optimal weight: 7.9990 chunk 161 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 190 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN E 85 GLN G 38 ASN K 85 GLN K 108 ASN L 93 GLN M 31 HIS M 38 ASN ** O 113 HIS ** 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: 0.4643 moved from start: 1.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 24747 Z= 0.194 Angle : 0.630 16.799 35755 Z= 0.357 Chirality : 0.035 0.169 4065 Planarity : 0.005 0.065 2638 Dihedral : 32.697 179.683 7733 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.04 % Favored : 95.90 % Rotamer: Outliers : 0.16 % Allowed : 1.66 % Favored : 98.18 % 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: 0.53 (0.21), residues: 1486 helix: 1.41 (0.15), residues: 1050 sheet: None (None), residues: 0 loop : -2.39 (0.26), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS M 31 PHE 0.026 0.002 PHE K 67 TYR 0.023 0.002 TYR E 54 ARG 0.009 0.001 ARG E 49 *********************** 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 162 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 160 time to evaluate : 1.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 ILE cc_start: 0.7718 (mt) cc_final: 0.7337 (mm) REVERT: B 39 ARG cc_start: 0.6903 (mmt-90) cc_final: 0.6619 (mmt-90) REVERT: B 70 VAL cc_start: 0.7411 (t) cc_final: 0.7187 (p) REVERT: G 38 ASN cc_start: 0.7175 (OUTLIER) cc_final: 0.6972 (t0) REVERT: G 118 LYS cc_start: 0.7489 (tmtt) cc_final: 0.7115 (ptmt) REVERT: H 82 LYS cc_start: 0.7118 (mppt) cc_final: 0.6733 (mtmt) REVERT: P 34 ILE cc_start: -0.0313 (mp) cc_final: -0.1305 (tt) REVERT: Q 29 ARG cc_start: 0.3028 (mpt90) cc_final: 0.2027 (mtt90) REVERT: Q 35 ARG cc_start: 0.5556 (mtm110) cc_final: 0.4899 (ttt180) REVERT: Q 99 ARG cc_start: 0.2145 (mpt-90) cc_final: -0.0723 (mmt180) REVERT: R 103 LEU cc_start: 0.4570 (mm) cc_final: 0.4363 (mt) REVERT: R 105 LYS cc_start: 0.3487 (mptt) cc_final: 0.2473 (tppt) outliers start: 2 outliers final: 0 residues processed: 160 average time/residue: 0.3535 time to fit residues: 88.2892 Evaluate side-chains 117 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 116 time to evaluate : 1.841 ------------------------------------------------------------------------------- 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: 6.9990 chunk 113 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 94 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 150 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN K 85 GLN L 93 GLN M 38 ASN ** O 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 31 HIS ** 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: 0.4754 moved from start: 1.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 24747 Z= 0.274 Angle : 0.749 18.050 35755 Z= 0.420 Chirality : 0.040 0.167 4065 Planarity : 0.006 0.066 2638 Dihedral : 32.848 179.155 7733 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 20.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.05 % Favored : 94.82 % Rotamer: Outliers : 0.08 % Allowed : 1.19 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.06 (0.21), residues: 1486 helix: 0.92 (0.15), residues: 1038 sheet: None (None), residues: 0 loop : -2.37 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS M 31 PHE 0.020 0.003 PHE P 61 TYR 0.026 0.003 TYR E 54 ARG 0.009 0.001 ARG B 36 *********************** 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 146 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 145 time to evaluate : 1.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 ILE cc_start: 0.7846 (mt) cc_final: 0.7415 (mm) REVERT: C 78 ILE cc_start: 0.5801 (mt) cc_final: 0.4987 (mm) REVERT: F 39 ARG cc_start: 0.7135 (mmt-90) cc_final: 0.6858 (mmm-85) REVERT: Q 35 ARG cc_start: 0.5348 (mtm110) cc_final: 0.4942 (mpt180) REVERT: Q 99 ARG cc_start: 0.2207 (mpt-90) cc_final: -0.0731 (mmt180) REVERT: R 105 LYS cc_start: 0.3604 (mptt) cc_final: 0.2782 (tppt) REVERT: R 118 TYR cc_start: 0.1953 (t80) cc_final: 0.1673 (t80) outliers start: 1 outliers final: 0 residues processed: 145 average time/residue: 0.3462 time to fit residues: 78.9941 Evaluate side-chains 104 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.756 ------------------------------------------------------------------------------- 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: 6.9990 chunk 182 optimal weight: 0.7980 chunk 166 optimal weight: 7.9990 chunk 177 optimal weight: 20.0000 chunk 107 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 139 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 160 optimal weight: 5.9990 chunk 168 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN G 38 ASN K 85 GLN K 93 GLN L 93 GLN M 24 GLN M 38 ASN ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 104 GLN ** O 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 31 HIS ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4700 moved from start: 1.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 24747 Z= 0.217 Angle : 0.663 16.864 35755 Z= 0.373 Chirality : 0.036 0.187 4065 Planarity : 0.005 0.107 2638 Dihedral : 32.792 178.319 7733 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.17 % Favored : 95.76 % Rotamer: Outliers : 0.16 % Allowed : 0.48 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.36 (0.21), residues: 1486 helix: 1.23 (0.15), residues: 1052 sheet: None (None), residues: 0 loop : -2.30 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS Q 31 PHE 0.013 0.002 PHE R 67 TYR 0.021 0.002 TYR H 34 ARG 0.006 0.001 ARG B 36 *********************** 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 149 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 147 time to evaluate : 1.644 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 34 ILE cc_start: 0.7702 (mt) cc_final: 0.7317 (mm) REVERT: E 101 VAL cc_start: 0.8319 (t) cc_final: 0.8060 (m) REVERT: F 39 ARG cc_start: 0.7255 (mmt-90) cc_final: 0.6879 (mmt90) REVERT: H 82 LYS cc_start: 0.7019 (mppt) cc_final: 0.6485 (mtmt) REVERT: P 34 ILE cc_start: -0.0163 (mp) cc_final: -0.1295 (tt) REVERT: Q 29 ARG cc_start: 0.3090 (mpt90) cc_final: 0.1750 (mtt90) REVERT: Q 35 ARG cc_start: 0.5677 (mtm110) cc_final: 0.5210 (mtt90) REVERT: Q 99 ARG cc_start: 0.2355 (mpt-90) cc_final: -0.0741 (mmt180) REVERT: R 105 LYS cc_start: 0.3468 (mptt) cc_final: 0.2642 (tppt) outliers start: 2 outliers final: 0 residues processed: 148 average time/residue: 0.3316 time to fit residues: 77.3340 Evaluate side-chains 115 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.650 ------------------------------------------------------------------------------- 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: 7.9990 chunk 114 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 197 optimal weight: 7.9990 chunk 181 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN K 85 GLN L 93 GLN M 38 ASN ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 31 HIS ** 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: 0.4758 moved from start: 1.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 24747 Z= 0.245 Angle : 0.710 17.433 35755 Z= 0.398 Chirality : 0.039 0.301 4065 Planarity : 0.006 0.095 2638 Dihedral : 32.837 179.986 7733 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.25 % Favored : 94.62 % Rotamer: Outliers : 0.08 % Allowed : 0.55 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.22 (0.21), residues: 1486 helix: 1.09 (0.15), residues: 1040 sheet: None (None), residues: 0 loop : -2.15 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS Q 31 PHE 0.039 0.002 PHE P 61 TYR 0.025 0.002 TYR C 50 ARG 0.007 0.001 ARG B 36 ********************** 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 134 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 133 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 ILE cc_start: 0.7786 (mt) cc_final: 0.7367 (mm) REVERT: C 78 ILE cc_start: 0.5483 (mt) cc_final: 0.4673 (mm) REVERT: D 56 MET cc_start: 0.7726 (tpt) cc_final: 0.7465 (tpp) REVERT: F 39 ARG cc_start: 0.7258 (mmt-90) cc_final: 0.6994 (mmm-85) REVERT: Q 35 ARG cc_start: 0.5596 (mtm110) cc_final: 0.5008 (mtt90) REVERT: Q 99 ARG cc_start: 0.2086 (mpt-90) cc_final: -0.0770 (mmt180) REVERT: R 105 LYS cc_start: 0.3489 (mptt) cc_final: 0.2703 (tppt) outliers start: 1 outliers final: 0 residues processed: 134 average time/residue: 0.3277 time to fit residues: 69.6624 Evaluate side-chains 103 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.684 ------------------------------------------------------------------------------- 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: 8.9990 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: 6.9990 chunk 65 optimal weight: 10.0000 chunk 161 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 138 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN K 85 GLN K 93 GLN L 93 GLN ** M 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 31 HIS ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 64 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.073295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.055938 restraints weight = 235398.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.057337 restraints weight = 146055.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.058316 restraints weight = 103367.107| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6037 moved from start: 1.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 24747 Z= 0.297 Angle : 0.799 19.797 35755 Z= 0.445 Chirality : 0.043 0.203 4065 Planarity : 0.007 0.090 2638 Dihedral : 33.117 177.996 7733 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 22.85 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.85 % Favored : 94.82 % Rotamer: Outliers : 0.08 % Allowed : 0.87 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.49 (0.21), residues: 1486 helix: 0.51 (0.15), residues: 1045 sheet: None (None), residues: 0 loop : -2.32 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.019 0.002 HIS M 31 PHE 0.023 0.003 PHE K 78 TYR 0.027 0.003 TYR H 34 ARG 0.009 0.001 ARG A 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3518.48 seconds wall clock time: 64 minutes 14.89 seconds (3854.89 seconds total)