Starting phenix.real_space_refine on Sun Oct 13 21:08:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vfx_43193/10_2024/8vfx_43193.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vfx_43193/10_2024/8vfx_43193.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vfx_43193/10_2024/8vfx_43193.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vfx_43193/10_2024/8vfx_43193.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vfx_43193/10_2024/8vfx_43193.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vfx_43193/10_2024/8vfx_43193.cif" } resolution = 2.65 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= 0.001 sd= 0.024 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 316 5.49 5 S 32 5.16 5 C 9172 2.51 5 N 2922 2.21 5 O 3682 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 16124 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "M" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1777 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain breaks: 1 Chain: "N" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1777 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain breaks: 1 Chain: "I" Number of atoms: 3239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3239 Classifications: {'DNA': 158} Link IDs: {'rna3p': 157} Chain: "J" Number of atoms: 3239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3239 Classifications: {'DNA': 158} Link IDs: {'rna3p': 157} Time building chain proxies: 9.89, per 1000 atoms: 0.61 Number of scatterers: 16124 At special positions: 0 Unit cell: (133.65, 141.075, 128.7, 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 32 16.00 P 316 15.00 O 3682 8.00 N 2922 7.00 C 9172 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS M 42 " - pdb=" SG CYS M 107 " distance=2.03 Simple disulfide: pdb=" SG CYS M 171 " - pdb=" SG CYS M 245 " distance=2.03 Simple disulfide: pdb=" SG CYS N 42 " - pdb=" SG CYS N 107 " distance=2.04 Simple disulfide: pdb=" SG CYS N 171 " - pdb=" SG CYS N 245 " distance=2.03 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: 4.23 Conformation dependent library (CDL) restraints added in 1.2 seconds 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2272 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 22 sheets defined 48.1% alpha, 21.9% beta 158 base pairs and 285 stacking pairs defined. Time for finding SS restraints: 8.54 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.652A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.264A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.640A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.557A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.974A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.678A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.323A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.619A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 102 removed outlier: 4.260A pdb=" N THR M 102 " --> pdb=" O SER M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 179 No H-bonds generated for 'chain 'M' and resid 177 through 179' Processing helix chain 'M' and resid 211 through 214 Processing helix chain 'M' and resid 236 through 240 Processing helix chain 'N' and resid 98 through 102 removed outlier: 3.668A pdb=" N THR N 102 " --> pdb=" O SER N 99 " (cutoff:3.500A) Processing helix chain 'N' and resid 177 through 179 No H-bonds generated for 'chain 'N' and resid 177 through 179' Processing helix chain 'N' and resid 211 through 214 removed outlier: 3.592A pdb=" N LYS N 214 " --> pdb=" O GLU N 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 211 through 214' Processing helix chain 'N' and resid 236 through 240 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.952A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.548A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.466A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.636A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.863A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.170A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'M' and resid 23 through 25 removed outlier: 3.923A pdb=" N ASP M 89 " --> pdb=" O SER M 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 29 through 32 removed outlier: 6.167A pdb=" N MET M 30 " --> pdb=" O GLU M 124 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU M 52 " --> pdb=" O TYR M 68 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TYR M 68 " --> pdb=" O LEU M 52 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP M 54 " --> pdb=" O LEU M 66 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 29 through 32 removed outlier: 6.167A pdb=" N MET M 30 " --> pdb=" O GLU M 124 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR M 116 " --> pdb=" O GLN M 109 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 152 through 155 Processing sheet with id=AB6, first strand: chain 'M' and resid 159 through 161 removed outlier: 6.576A pdb=" N ILE M 183 " --> pdb=" O TYR M 199 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TYR M 199 " --> pdb=" O ILE M 183 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TRP M 185 " --> pdb=" O ILE M 197 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 159 through 161 removed outlier: 4.022A pdb=" N TYR M 258 " --> pdb=" O ARG M 247 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 23 through 25 removed outlier: 3.664A pdb=" N ASP N 89 " --> pdb=" O SER N 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 29 through 32 removed outlier: 3.707A pdb=" N GLU N 124 " --> pdb=" O MET N 30 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU N 52 " --> pdb=" O TYR N 68 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TYR N 68 " --> pdb=" O LEU N 52 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TRP N 54 " --> pdb=" O LEU N 66 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 29 through 32 removed outlier: 3.707A pdb=" N GLU N 124 " --> pdb=" O MET N 30 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 152 through 155 Processing sheet with id=AC3, first strand: chain 'N' and resid 159 through 161 removed outlier: 6.617A pdb=" N ILE N 183 " --> pdb=" O TYR N 199 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N TYR N 199 " --> pdb=" O ILE N 183 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TRP N 185 " --> pdb=" O ILE N 197 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 159 through 161 removed outlier: 4.025A pdb=" N TYR N 258 " --> pdb=" O ARG N 247 " (cutoff:3.500A) 579 hydrogen bonds defined for protein. 1590 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 384 hydrogen bonds 768 hydrogen bond angles 0 basepair planarities 158 basepair parallelities 285 stacking parallelities Total time for adding SS restraints: 7.36 Time building geometry restraints manager: 4.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3477 1.33 - 1.45: 4881 1.45 - 1.57: 8036 1.57 - 1.69: 630 1.69 - 1.81: 52 Bond restraints: 17076 Sorted by residual: bond pdb=" C3' DT J 92 " pdb=" O3' DT J 92 " ideal model delta sigma weight residual 1.422 1.478 -0.056 3.00e-02 1.11e+03 3.45e+00 bond pdb=" N MET M 19 " pdb=" CA MET M 19 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.15e+00 bond pdb=" N LYS H 30 " pdb=" CA LYS H 30 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.09e+00 bond pdb=" C3' DT J 126 " pdb=" O3' DT J 126 " ideal model delta sigma weight residual 1.422 1.475 -0.053 3.00e-02 1.11e+03 3.07e+00 bond pdb=" N LYS B 20 " pdb=" CA LYS B 20 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 ... (remaining 17071 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 22527 1.09 - 2.17: 1411 2.17 - 3.26: 424 3.26 - 4.34: 54 4.34 - 5.43: 12 Bond angle restraints: 24428 Sorted by residual: angle pdb=" C3' DT J 126 " pdb=" O3' DT J 126 " pdb=" P DG J 127 " ideal model delta sigma weight residual 120.20 124.50 -4.30 1.50e+00 4.44e-01 8.22e+00 angle pdb=" C3' DT J 92 " pdb=" O3' DT J 92 " pdb=" P DC J 93 " ideal model delta sigma weight residual 120.20 124.47 -4.27 1.50e+00 4.44e-01 8.12e+00 angle pdb=" C3' DA I 126 " pdb=" C2' DA I 126 " pdb=" C1' DA I 126 " ideal model delta sigma weight residual 101.60 105.75 -4.15 1.50e+00 4.44e-01 7.65e+00 angle pdb=" C2' DC I 162 " pdb=" C1' DC I 162 " pdb=" N1 DC I 162 " ideal model delta sigma weight residual 113.50 117.62 -4.12 1.50e+00 4.44e-01 7.55e+00 angle pdb=" C2' DT I 70 " pdb=" C1' DT I 70 " pdb=" N1 DT I 70 " ideal model delta sigma weight residual 113.50 117.60 -4.10 1.50e+00 4.44e-01 7.48e+00 ... (remaining 24423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.85: 8130 34.85 - 69.71: 1385 69.71 - 104.56: 11 104.56 - 139.41: 0 139.41 - 174.27: 4 Dihedral angle restraints: 9530 sinusoidal: 5984 harmonic: 3546 Sorted by residual: dihedral pdb=" C4' DT J 126 " pdb=" C3' DT J 126 " pdb=" O3' DT J 126 " pdb=" P DG J 127 " ideal model delta sinusoidal sigma weight residual 220.00 45.73 174.27 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT J 92 " pdb=" C3' DT J 92 " pdb=" O3' DT J 92 " pdb=" P DC J 93 " ideal model delta sinusoidal sigma weight residual 220.00 51.47 168.53 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DA J 106 " pdb=" C3' DA J 106 " pdb=" O3' DA J 106 " pdb=" P DT J 107 " ideal model delta sinusoidal sigma weight residual 220.00 53.64 166.36 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 9527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1750 0.032 - 0.064: 674 0.064 - 0.095: 253 0.095 - 0.127: 64 0.127 - 0.159: 11 Chirality restraints: 2752 Sorted by residual: chirality pdb=" C3' DG I 122 " pdb=" C4' DG I 122 " pdb=" O3' DG I 122 " pdb=" C2' DG I 122 " both_signs ideal model delta sigma weight residual False -2.66 -2.50 -0.16 2.00e-01 2.50e+01 6.33e-01 chirality pdb=" CA ILE M 200 " pdb=" N ILE M 200 " pdb=" C ILE M 200 " pdb=" CB ILE M 200 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA VAL M 77 " pdb=" N VAL M 77 " pdb=" C VAL M 77 " pdb=" CB VAL M 77 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.83e-01 ... (remaining 2749 not shown) Planarity restraints: 1988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 132 " 0.024 2.00e-02 2.50e+03 1.13e-02 3.52e+00 pdb=" N9 DA I 132 " -0.026 2.00e-02 2.50e+03 pdb=" C8 DA I 132 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DA I 132 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA I 132 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DA I 132 " 0.003 2.00e-02 2.50e+03 pdb=" N6 DA I 132 " 0.009 2.00e-02 2.50e+03 pdb=" N1 DA I 132 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA I 132 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA I 132 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DA I 132 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 162 " -0.023 2.00e-02 2.50e+03 1.25e-02 3.52e+00 pdb=" N1 DC I 162 " 0.025 2.00e-02 2.50e+03 pdb=" C2 DC I 162 " -0.002 2.00e-02 2.50e+03 pdb=" O2 DC I 162 " 0.008 2.00e-02 2.50e+03 pdb=" N3 DC I 162 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DC I 162 " -0.005 2.00e-02 2.50e+03 pdb=" N4 DC I 162 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DC I 162 " 0.009 2.00e-02 2.50e+03 pdb=" C6 DC I 162 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 89 " -0.024 2.00e-02 2.50e+03 1.18e-02 3.51e+00 pdb=" N1 DT I 89 " 0.026 2.00e-02 2.50e+03 pdb=" C2 DT I 89 " 0.003 2.00e-02 2.50e+03 pdb=" O2 DT I 89 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DT I 89 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DT I 89 " -0.005 2.00e-02 2.50e+03 pdb=" O4 DT I 89 " -0.009 2.00e-02 2.50e+03 pdb=" C5 DT I 89 " -0.002 2.00e-02 2.50e+03 pdb=" C7 DT I 89 " 0.006 2.00e-02 2.50e+03 pdb=" C6 DT I 89 " 0.002 2.00e-02 2.50e+03 ... (remaining 1985 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 161 2.63 - 3.20: 13135 3.20 - 3.77: 28189 3.77 - 4.33: 39477 4.33 - 4.90: 57714 Nonbonded interactions: 138676 Sorted by model distance: nonbonded pdb=" OG SER H 32 " pdb=" OP1 DC I 145 " model vdw 2.067 3.040 nonbonded pdb=" OD2 ASP A 106 " pdb=" NH1 ARG A 131 " model vdw 2.334 3.120 nonbonded pdb=" OE1 GLU G 91 " pdb=" OG SER N 180 " model vdw 2.343 3.040 nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.395 3.040 nonbonded pdb=" NH2 ARG M 80 " pdb=" OD2 ASP M 101 " model vdw 2.395 3.120 ... (remaining 138671 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' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'M' selection = chain 'N' } 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 individual isotropic 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.150 Set scattering table: 0.160 Process input model: 44.010 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 17076 Z= 0.256 Angle : 0.639 5.430 24428 Z= 0.396 Chirality : 0.040 0.159 2752 Planarity : 0.004 0.035 1988 Dihedral : 24.467 174.268 7246 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.39 % Allowed : 1.64 % Favored : 97.98 % 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: 2.04 (0.24), residues: 1198 helix: 2.56 (0.22), residues: 536 sheet: 0.84 (0.33), residues: 248 loop : 0.11 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 259 HIS 0.004 0.001 HIS N 110 PHE 0.006 0.001 PHE E 84 TYR 0.012 0.001 TYR M 199 ARG 0.003 0.000 ARG E 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 247 time to evaluate : 1.283 Fit side-chains REVERT: A 64 LYS cc_start: 0.8102 (mmtm) cc_final: 0.7577 (mtpt) REVERT: B 31 LYS cc_start: 0.8291 (tttt) cc_final: 0.7896 (tttm) REVERT: B 79 LYS cc_start: 0.8354 (mtmm) cc_final: 0.8006 (mtpt) REVERT: C 99 ARG cc_start: 0.8229 (mmm-85) cc_final: 0.7855 (mmm160) REVERT: C 114 VAL cc_start: 0.8971 (t) cc_final: 0.8762 (p) REVERT: D 76 GLU cc_start: 0.8883 (tp30) cc_final: 0.8540 (tp30) REVERT: E 122 LYS cc_start: 0.8484 (pttt) cc_final: 0.8157 (pttt) REVERT: E 129 ARG cc_start: 0.8438 (tpt90) cc_final: 0.8180 (tpt-90) REVERT: F 79 LYS cc_start: 0.8437 (mttt) cc_final: 0.8206 (mtpm) REVERT: F 91 LYS cc_start: 0.8678 (ttpt) cc_final: 0.8390 (tttp) REVERT: G 36 LYS cc_start: 0.8731 (mmtm) cc_final: 0.8439 (mptt) REVERT: G 95 LYS cc_start: 0.8933 (tttm) cc_final: 0.8691 (tptp) REVERT: H 34 LYS cc_start: 0.8421 (mtpp) cc_final: 0.7877 (mttp) REVERT: H 68 ASP cc_start: 0.9090 (t70) cc_final: 0.8192 (t0) REVERT: H 72 ARG cc_start: 0.8657 (mtt180) cc_final: 0.8436 (mtm180) REVERT: H 87 SER cc_start: 0.8756 (m) cc_final: 0.8169 (p) REVERT: H 105 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8378 (mm-30) REVERT: H 116 LYS cc_start: 0.8511 (tttt) cc_final: 0.8306 (tttp) REVERT: H 120 LYS cc_start: 0.8610 (tttm) cc_final: 0.8112 (tttm) REVERT: M 30 MET cc_start: 0.8958 (ptp) cc_final: 0.8391 (ptm) REVERT: M 31 HIS cc_start: 0.8152 (m90) cc_final: 0.6894 (m-70) REVERT: M 33 SER cc_start: 0.8400 (m) cc_final: 0.7958 (p) REVERT: M 36 GLU cc_start: 0.8543 (pt0) cc_final: 0.8310 (pt0) REVERT: M 46 GLN cc_start: 0.7751 (tt0) cc_final: 0.7417 (mt0) REVERT: M 124 GLU cc_start: 0.8129 (pt0) cc_final: 0.7851 (pm20) REVERT: M 154 GLN cc_start: 0.8047 (tp40) cc_final: 0.7783 (mm110) REVERT: M 222 ASP cc_start: 0.8579 (t0) cc_final: 0.7879 (t0) REVERT: M 231 GLU cc_start: 0.8225 (tp30) cc_final: 0.7859 (tp30) REVERT: M 238 GLU cc_start: 0.8356 (pt0) cc_final: 0.7943 (pm20) REVERT: N 19 MET cc_start: 0.7012 (tpp) cc_final: 0.6723 (pmt) REVERT: N 30 MET cc_start: 0.8885 (ptp) cc_final: 0.7916 (ptp) REVERT: N 49 ARG cc_start: 0.7928 (mtm110) cc_final: 0.7504 (mtm-85) REVERT: N 89 ASP cc_start: 0.8334 (m-30) cc_final: 0.7888 (p0) REVERT: N 112 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7542 (mm-30) REVERT: N 152 GLN cc_start: 0.8664 (tt0) cc_final: 0.8237 (tt0) REVERT: N 159 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8412 (mt-10) REVERT: N 191 ARG cc_start: 0.8824 (ttp-170) cc_final: 0.8482 (ttp80) outliers start: 4 outliers final: 1 residues processed: 250 average time/residue: 2.3036 time to fit residues: 615.0062 Evaluate side-chains 174 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 173 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 74 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 76 GLN D 63 ASN F 93 GLN H 63 ASN H 67 ASN N 154 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 17076 Z= 0.317 Angle : 0.606 7.379 24428 Z= 0.355 Chirality : 0.039 0.152 2752 Planarity : 0.004 0.034 1988 Dihedral : 29.359 177.032 4892 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.73 % Allowed : 8.96 % Favored : 89.31 % 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: 2.05 (0.24), residues: 1198 helix: 2.45 (0.22), residues: 548 sheet: 1.05 (0.35), residues: 228 loop : 0.12 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 259 HIS 0.006 0.001 HIS F 75 PHE 0.010 0.002 PHE E 67 TYR 0.014 0.002 TYR M 199 ARG 0.008 0.001 ARG H 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 182 time to evaluate : 1.780 Fit side-chains REVERT: A 64 LYS cc_start: 0.8376 (mmtm) cc_final: 0.7891 (mtmt) REVERT: A 106 ASP cc_start: 0.8702 (m-30) cc_final: 0.8466 (m-30) REVERT: B 24 ASP cc_start: 0.8041 (t0) cc_final: 0.7744 (t0) REVERT: B 79 LYS cc_start: 0.8579 (mtmm) cc_final: 0.8192 (mtpt) REVERT: B 88 TYR cc_start: 0.8528 (m-10) cc_final: 0.8270 (m-80) REVERT: C 56 GLU cc_start: 0.8942 (tt0) cc_final: 0.8731 (tt0) REVERT: C 91 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8431 (tp30) REVERT: C 99 ARG cc_start: 0.8241 (mmm-85) cc_final: 0.7901 (mmm160) REVERT: D 33 ARG cc_start: 0.8452 (ptp-170) cc_final: 0.7957 (ptm-80) REVERT: D 76 GLU cc_start: 0.8896 (tp30) cc_final: 0.8488 (tp30) REVERT: D 95 GLN cc_start: 0.8977 (tt0) cc_final: 0.8729 (tt0) REVERT: E 122 LYS cc_start: 0.8357 (pttt) cc_final: 0.8067 (pttt) REVERT: E 129 ARG cc_start: 0.8476 (tpt90) cc_final: 0.8271 (ttt-90) REVERT: F 79 LYS cc_start: 0.8529 (mttt) cc_final: 0.8274 (mtpm) REVERT: G 36 LYS cc_start: 0.8776 (mmtm) cc_final: 0.8463 (mptt) REVERT: H 34 LYS cc_start: 0.8357 (mtpp) cc_final: 0.7785 (mttp) REVERT: H 36 SER cc_start: 0.8965 (p) cc_final: 0.8614 (p) REVERT: H 68 ASP cc_start: 0.9072 (t70) cc_final: 0.8213 (t0) REVERT: H 71 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7943 (mt-10) REVERT: H 87 SER cc_start: 0.8524 (m) cc_final: 0.8180 (p) REVERT: H 105 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8483 (mm-30) REVERT: H 116 LYS cc_start: 0.8596 (tttt) cc_final: 0.8328 (tttm) REVERT: H 120 LYS cc_start: 0.8385 (tttm) cc_final: 0.8148 (ttmt) REVERT: M 30 MET cc_start: 0.8581 (ptp) cc_final: 0.7512 (ptm) REVERT: M 31 HIS cc_start: 0.8301 (m90) cc_final: 0.7277 (m-70) REVERT: M 33 SER cc_start: 0.8625 (m) cc_final: 0.8299 (p) REVERT: M 46 GLN cc_start: 0.7956 (tt0) cc_final: 0.7464 (mt0) REVERT: M 102 THR cc_start: 0.9338 (OUTLIER) cc_final: 0.9074 (t) REVERT: M 124 GLU cc_start: 0.8290 (pt0) cc_final: 0.7942 (pm20) REVERT: M 221 SER cc_start: 0.9323 (p) cc_final: 0.9084 (m) REVERT: M 222 ASP cc_start: 0.8561 (t0) cc_final: 0.7823 (t0) REVERT: N 19 MET cc_start: 0.7014 (tpp) cc_final: 0.6655 (pmt) REVERT: N 20 ASP cc_start: 0.8928 (m-30) cc_final: 0.8575 (m-30) REVERT: N 49 ARG cc_start: 0.7949 (mtm110) cc_final: 0.7557 (mtm-85) REVERT: N 154 GLN cc_start: 0.8475 (mm-40) cc_final: 0.8187 (mm110) REVERT: N 191 ARG cc_start: 0.8702 (ttp-170) cc_final: 0.8335 (ttp80) REVERT: N 222 ASP cc_start: 0.7899 (t0) cc_final: 0.7661 (t0) outliers start: 18 outliers final: 7 residues processed: 188 average time/residue: 2.1546 time to fit residues: 433.6411 Evaluate side-chains 186 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 176 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain M residue 265 VAL Chi-restraints excluded: chain N residue 22 LYS Chi-restraints excluded: chain N residue 186 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN M 154 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 17076 Z= 0.291 Angle : 0.582 8.564 24428 Z= 0.343 Chirality : 0.037 0.138 2752 Planarity : 0.004 0.038 1988 Dihedral : 29.461 178.424 4892 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.93 % Allowed : 9.92 % Favored : 88.15 % 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: 2.06 (0.24), residues: 1198 helix: 2.47 (0.22), residues: 548 sheet: 1.08 (0.35), residues: 228 loop : 0.08 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 259 HIS 0.005 0.001 HIS F 75 PHE 0.008 0.001 PHE E 67 TYR 0.013 0.001 TYR M 199 ARG 0.007 0.001 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 179 time to evaluate : 1.340 Fit side-chains revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8493 (mmtm) cc_final: 0.8098 (mtmt) REVERT: A 106 ASP cc_start: 0.8636 (m-30) cc_final: 0.8401 (m-30) REVERT: B 79 LYS cc_start: 0.8586 (mtmm) cc_final: 0.8188 (mtpt) REVERT: B 88 TYR cc_start: 0.8534 (m-10) cc_final: 0.8305 (m-80) REVERT: C 56 GLU cc_start: 0.8964 (tt0) cc_final: 0.8753 (tt0) REVERT: C 71 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7915 (mtm-85) REVERT: C 91 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8597 (tt0) REVERT: C 99 ARG cc_start: 0.8255 (mmm-85) cc_final: 0.7929 (mmm160) REVERT: D 33 ARG cc_start: 0.8459 (ptp-170) cc_final: 0.8090 (ptp-170) REVERT: D 76 GLU cc_start: 0.8920 (tp30) cc_final: 0.8448 (tp30) REVERT: D 95 GLN cc_start: 0.8918 (tt0) cc_final: 0.8691 (tt0) REVERT: E 73 GLU cc_start: 0.8686 (tt0) cc_final: 0.8460 (tt0) REVERT: E 122 LYS cc_start: 0.8367 (pttt) cc_final: 0.8084 (pttt) REVERT: E 129 ARG cc_start: 0.8505 (tpt90) cc_final: 0.8209 (tpt-90) REVERT: F 79 LYS cc_start: 0.8580 (mttt) cc_final: 0.8329 (mtpm) REVERT: G 36 LYS cc_start: 0.8871 (mmtm) cc_final: 0.8559 (mptt) REVERT: G 104 GLN cc_start: 0.8659 (mm-40) cc_final: 0.8429 (mm110) REVERT: H 34 LYS cc_start: 0.8345 (mtpp) cc_final: 0.7805 (mttp) REVERT: H 36 SER cc_start: 0.9027 (p) cc_final: 0.8662 (p) REVERT: H 68 ASP cc_start: 0.9047 (t70) cc_final: 0.8187 (t0) REVERT: H 71 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7943 (mt-10) REVERT: H 86 ARG cc_start: 0.8188 (mtp85) cc_final: 0.7972 (mtp85) REVERT: H 87 SER cc_start: 0.8536 (m) cc_final: 0.8179 (p) REVERT: H 105 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8476 (mm-30) REVERT: H 116 LYS cc_start: 0.8507 (tttt) cc_final: 0.8213 (tttp) REVERT: H 120 LYS cc_start: 0.8449 (tttm) cc_final: 0.8178 (ttmt) REVERT: M 30 MET cc_start: 0.8528 (ptp) cc_final: 0.8283 (ptm) REVERT: M 46 GLN cc_start: 0.7940 (tt0) cc_final: 0.7521 (mt0) REVERT: M 102 THR cc_start: 0.9205 (OUTLIER) cc_final: 0.8943 (t) REVERT: M 222 ASP cc_start: 0.8562 (t0) cc_final: 0.7921 (t0) REVERT: N 19 MET cc_start: 0.7162 (tpp) cc_final: 0.6879 (pmt) REVERT: N 49 ARG cc_start: 0.8084 (mtm110) cc_final: 0.7718 (mtm-85) REVERT: N 89 ASP cc_start: 0.8055 (m-30) cc_final: 0.7537 (p0) REVERT: N 154 GLN cc_start: 0.8445 (mm-40) cc_final: 0.8241 (mm110) REVERT: N 191 ARG cc_start: 0.8709 (ttp-170) cc_final: 0.8381 (ttp80) REVERT: N 222 ASP cc_start: 0.7893 (t0) cc_final: 0.7499 (t0) outliers start: 20 outliers final: 7 residues processed: 187 average time/residue: 2.2248 time to fit residues: 445.2251 Evaluate side-chains 187 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 176 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain N residue 22 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 133 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 126 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN G 84 GLN M 31 HIS M 152 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17076 Z= 0.229 Angle : 0.572 10.230 24428 Z= 0.337 Chirality : 0.036 0.136 2752 Planarity : 0.004 0.037 1988 Dihedral : 29.477 178.635 4890 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.02 % Allowed : 10.89 % Favored : 87.09 % 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: 2.17 (0.24), residues: 1198 helix: 2.56 (0.22), residues: 548 sheet: 1.13 (0.35), residues: 228 loop : 0.14 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 259 HIS 0.004 0.001 HIS F 75 PHE 0.009 0.001 PHE E 67 TYR 0.011 0.001 TYR B 51 ARG 0.011 0.001 ARG M 37 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 177 time to evaluate : 1.725 Fit side-chains REVERT: A 64 LYS cc_start: 0.8451 (mmtm) cc_final: 0.8096 (mtmt) REVERT: A 106 ASP cc_start: 0.8586 (m-30) cc_final: 0.8359 (m-30) REVERT: B 24 ASP cc_start: 0.8033 (t0) cc_final: 0.7763 (t0) REVERT: B 79 LYS cc_start: 0.8581 (mtmm) cc_final: 0.8174 (mtpt) REVERT: C 56 GLU cc_start: 0.8908 (tt0) cc_final: 0.8698 (tt0) REVERT: C 71 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7848 (mtm-85) REVERT: C 91 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8556 (tt0) REVERT: C 99 ARG cc_start: 0.8271 (mmm-85) cc_final: 0.7919 (mmm160) REVERT: D 33 ARG cc_start: 0.8483 (ptp-170) cc_final: 0.8121 (ptp-170) REVERT: D 76 GLU cc_start: 0.8921 (tp30) cc_final: 0.8489 (tp30) REVERT: D 95 GLN cc_start: 0.8914 (tt0) cc_final: 0.8685 (tt0) REVERT: E 73 GLU cc_start: 0.8711 (tt0) cc_final: 0.8434 (tt0) REVERT: E 122 LYS cc_start: 0.8356 (pttt) cc_final: 0.8073 (pttt) REVERT: E 129 ARG cc_start: 0.8506 (tpt90) cc_final: 0.8215 (tpt-90) REVERT: F 79 LYS cc_start: 0.8569 (mttt) cc_final: 0.8309 (mtpm) REVERT: G 36 LYS cc_start: 0.8908 (mmtm) cc_final: 0.8584 (mptt) REVERT: H 34 LYS cc_start: 0.8343 (mtpp) cc_final: 0.7800 (mttp) REVERT: H 36 SER cc_start: 0.9012 (p) cc_final: 0.8661 (p) REVERT: H 68 ASP cc_start: 0.9053 (t70) cc_final: 0.8242 (t0) REVERT: H 71 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7936 (mt-10) REVERT: H 87 SER cc_start: 0.8533 (m) cc_final: 0.8183 (p) REVERT: H 105 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8564 (mm-30) REVERT: H 120 LYS cc_start: 0.8406 (tttm) cc_final: 0.8143 (ttmt) REVERT: M 30 MET cc_start: 0.8447 (ptp) cc_final: 0.8172 (ptm) REVERT: M 33 SER cc_start: 0.8598 (m) cc_final: 0.8224 (p) REVERT: M 46 GLN cc_start: 0.7920 (tt0) cc_final: 0.7512 (mt0) REVERT: M 102 THR cc_start: 0.9201 (OUTLIER) cc_final: 0.8935 (t) REVERT: M 222 ASP cc_start: 0.8488 (t0) cc_final: 0.7884 (t0) REVERT: N 19 MET cc_start: 0.7167 (tpp) cc_final: 0.6881 (pmt) REVERT: N 20 ASP cc_start: 0.8909 (m-30) cc_final: 0.8549 (m-30) REVERT: N 49 ARG cc_start: 0.8070 (mtm110) cc_final: 0.7681 (mtm-85) REVERT: N 154 GLN cc_start: 0.8495 (mm-40) cc_final: 0.8189 (mm110) REVERT: N 191 ARG cc_start: 0.8695 (ttp-170) cc_final: 0.8380 (ttp80) REVERT: N 222 ASP cc_start: 0.7926 (t0) cc_final: 0.7476 (OUTLIER) REVERT: N 235 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8354 (mm) outliers start: 21 outliers final: 10 residues processed: 187 average time/residue: 2.1111 time to fit residues: 423.7521 Evaluate side-chains 187 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 173 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 221 SER Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain N residue 22 LYS Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 235 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN E 125 GLN M 152 GLN N 152 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17076 Z= 0.262 Angle : 0.571 9.352 24428 Z= 0.337 Chirality : 0.036 0.131 2752 Planarity : 0.004 0.053 1988 Dihedral : 29.436 178.100 4890 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.83 % Allowed : 11.95 % Favored : 86.22 % 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: 2.18 (0.24), residues: 1198 helix: 2.62 (0.22), residues: 548 sheet: 0.94 (0.34), residues: 240 loop : 0.20 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 259 HIS 0.004 0.001 HIS M 110 PHE 0.009 0.001 PHE E 67 TYR 0.013 0.001 TYR M 199 ARG 0.010 0.001 ARG M 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 182 time to evaluate : 1.410 Fit side-chains REVERT: A 64 LYS cc_start: 0.8490 (mmtm) cc_final: 0.8067 (mtmt) REVERT: B 24 ASP cc_start: 0.8133 (t0) cc_final: 0.7862 (t0) REVERT: B 79 LYS cc_start: 0.8672 (mtmm) cc_final: 0.8178 (mtpt) REVERT: B 88 TYR cc_start: 0.8752 (m-10) cc_final: 0.8484 (m-80) REVERT: C 56 GLU cc_start: 0.8945 (tt0) cc_final: 0.8729 (tt0) REVERT: C 91 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8570 (tt0) REVERT: C 99 ARG cc_start: 0.8189 (mmm-85) cc_final: 0.7823 (mmm160) REVERT: D 33 ARG cc_start: 0.8480 (ptp-170) cc_final: 0.8109 (ptp-170) REVERT: D 76 GLU cc_start: 0.8893 (tp30) cc_final: 0.8455 (tp30) REVERT: D 95 GLN cc_start: 0.8899 (tt0) cc_final: 0.8679 (tt0) REVERT: E 122 LYS cc_start: 0.8360 (pttt) cc_final: 0.8069 (pttt) REVERT: E 129 ARG cc_start: 0.8520 (tpt90) cc_final: 0.8248 (tpt-90) REVERT: F 79 LYS cc_start: 0.8600 (mttt) cc_final: 0.8332 (mtpm) REVERT: G 36 LYS cc_start: 0.8909 (mmtm) cc_final: 0.8594 (mptt) REVERT: H 34 LYS cc_start: 0.8266 (mtpp) cc_final: 0.7726 (mttp) REVERT: H 36 SER cc_start: 0.8985 (p) cc_final: 0.8636 (p) REVERT: H 68 ASP cc_start: 0.9051 (t70) cc_final: 0.8239 (t0) REVERT: H 86 ARG cc_start: 0.8145 (mtp85) cc_final: 0.7916 (mtp85) REVERT: H 87 SER cc_start: 0.8537 (m) cc_final: 0.8205 (p) REVERT: H 105 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8569 (mm-30) REVERT: H 120 LYS cc_start: 0.8452 (tttm) cc_final: 0.8181 (ttmt) REVERT: M 30 MET cc_start: 0.8483 (ptp) cc_final: 0.7870 (ptm) REVERT: M 46 GLN cc_start: 0.7930 (tt0) cc_final: 0.7511 (mt0) REVERT: M 102 THR cc_start: 0.9217 (OUTLIER) cc_final: 0.8946 (t) REVERT: M 222 ASP cc_start: 0.8382 (t0) cc_final: 0.7629 (t0) REVERT: N 19 MET cc_start: 0.7191 (tpp) cc_final: 0.6864 (pmt) REVERT: N 49 ARG cc_start: 0.8274 (mtm110) cc_final: 0.7756 (mtm-85) REVERT: N 89 ASP cc_start: 0.8059 (m-30) cc_final: 0.7511 (p0) REVERT: N 154 GLN cc_start: 0.8491 (mm-40) cc_final: 0.8240 (mm110) REVERT: N 191 ARG cc_start: 0.8704 (ttp-170) cc_final: 0.8438 (ttp80) REVERT: N 192 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.7946 (mt0) REVERT: N 222 ASP cc_start: 0.7992 (t0) cc_final: 0.7503 (t0) outliers start: 19 outliers final: 6 residues processed: 191 average time/residue: 2.0323 time to fit residues: 415.9128 Evaluate side-chains 181 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 172 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 221 SER Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 192 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 27 optimal weight: 0.0070 chunk 82 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 overall best weight: 1.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN E 125 GLN G 73 ASN G 104 GLN N 152 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 17076 Z= 0.293 Angle : 0.586 9.855 24428 Z= 0.343 Chirality : 0.037 0.132 2752 Planarity : 0.004 0.037 1988 Dihedral : 29.546 179.087 4890 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.93 % Allowed : 12.04 % Favored : 86.03 % 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: 2.12 (0.24), residues: 1198 helix: 2.60 (0.22), residues: 544 sheet: 0.92 (0.34), residues: 240 loop : 0.13 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 259 HIS 0.005 0.001 HIS F 75 PHE 0.008 0.001 PHE E 67 TYR 0.012 0.001 TYR M 199 ARG 0.010 0.001 ARG M 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 178 time to evaluate : 1.839 Fit side-chains REVERT: A 64 LYS cc_start: 0.8495 (mmtm) cc_final: 0.8098 (mtmt) REVERT: A 106 ASP cc_start: 0.8615 (m-30) cc_final: 0.8407 (m-30) REVERT: B 79 LYS cc_start: 0.8676 (mtmm) cc_final: 0.8225 (mtpt) REVERT: B 88 TYR cc_start: 0.8532 (m-10) cc_final: 0.8282 (m-80) REVERT: C 56 GLU cc_start: 0.8951 (tt0) cc_final: 0.8710 (tt0) REVERT: C 91 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8575 (tt0) REVERT: C 99 ARG cc_start: 0.8169 (mmm-85) cc_final: 0.7762 (mmm160) REVERT: D 33 ARG cc_start: 0.8369 (ptp-170) cc_final: 0.8026 (ptp-170) REVERT: D 76 GLU cc_start: 0.8900 (tp30) cc_final: 0.8427 (tp30) REVERT: D 95 GLN cc_start: 0.8895 (tt0) cc_final: 0.8685 (tt0) REVERT: E 122 LYS cc_start: 0.8374 (pttt) cc_final: 0.8078 (pttt) REVERT: E 129 ARG cc_start: 0.8526 (tpt90) cc_final: 0.8231 (tpt-90) REVERT: F 79 LYS cc_start: 0.8588 (mttt) cc_final: 0.8312 (mtpm) REVERT: G 36 LYS cc_start: 0.8825 (mmtm) cc_final: 0.8511 (mptt) REVERT: G 91 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7590 (tt0) REVERT: G 104 GLN cc_start: 0.8709 (mm-40) cc_final: 0.8456 (mm110) REVERT: H 34 LYS cc_start: 0.8313 (mtpp) cc_final: 0.7768 (mttp) REVERT: H 36 SER cc_start: 0.9004 (p) cc_final: 0.8651 (p) REVERT: H 68 ASP cc_start: 0.9041 (t70) cc_final: 0.8234 (t0) REVERT: H 87 SER cc_start: 0.8541 (m) cc_final: 0.8186 (p) REVERT: H 120 LYS cc_start: 0.8455 (tttm) cc_final: 0.8182 (ttmt) REVERT: M 31 HIS cc_start: 0.8250 (m-70) cc_final: 0.7662 (m-70) REVERT: M 46 GLN cc_start: 0.7849 (tt0) cc_final: 0.7373 (mt0) REVERT: M 102 THR cc_start: 0.9294 (OUTLIER) cc_final: 0.9049 (t) REVERT: M 222 ASP cc_start: 0.8424 (t0) cc_final: 0.7731 (t0) REVERT: M 230 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.7341 (tmm) REVERT: N 19 MET cc_start: 0.7223 (tpp) cc_final: 0.6877 (pmt) REVERT: N 49 ARG cc_start: 0.8285 (mtm110) cc_final: 0.7758 (mtm-85) REVERT: N 152 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8192 (tt0) REVERT: N 154 GLN cc_start: 0.8518 (mm-40) cc_final: 0.8246 (mm110) REVERT: N 191 ARG cc_start: 0.8687 (ttp-170) cc_final: 0.8376 (ttp80) REVERT: N 222 ASP cc_start: 0.7997 (t0) cc_final: 0.7496 (t0) outliers start: 20 outliers final: 8 residues processed: 190 average time/residue: 2.1820 time to fit residues: 443.3589 Evaluate side-chains 187 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 174 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 221 SER Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 152 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 80 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 79 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN E 125 GLN H 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17076 Z= 0.252 Angle : 0.577 10.694 24428 Z= 0.339 Chirality : 0.036 0.132 2752 Planarity : 0.004 0.048 1988 Dihedral : 29.536 178.776 4890 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.83 % Allowed : 12.91 % Favored : 85.26 % 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: 2.18 (0.24), residues: 1198 helix: 2.65 (0.22), residues: 544 sheet: 0.92 (0.34), residues: 240 loop : 0.16 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 259 HIS 0.004 0.001 HIS F 75 PHE 0.009 0.001 PHE E 67 TYR 0.011 0.001 TYR M 199 ARG 0.011 0.001 ARG M 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 172 time to evaluate : 1.530 Fit side-chains REVERT: A 64 LYS cc_start: 0.8456 (mmtm) cc_final: 0.8077 (mtmt) REVERT: A 106 ASP cc_start: 0.8598 (m-30) cc_final: 0.8392 (m-30) REVERT: B 79 LYS cc_start: 0.8676 (mtmm) cc_final: 0.8220 (mtpt) REVERT: B 88 TYR cc_start: 0.8546 (m-10) cc_final: 0.8268 (m-80) REVERT: C 56 GLU cc_start: 0.8950 (tt0) cc_final: 0.8713 (tt0) REVERT: C 90 ASP cc_start: 0.9026 (t0) cc_final: 0.8765 (t70) REVERT: C 91 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8591 (tt0) REVERT: C 99 ARG cc_start: 0.8180 (mmm-85) cc_final: 0.7750 (mmm160) REVERT: D 76 GLU cc_start: 0.8898 (tp30) cc_final: 0.8469 (tp30) REVERT: D 95 GLN cc_start: 0.8892 (tt0) cc_final: 0.8683 (tt0) REVERT: E 122 LYS cc_start: 0.8362 (pttt) cc_final: 0.8069 (pttt) REVERT: E 129 ARG cc_start: 0.8521 (tpt90) cc_final: 0.8242 (tpt-90) REVERT: F 79 LYS cc_start: 0.8587 (mttt) cc_final: 0.8309 (mtpm) REVERT: G 36 LYS cc_start: 0.8902 (mmtm) cc_final: 0.8596 (mptt) REVERT: G 91 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7586 (tt0) REVERT: H 34 LYS cc_start: 0.8266 (mtpp) cc_final: 0.7730 (mttp) REVERT: H 36 SER cc_start: 0.8947 (p) cc_final: 0.8636 (p) REVERT: H 68 ASP cc_start: 0.9043 (t70) cc_final: 0.8232 (t0) REVERT: H 87 SER cc_start: 0.8577 (m) cc_final: 0.8219 (p) REVERT: H 120 LYS cc_start: 0.8457 (tttm) cc_final: 0.8224 (ttmt) REVERT: M 31 HIS cc_start: 0.8225 (m-70) cc_final: 0.7628 (m-70) REVERT: M 46 GLN cc_start: 0.7835 (tt0) cc_final: 0.7368 (mt0) REVERT: M 102 THR cc_start: 0.9302 (OUTLIER) cc_final: 0.9057 (t) REVERT: M 222 ASP cc_start: 0.8414 (t0) cc_final: 0.7715 (t0) REVERT: M 230 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.7319 (tmm) REVERT: N 19 MET cc_start: 0.7229 (tpp) cc_final: 0.6877 (pmt) REVERT: N 49 ARG cc_start: 0.8280 (mtm110) cc_final: 0.7754 (mtm-85) REVERT: N 154 GLN cc_start: 0.8504 (mm-40) cc_final: 0.8234 (mm110) REVERT: N 191 ARG cc_start: 0.8686 (ttp-170) cc_final: 0.8442 (ttp80) REVERT: N 192 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.7949 (mt0) REVERT: N 222 ASP cc_start: 0.7998 (t0) cc_final: 0.7483 (t0) outliers start: 19 outliers final: 12 residues processed: 179 average time/residue: 2.1565 time to fit residues: 413.4189 Evaluate side-chains 186 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 169 time to evaluate : 2.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 152 GLN Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 221 SER Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 192 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 95 optimal weight: 0.0270 chunk 69 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN E 125 GLN G 73 ASN N 152 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17076 Z= 0.217 Angle : 0.576 12.491 24428 Z= 0.337 Chirality : 0.035 0.132 2752 Planarity : 0.004 0.069 1988 Dihedral : 29.536 178.760 4890 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.50 % Allowed : 12.52 % Favored : 84.97 % 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: 2.23 (0.24), residues: 1198 helix: 2.70 (0.22), residues: 544 sheet: 0.93 (0.34), residues: 240 loop : 0.21 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 259 HIS 0.004 0.001 HIS F 75 PHE 0.010 0.001 PHE E 67 TYR 0.010 0.001 TYR N 244 ARG 0.014 0.001 ARG M 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 173 time to evaluate : 1.837 Fit side-chains REVERT: A 64 LYS cc_start: 0.8452 (mmtm) cc_final: 0.8075 (mtmt) REVERT: B 79 LYS cc_start: 0.8646 (mtmm) cc_final: 0.8200 (mtpt) REVERT: B 88 TYR cc_start: 0.8546 (m-10) cc_final: 0.8269 (m-80) REVERT: C 56 GLU cc_start: 0.8948 (tt0) cc_final: 0.8700 (tt0) REVERT: C 90 ASP cc_start: 0.9022 (t0) cc_final: 0.8768 (t70) REVERT: C 91 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8595 (tt0) REVERT: C 99 ARG cc_start: 0.8164 (mmm-85) cc_final: 0.7755 (mmm160) REVERT: D 76 GLU cc_start: 0.8925 (tp30) cc_final: 0.8488 (tp30) REVERT: D 95 GLN cc_start: 0.8887 (tt0) cc_final: 0.8678 (tt0) REVERT: E 122 LYS cc_start: 0.8355 (pttt) cc_final: 0.8067 (pttt) REVERT: E 129 ARG cc_start: 0.8519 (tpt90) cc_final: 0.8241 (tpt-90) REVERT: F 79 LYS cc_start: 0.8585 (mttt) cc_final: 0.8306 (mtpm) REVERT: G 36 LYS cc_start: 0.8902 (mmtm) cc_final: 0.8597 (mptt) REVERT: G 91 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7579 (tt0) REVERT: H 34 LYS cc_start: 0.8266 (mtpp) cc_final: 0.7729 (mttp) REVERT: H 36 SER cc_start: 0.8941 (p) cc_final: 0.8622 (p) REVERT: H 68 ASP cc_start: 0.9040 (t70) cc_final: 0.8201 (t0) REVERT: H 87 SER cc_start: 0.8577 (m) cc_final: 0.8222 (p) REVERT: H 120 LYS cc_start: 0.8474 (tttm) cc_final: 0.8250 (ttmt) REVERT: M 31 HIS cc_start: 0.8224 (m-70) cc_final: 0.7621 (m-70) REVERT: M 46 GLN cc_start: 0.7826 (tt0) cc_final: 0.7360 (mt0) REVERT: M 102 THR cc_start: 0.9300 (OUTLIER) cc_final: 0.9057 (t) REVERT: M 222 ASP cc_start: 0.8410 (t0) cc_final: 0.7707 (t0) REVERT: M 230 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.7312 (tmm) REVERT: N 19 MET cc_start: 0.7230 (tpp) cc_final: 0.6876 (pmt) REVERT: N 37 ARG cc_start: 0.8444 (ttm-80) cc_final: 0.7534 (ttm-80) REVERT: N 49 ARG cc_start: 0.8275 (mtm110) cc_final: 0.7743 (mtm-85) REVERT: N 95 ASN cc_start: 0.9097 (OUTLIER) cc_final: 0.7892 (m-40) REVERT: N 154 GLN cc_start: 0.8503 (mm-40) cc_final: 0.8255 (mm110) REVERT: N 191 ARG cc_start: 0.8685 (ttp-170) cc_final: 0.8444 (ttp80) REVERT: N 192 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.7956 (mt0) REVERT: N 222 ASP cc_start: 0.8018 (t0) cc_final: 0.7568 (t0) outliers start: 26 outliers final: 11 residues processed: 184 average time/residue: 2.1074 time to fit residues: 416.6698 Evaluate side-chains 188 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 171 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 152 GLN Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain M residue 221 SER Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 95 ASN Chi-restraints excluded: chain N residue 192 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN E 125 GLN F 93 GLN G 104 GLN N 31 HIS N 57 GLN N 152 GLN N 188 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 17076 Z= 0.411 Angle : 0.631 11.584 24428 Z= 0.366 Chirality : 0.040 0.139 2752 Planarity : 0.005 0.045 1988 Dihedral : 29.831 179.694 4890 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.02 % Allowed : 13.10 % Favored : 84.87 % 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: 1.92 (0.24), residues: 1198 helix: 2.43 (0.22), residues: 544 sheet: 0.84 (0.34), residues: 240 loop : 0.01 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 259 HIS 0.007 0.001 HIS M 110 PHE 0.011 0.002 PHE M 117 TYR 0.016 0.002 TYR H 37 ARG 0.013 0.001 ARG M 191 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 178 time to evaluate : 1.346 Fit side-chains REVERT: A 64 LYS cc_start: 0.8534 (mmtm) cc_final: 0.8095 (mtmt) REVERT: B 79 LYS cc_start: 0.8632 (mtmm) cc_final: 0.8113 (mtpt) REVERT: C 56 GLU cc_start: 0.8937 (tt0) cc_final: 0.8710 (tt0) REVERT: C 91 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8568 (tt0) REVERT: C 99 ARG cc_start: 0.8216 (mmm-85) cc_final: 0.7848 (mmm160) REVERT: D 33 ARG cc_start: 0.8285 (ptp-170) cc_final: 0.8000 (ptp-170) REVERT: D 95 GLN cc_start: 0.8896 (tt0) cc_final: 0.8686 (tt0) REVERT: E 122 LYS cc_start: 0.8400 (pttt) cc_final: 0.8094 (pttt) REVERT: E 129 ARG cc_start: 0.8552 (tpt90) cc_final: 0.8241 (tpt-90) REVERT: F 79 LYS cc_start: 0.8609 (mttt) cc_final: 0.8320 (mtpm) REVERT: G 36 LYS cc_start: 0.8827 (mmtm) cc_final: 0.8523 (mptt) REVERT: G 91 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7618 (tt0) REVERT: G 104 GLN cc_start: 0.8794 (mm-40) cc_final: 0.8571 (mm110) REVERT: H 34 LYS cc_start: 0.8339 (mtpp) cc_final: 0.7786 (mttp) REVERT: H 36 SER cc_start: 0.9021 (p) cc_final: 0.8683 (p) REVERT: H 68 ASP cc_start: 0.9028 (t70) cc_final: 0.8214 (t0) REVERT: H 86 ARG cc_start: 0.8216 (mtp85) cc_final: 0.7958 (mtp85) REVERT: H 105 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8469 (mm-30) REVERT: H 120 LYS cc_start: 0.8393 (tttm) cc_final: 0.8107 (ttmt) REVERT: M 46 GLN cc_start: 0.8009 (tt0) cc_final: 0.7553 (mt0) REVERT: M 102 THR cc_start: 0.9329 (OUTLIER) cc_final: 0.9061 (t) REVERT: M 222 ASP cc_start: 0.8433 (t0) cc_final: 0.7853 (t0) REVERT: M 230 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.7390 (tmm) REVERT: N 19 MET cc_start: 0.7277 (tpp) cc_final: 0.6896 (pmt) REVERT: N 49 ARG cc_start: 0.8364 (mtm110) cc_final: 0.7786 (mtm-85) REVERT: N 100 ASP cc_start: 0.8684 (t0) cc_final: 0.8459 (t0) REVERT: N 154 GLN cc_start: 0.8548 (mm-40) cc_final: 0.8273 (mm110) REVERT: N 192 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8032 (mm-40) REVERT: N 222 ASP cc_start: 0.8031 (t0) cc_final: 0.7498 (t0) outliers start: 21 outliers final: 12 residues processed: 186 average time/residue: 2.1649 time to fit residues: 431.0728 Evaluate side-chains 189 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 172 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain M residue 221 SER Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 192 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 65 optimal weight: 0.1980 chunk 96 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 GLN G 73 ASN N 31 HIS N 152 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17076 Z= 0.249 Angle : 0.607 11.796 24428 Z= 0.355 Chirality : 0.037 0.141 2752 Planarity : 0.004 0.058 1988 Dihedral : 29.848 179.559 4890 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.83 % Allowed : 13.49 % Favored : 84.68 % 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: 1.98 (0.24), residues: 1198 helix: 2.46 (0.22), residues: 544 sheet: 0.86 (0.34), residues: 240 loop : 0.09 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 259 HIS 0.005 0.001 HIS F 75 PHE 0.009 0.001 PHE E 67 TYR 0.013 0.002 TYR D 83 ARG 0.014 0.001 ARG M 191 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 174 time to evaluate : 1.256 Fit side-chains REVERT: A 64 LYS cc_start: 0.8516 (mmtm) cc_final: 0.8090 (mtmt) REVERT: A 106 ASP cc_start: 0.8637 (m-30) cc_final: 0.8428 (m-30) REVERT: B 79 LYS cc_start: 0.8636 (mtmm) cc_final: 0.8120 (mtpt) REVERT: C 56 GLU cc_start: 0.8927 (tt0) cc_final: 0.8701 (tt0) REVERT: C 91 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8550 (tt0) REVERT: C 99 ARG cc_start: 0.8211 (mmm-85) cc_final: 0.7840 (mmm160) REVERT: D 76 GLU cc_start: 0.8868 (tp30) cc_final: 0.8438 (tp30) REVERT: D 95 GLN cc_start: 0.8884 (tt0) cc_final: 0.8672 (tt0) REVERT: E 122 LYS cc_start: 0.8380 (pttt) cc_final: 0.8075 (pttt) REVERT: E 129 ARG cc_start: 0.8549 (tpt90) cc_final: 0.8240 (tpt-90) REVERT: F 79 LYS cc_start: 0.8599 (mttt) cc_final: 0.8307 (mtpm) REVERT: G 36 LYS cc_start: 0.8781 (mmtm) cc_final: 0.8459 (mptt) REVERT: G 91 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7568 (tt0) REVERT: H 34 LYS cc_start: 0.8319 (mtpp) cc_final: 0.7746 (mttp) REVERT: H 36 SER cc_start: 0.8984 (p) cc_final: 0.8647 (p) REVERT: H 68 ASP cc_start: 0.9038 (t70) cc_final: 0.8158 (t0) REVERT: H 86 ARG cc_start: 0.8171 (mtp85) cc_final: 0.7907 (mtp85) REVERT: H 120 LYS cc_start: 0.8391 (tttm) cc_final: 0.8144 (ttmt) REVERT: M 37 ARG cc_start: 0.8779 (ttm-80) cc_final: 0.8504 (ttm-80) REVERT: M 46 GLN cc_start: 0.7972 (tt0) cc_final: 0.7517 (mt0) REVERT: M 102 THR cc_start: 0.9338 (OUTLIER) cc_final: 0.9066 (t) REVERT: M 222 ASP cc_start: 0.8425 (t0) cc_final: 0.7810 (t0) REVERT: M 230 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.7346 (tmm) REVERT: N 19 MET cc_start: 0.7271 (tpp) cc_final: 0.6894 (pmt) REVERT: N 49 ARG cc_start: 0.8342 (mtm110) cc_final: 0.7765 (mtm-85) REVERT: N 100 ASP cc_start: 0.8695 (t0) cc_final: 0.8489 (t0) REVERT: N 154 GLN cc_start: 0.8544 (mm-40) cc_final: 0.8268 (mm110) REVERT: N 222 ASP cc_start: 0.8011 (t0) cc_final: 0.7477 (t0) outliers start: 19 outliers final: 12 residues processed: 184 average time/residue: 2.1145 time to fit residues: 417.3054 Evaluate side-chains 188 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 172 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 152 GLN Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain M residue 221 SER Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 38 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 32 optimal weight: 0.9990 chunk 116 optimal weight: 40.0000 chunk 48 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 104 GLN N 31 HIS N 152 GLN N 192 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.112228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.070475 restraints weight = 24266.656| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.59 r_work: 0.2759 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17076 Z= 0.250 Angle : 0.596 12.191 24428 Z= 0.348 Chirality : 0.036 0.135 2752 Planarity : 0.004 0.042 1988 Dihedral : 29.796 179.849 4890 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.02 % Allowed : 13.49 % Favored : 84.49 % 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: 2.06 (0.24), residues: 1198 helix: 2.55 (0.22), residues: 544 sheet: 0.87 (0.34), residues: 240 loop : 0.10 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 185 HIS 0.004 0.001 HIS F 75 PHE 0.010 0.001 PHE E 67 TYR 0.017 0.002 TYR D 83 ARG 0.009 0.001 ARG H 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6621.77 seconds wall clock time: 129 minutes 33.11 seconds (7773.11 seconds total)