Starting phenix.real_space_refine on Sat Jun 14 06:28:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vfx_43193/06_2025/8vfx_43193.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vfx_43193/06_2025/8vfx_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/cci-nas-00/data/ceres_data/8vfx_43193/06_2025/8vfx_43193.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vfx_43193/06_2025/8vfx_43193.map" model { file = "/net/cci-nas-00/data/ceres_data/8vfx_43193/06_2025/8vfx_43193.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vfx_43193/06_2025/8vfx_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-5710/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: 10.51, per 1000 atoms: 0.65 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: 4.40 Conformation dependent library (CDL) restraints added in 1.3 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: 8.64 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: 6.96 Time building geometry restraints manager: 5.18 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: 1.220 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: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 47.140 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.080 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:15.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.470 ------------------------------------------------------------------------------- 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 17080 Z= 0.205 Angle : 0.639 5.430 24436 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 Details of bonding type rmsd hydrogen bonds : bond 0.12648 ( 939) hydrogen bonds : angle 4.82521 ( 2358) SS BOND : bond 0.00288 ( 4) SS BOND : angle 0.62868 ( 8) covalent geometry : bond 0.00467 (17076) covalent geometry : angle 0.63900 (24428) *********************** 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 to be fit. rotamer outliers: 4 poor density : 247 time to evaluate : 1.330 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: 1.9613 time to fit residues: 523.7735 Evaluate side-chains 174 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 173 time to evaluate : 1.438 ------------------------------------------------------------------------------- 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: 2.9990 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.115263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.076117 restraints weight = 24075.405| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.51 r_work: 0.2889 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 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 17080 Z= 0.237 Angle : 0.606 7.379 24436 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 Details of bonding type rmsd hydrogen bonds : bond 0.04510 ( 939) hydrogen bonds : angle 3.54918 ( 2358) SS BOND : bond 0.00520 ( 4) SS BOND : angle 0.72246 ( 8) covalent geometry : bond 0.00546 (17076) covalent geometry : angle 0.60639 (24428) *********************** 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 to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 1.494 Fit side-chains REVERT: A 64 LYS cc_start: 0.8944 (mmtm) cc_final: 0.8697 (mtmt) REVERT: B 24 ASP cc_start: 0.8083 (t0) cc_final: 0.7837 (t0) REVERT: B 79 LYS cc_start: 0.9026 (mtmm) cc_final: 0.8826 (mtpt) REVERT: C 91 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8714 (tp30) REVERT: D 33 ARG cc_start: 0.8563 (ptp-170) cc_final: 0.8089 (ptm-80) REVERT: D 76 GLU cc_start: 0.8962 (tp30) cc_final: 0.8735 (tp30) REVERT: E 122 LYS cc_start: 0.9027 (pttt) cc_final: 0.8786 (pttt) REVERT: G 36 LYS cc_start: 0.9106 (mmtm) cc_final: 0.8881 (mptt) REVERT: H 34 LYS cc_start: 0.8684 (mtpp) cc_final: 0.8245 (mttp) REVERT: H 36 SER cc_start: 0.9226 (p) cc_final: 0.8943 (p) REVERT: H 68 ASP cc_start: 0.9336 (t70) cc_final: 0.8747 (t0) REVERT: H 71 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8344 (mt-10) REVERT: M 30 MET cc_start: 0.8655 (ptp) cc_final: 0.7944 (ptm) REVERT: M 31 HIS cc_start: 0.8389 (m90) cc_final: 0.7546 (m-70) REVERT: M 33 SER cc_start: 0.8806 (m) cc_final: 0.8573 (p) REVERT: M 46 GLN cc_start: 0.8067 (tt0) cc_final: 0.7796 (mt0) REVERT: M 100 ASP cc_start: 0.9008 (p0) cc_final: 0.8790 (p0) REVERT: M 102 THR cc_start: 0.9518 (OUTLIER) cc_final: 0.9275 (t) REVERT: M 222 ASP cc_start: 0.8971 (t0) cc_final: 0.8467 (t0) REVERT: N 19 MET cc_start: 0.7214 (tpp) cc_final: 0.6812 (pmt) REVERT: N 20 ASP cc_start: 0.8792 (m-30) cc_final: 0.8562 (m-30) REVERT: N 49 ARG cc_start: 0.8053 (mtm110) cc_final: 0.7819 (mtm-85) REVERT: N 191 ARG cc_start: 0.8718 (ttp-170) cc_final: 0.8442 (ttp80) outliers start: 18 outliers final: 7 residues processed: 188 average time/residue: 1.7787 time to fit residues: 359.3637 Evaluate side-chains 181 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 171 time to evaluate : 1.303 ------------------------------------------------------------------------------- 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 99 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.111869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.069960 restraints weight = 24219.976| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.60 r_work: 0.2748 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 17080 Z= 0.258 Angle : 0.609 8.145 24436 Z= 0.356 Chirality : 0.039 0.138 2752 Planarity : 0.004 0.040 1988 Dihedral : 29.682 179.493 4892 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.12 % Allowed : 10.79 % 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: 1.89 (0.24), residues: 1198 helix: 2.40 (0.22), residues: 544 sheet: 1.06 (0.35), residues: 218 loop : -0.09 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 259 HIS 0.006 0.002 HIS F 75 PHE 0.009 0.002 PHE M 117 TYR 0.014 0.002 TYR M 199 ARG 0.007 0.001 ARG H 99 Details of bonding type rmsd hydrogen bonds : bond 0.04573 ( 939) hydrogen bonds : angle 3.46704 ( 2358) SS BOND : bond 0.00476 ( 4) SS BOND : angle 0.84511 ( 8) covalent geometry : bond 0.00595 (17076) covalent geometry : angle 0.60881 (24428) *********************** 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 196 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 1.449 Fit side-chains REVERT: A 64 LYS cc_start: 0.8879 (mmtm) cc_final: 0.8581 (mtmt) REVERT: B 79 LYS cc_start: 0.8944 (mtmm) cc_final: 0.8645 (mtpt) REVERT: C 71 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8174 (mtm-85) REVERT: D 33 ARG cc_start: 0.8563 (ptp-170) cc_final: 0.8171 (ptp-170) REVERT: D 76 GLU cc_start: 0.9115 (tp30) cc_final: 0.8913 (mm-30) REVERT: E 122 LYS cc_start: 0.8903 (pttt) cc_final: 0.8626 (pttt) REVERT: G 13 LYS cc_start: 0.8755 (tppp) cc_final: 0.8548 (tppp) REVERT: G 36 LYS cc_start: 0.9037 (mmtm) cc_final: 0.8726 (mptt) REVERT: H 34 LYS cc_start: 0.8602 (mtpp) cc_final: 0.8120 (mttp) REVERT: H 36 SER cc_start: 0.9260 (p) cc_final: 0.8927 (p) REVERT: H 68 ASP cc_start: 0.9310 (t70) cc_final: 0.8583 (t0) REVERT: H 71 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8297 (mt-10) REVERT: M 46 GLN cc_start: 0.8092 (tt0) cc_final: 0.7689 (mt0) REVERT: M 102 THR cc_start: 0.9438 (OUTLIER) cc_final: 0.9156 (t) REVERT: M 222 ASP cc_start: 0.8717 (t0) cc_final: 0.8201 (t0) REVERT: N 19 MET cc_start: 0.7357 (tpp) cc_final: 0.6977 (pmt) REVERT: N 49 ARG cc_start: 0.8193 (mtm110) cc_final: 0.7872 (mtm-85) REVERT: N 191 ARG cc_start: 0.8846 (ttp-170) cc_final: 0.8532 (ttp80) outliers start: 22 outliers final: 9 residues processed: 183 average time/residue: 1.9675 time to fit residues: 385.9305 Evaluate side-chains 178 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 166 time to evaluate : 1.493 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain N residue 186 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 144 optimal weight: 6.9990 chunk 110 optimal weight: 0.0870 overall best weight: 0.8760 ------------------------------------------------------------------------------- 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 152 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.113135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.070964 restraints weight = 24048.016| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.60 r_work: 0.2775 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17080 Z= 0.167 Angle : 0.576 9.586 24436 Z= 0.341 Chirality : 0.036 0.138 2752 Planarity : 0.004 0.054 1988 Dihedral : 29.653 179.501 4890 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.02 % Allowed : 12.04 % Favored : 85.93 % 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: 2.11 (0.24), residues: 1198 helix: 2.54 (0.22), residues: 544 sheet: 1.10 (0.35), residues: 228 loop : 0.11 (0.28), residues: 426 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 0.009 0.001 PHE E 67 TYR 0.014 0.001 TYR M 203 ARG 0.007 0.000 ARG H 99 Details of bonding type rmsd hydrogen bonds : bond 0.03978 ( 939) hydrogen bonds : angle 3.35519 ( 2358) SS BOND : bond 0.00382 ( 4) SS BOND : angle 0.72474 ( 8) covalent geometry : bond 0.00375 (17076) covalent geometry : angle 0.57641 (24428) *********************** 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 192 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 1.293 Fit side-chains REVERT: A 64 LYS cc_start: 0.8850 (mmtm) cc_final: 0.8580 (mtmt) REVERT: B 24 ASP cc_start: 0.8043 (t0) cc_final: 0.7827 (t0) REVERT: B 79 LYS cc_start: 0.8940 (mtmm) cc_final: 0.8624 (mtpt) REVERT: C 71 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8102 (mtm-85) REVERT: C 90 ASP cc_start: 0.9185 (t0) cc_final: 0.8948 (t70) REVERT: C 91 GLU cc_start: 0.8989 (tt0) cc_final: 0.8780 (tp30) REVERT: D 33 ARG cc_start: 0.8562 (ptp-170) cc_final: 0.8153 (ptp-170) REVERT: E 122 LYS cc_start: 0.8885 (pttt) cc_final: 0.8610 (pttt) REVERT: G 36 LYS cc_start: 0.9080 (mmtm) cc_final: 0.8808 (mptt) REVERT: H 34 LYS cc_start: 0.8589 (mtpp) cc_final: 0.8122 (mttp) REVERT: H 36 SER cc_start: 0.9236 (p) cc_final: 0.8929 (p) REVERT: H 68 ASP cc_start: 0.9321 (t70) cc_final: 0.8606 (t0) REVERT: H 71 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8294 (mt-10) REVERT: M 46 GLN cc_start: 0.8058 (tt0) cc_final: 0.7662 (mt0) REVERT: M 102 THR cc_start: 0.9438 (OUTLIER) cc_final: 0.9158 (t) REVERT: M 222 ASP cc_start: 0.8737 (t0) cc_final: 0.8206 (t0) REVERT: N 19 MET cc_start: 0.7380 (tpp) cc_final: 0.6982 (pmt) REVERT: N 49 ARG cc_start: 0.8170 (mtm110) cc_final: 0.7848 (mtm-85) REVERT: N 191 ARG cc_start: 0.8860 (ttp-170) cc_final: 0.8556 (ttp80) REVERT: N 235 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8563 (mm) outliers start: 21 outliers final: 7 residues processed: 183 average time/residue: 1.8201 time to fit residues: 357.6577 Evaluate side-chains 178 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 167 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 71 ARG 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 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 120 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 31 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.115945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.076721 restraints weight = 24322.926| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.54 r_work: 0.2901 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17080 Z= 0.173 Angle : 0.560 8.729 24436 Z= 0.332 Chirality : 0.035 0.130 2752 Planarity : 0.004 0.041 1988 Dihedral : 29.359 178.827 4890 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % 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: 2.26 (0.24), residues: 1198 helix: 2.67 (0.22), residues: 548 sheet: 0.97 (0.34), residues: 240 loop : 0.25 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 259 HIS 0.004 0.001 HIS M 110 PHE 0.010 0.001 PHE E 67 TYR 0.012 0.001 TYR M 199 ARG 0.009 0.001 ARG H 86 Details of bonding type rmsd hydrogen bonds : bond 0.03627 ( 939) hydrogen bonds : angle 3.20868 ( 2358) SS BOND : bond 0.00411 ( 4) SS BOND : angle 0.95875 ( 8) covalent geometry : bond 0.00391 (17076) covalent geometry : angle 0.55958 (24428) *********************** 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 to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 1.498 Fit side-chains REVERT: B 79 LYS cc_start: 0.9053 (mtmm) cc_final: 0.8840 (mtpt) REVERT: C 91 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8771 (tp30) REVERT: E 122 LYS cc_start: 0.9021 (pttt) cc_final: 0.8785 (pttt) REVERT: G 36 LYS cc_start: 0.9150 (mmtm) cc_final: 0.8916 (mptt) REVERT: H 34 LYS cc_start: 0.8658 (mtpp) cc_final: 0.8263 (mttp) REVERT: H 36 SER cc_start: 0.9288 (p) cc_final: 0.8983 (p) REVERT: H 68 ASP cc_start: 0.9308 (t70) cc_final: 0.8753 (t0) REVERT: H 86 ARG cc_start: 0.8505 (mtt-85) cc_final: 0.8107 (mtp-110) REVERT: M 46 GLN cc_start: 0.7997 (tt0) cc_final: 0.7716 (mt0) REVERT: M 102 THR cc_start: 0.9484 (OUTLIER) cc_final: 0.9256 (t) REVERT: M 222 ASP cc_start: 0.8846 (t0) cc_final: 0.8382 (t0) REVERT: N 19 MET cc_start: 0.7361 (tpp) cc_final: 0.6988 (pmt) REVERT: N 49 ARG cc_start: 0.8312 (mtm110) cc_final: 0.7961 (mtm-85) REVERT: N 89 ASP cc_start: 0.8367 (m-30) cc_final: 0.8003 (p0) REVERT: N 191 ARG cc_start: 0.8793 (ttp-170) cc_final: 0.8547 (ttp80) outliers start: 21 outliers final: 6 residues processed: 190 average time/residue: 1.9005 time to fit residues: 386.9779 Evaluate side-chains 178 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 170 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 76 GLN 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 27 optimal weight: 0.0040 chunk 96 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.9798 ------------------------------------------------------------------------------- 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 73 ASN H 63 ASN N 31 HIS N 57 GLN N 188 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.111761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.069900 restraints weight = 24410.315| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.60 r_work: 0.2746 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 17080 Z= 0.260 Angle : 0.608 9.566 24436 Z= 0.355 Chirality : 0.039 0.137 2752 Planarity : 0.004 0.035 1988 Dihedral : 29.678 179.919 4890 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.83 % Allowed : 13.10 % Favored : 85.07 % 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: 2.01 (0.24), residues: 1198 helix: 2.50 (0.22), residues: 544 sheet: 0.88 (0.34), residues: 240 loop : 0.07 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 259 HIS 0.006 0.001 HIS F 75 PHE 0.010 0.002 PHE M 117 TYR 0.014 0.002 TYR M 199 ARG 0.009 0.001 ARG M 191 Details of bonding type rmsd hydrogen bonds : bond 0.04380 ( 939) hydrogen bonds : angle 3.35683 ( 2358) SS BOND : bond 0.00504 ( 4) SS BOND : angle 1.19132 ( 8) covalent geometry : bond 0.00600 (17076) covalent geometry : angle 0.60755 (24428) *********************** 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 191 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 172 time to evaluate : 1.445 Fit side-chains REVERT: B 79 LYS cc_start: 0.8998 (mtmm) cc_final: 0.8654 (mtpt) REVERT: D 33 ARG cc_start: 0.8473 (ptp-170) cc_final: 0.8080 (ptp-170) REVERT: E 122 LYS cc_start: 0.8910 (pttt) cc_final: 0.8621 (pttt) REVERT: G 36 LYS cc_start: 0.9060 (mmtm) cc_final: 0.8783 (mptt) REVERT: G 91 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8152 (tt0) REVERT: H 34 LYS cc_start: 0.8601 (mtpp) cc_final: 0.8115 (mttp) REVERT: H 36 SER cc_start: 0.9196 (p) cc_final: 0.8926 (p) REVERT: H 68 ASP cc_start: 0.9319 (t70) cc_final: 0.8645 (t0) REVERT: M 46 GLN cc_start: 0.8103 (tt0) cc_final: 0.7700 (mt0) REVERT: M 102 THR cc_start: 0.9446 (OUTLIER) cc_final: 0.9169 (t) REVERT: M 222 ASP cc_start: 0.8780 (t0) cc_final: 0.8256 (t0) REVERT: M 230 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.7743 (tmm) REVERT: N 19 MET cc_start: 0.7409 (tpp) cc_final: 0.6966 (pmt) REVERT: N 49 ARG cc_start: 0.8419 (mtm110) cc_final: 0.7918 (mtm-85) REVERT: N 192 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8302 (mm-40) outliers start: 19 outliers final: 9 residues processed: 182 average time/residue: 1.8951 time to fit residues: 369.9420 Evaluate side-chains 179 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain G residue 91 GLU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 129 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 23 optimal weight: 0.2980 chunk 57 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 N 31 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.114808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.075663 restraints weight = 23941.102| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.50 r_work: 0.2881 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17080 Z= 0.174 Angle : 0.586 10.610 24436 Z= 0.343 Chirality : 0.036 0.133 2752 Planarity : 0.004 0.049 1988 Dihedral : 29.647 179.387 4890 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.22 % Allowed : 13.39 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.14 (0.24), residues: 1198 helix: 2.59 (0.22), residues: 544 sheet: 0.96 (0.34), residues: 240 loop : 0.15 (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 0.011 0.001 PHE E 67 TYR 0.012 0.001 TYR M 203 ARG 0.009 0.000 ARG M 191 Details of bonding type rmsd hydrogen bonds : bond 0.03882 ( 939) hydrogen bonds : angle 3.27938 ( 2358) SS BOND : bond 0.00418 ( 4) SS BOND : angle 1.06880 ( 8) covalent geometry : bond 0.00391 (17076) covalent geometry : angle 0.58567 (24428) *********************** 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 193 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 1.489 Fit side-chains REVERT: B 79 LYS cc_start: 0.9064 (mtmm) cc_final: 0.8798 (mtpt) REVERT: B 88 TYR cc_start: 0.9278 (m-10) cc_final: 0.8920 (m-80) REVERT: C 90 ASP cc_start: 0.9160 (t0) cc_final: 0.8959 (t70) REVERT: C 91 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8768 (tp30) REVERT: E 122 LYS cc_start: 0.9016 (pttt) cc_final: 0.8766 (pttt) REVERT: G 36 LYS cc_start: 0.9118 (mmtm) cc_final: 0.8874 (mptt) REVERT: H 34 LYS cc_start: 0.8672 (mtpp) cc_final: 0.8236 (mttp) REVERT: H 36 SER cc_start: 0.9223 (p) cc_final: 0.8975 (p) REVERT: H 68 ASP cc_start: 0.9315 (t70) cc_final: 0.8762 (t0) REVERT: M 46 GLN cc_start: 0.8048 (tt0) cc_final: 0.7783 (mt0) REVERT: M 102 THR cc_start: 0.9463 (OUTLIER) cc_final: 0.9209 (t) REVERT: M 222 ASP cc_start: 0.8862 (t0) cc_final: 0.8421 (t0) REVERT: M 230 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.7758 (tmm) REVERT: N 19 MET cc_start: 0.7384 (tpp) cc_final: 0.7000 (pmt) REVERT: N 49 ARG cc_start: 0.8339 (mtm110) cc_final: 0.7998 (mtm-85) outliers start: 23 outliers final: 11 residues processed: 180 average time/residue: 1.9980 time to fit residues: 389.7689 Evaluate side-chains 180 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 166 time to evaluate : 1.563 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 68 optimal weight: 0.3980 chunk 97 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 65 optimal weight: 0.0570 chunk 75 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 116 optimal weight: 40.0000 chunk 12 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 overall best weight: 0.6898 ------------------------------------------------------------------------------- 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 M 31 HIS N 31 HIS N 192 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.115172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.076238 restraints weight = 23731.733| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.48 r_work: 0.2892 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17080 Z= 0.155 Angle : 0.578 11.565 24436 Z= 0.339 Chirality : 0.036 0.144 2752 Planarity : 0.004 0.060 1988 Dihedral : 29.613 179.202 4890 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.83 % Allowed : 13.87 % Favored : 84.30 % 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: 2.21 (0.24), residues: 1198 helix: 2.69 (0.22), residues: 542 sheet: 0.96 (0.34), residues: 240 loop : 0.17 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 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 M 203 ARG 0.011 0.000 ARG M 191 Details of bonding type rmsd hydrogen bonds : bond 0.03708 ( 939) hydrogen bonds : angle 3.25532 ( 2358) SS BOND : bond 0.00371 ( 4) SS BOND : angle 1.03298 ( 8) covalent geometry : bond 0.00344 (17076) covalent geometry : angle 0.57766 (24428) *********************** 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 194 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 1.344 Fit side-chains REVERT: B 79 LYS cc_start: 0.9069 (mtmm) cc_final: 0.8817 (mtpt) REVERT: C 90 ASP cc_start: 0.9145 (t0) cc_final: 0.8944 (t70) REVERT: C 91 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8726 (tp30) REVERT: E 122 LYS cc_start: 0.9020 (pttt) cc_final: 0.8780 (pttt) REVERT: G 36 LYS cc_start: 0.9132 (mmtm) cc_final: 0.8897 (mptt) REVERT: G 104 GLN cc_start: 0.9033 (mm110) cc_final: 0.8599 (mm110) REVERT: H 34 LYS cc_start: 0.8677 (mtpp) cc_final: 0.8273 (mttp) REVERT: H 36 SER cc_start: 0.9223 (p) cc_final: 0.8981 (p) REVERT: H 68 ASP cc_start: 0.9308 (t70) cc_final: 0.8703 (t0) REVERT: M 102 THR cc_start: 0.9477 (OUTLIER) cc_final: 0.9240 (t) REVERT: M 222 ASP cc_start: 0.8860 (t0) cc_final: 0.8435 (t0) REVERT: M 230 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.7643 (tmm) REVERT: N 19 MET cc_start: 0.7373 (tpp) cc_final: 0.7004 (pmt) REVERT: N 20 ASP cc_start: 0.8732 (m-30) cc_final: 0.8501 (m-30) REVERT: N 49 ARG cc_start: 0.8346 (mtm110) cc_final: 0.8040 (mtm-85) outliers start: 19 outliers final: 13 residues processed: 183 average time/residue: 1.8385 time to fit residues: 361.5608 Evaluate side-chains 183 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 1.363 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 129 optimal weight: 4.9990 chunk 66 optimal weight: 0.0010 chunk 103 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 40 optimal weight: 0.0980 chunk 140 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- 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 46 GLN N 31 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.115952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.076639 restraints weight = 24075.556| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.53 r_work: 0.2898 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17080 Z= 0.172 Angle : 0.572 12.061 24436 Z= 0.334 Chirality : 0.035 0.130 2752 Planarity : 0.004 0.054 1988 Dihedral : 29.431 179.643 4890 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.83 % Allowed : 14.26 % Favored : 83.91 % 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: 2.24 (0.24), residues: 1198 helix: 2.70 (0.22), residues: 546 sheet: 0.96 (0.34), residues: 240 loop : 0.18 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 259 HIS 0.003 0.001 HIS F 75 PHE 0.010 0.001 PHE E 67 TYR 0.011 0.001 TYR M 199 ARG 0.014 0.001 ARG M 49 Details of bonding type rmsd hydrogen bonds : bond 0.03555 ( 939) hydrogen bonds : angle 3.17879 ( 2358) SS BOND : bond 0.00399 ( 4) SS BOND : angle 1.04484 ( 8) covalent geometry : bond 0.00389 (17076) covalent geometry : angle 0.57130 (24428) *********************** 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 194 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 1.942 Fit side-chains REVERT: B 79 LYS cc_start: 0.9081 (mtmm) cc_final: 0.8801 (mtpt) REVERT: C 91 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8750 (tp30) REVERT: E 122 LYS cc_start: 0.9028 (pttt) cc_final: 0.8794 (pttt) REVERT: G 36 LYS cc_start: 0.9137 (mmtm) cc_final: 0.8901 (mptt) REVERT: G 91 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8254 (tt0) REVERT: H 34 LYS cc_start: 0.8660 (mtpp) cc_final: 0.8239 (mttp) REVERT: H 36 SER cc_start: 0.9220 (p) cc_final: 0.8978 (p) REVERT: H 68 ASP cc_start: 0.9311 (t70) cc_final: 0.8757 (t0) REVERT: M 23 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.8203 (mmm) REVERT: M 102 THR cc_start: 0.9453 (OUTLIER) cc_final: 0.9253 (t) REVERT: M 222 ASP cc_start: 0.8873 (t0) cc_final: 0.8452 (t0) REVERT: M 230 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.7759 (tmm) REVERT: N 19 MET cc_start: 0.7398 (tpp) cc_final: 0.7014 (pmt) REVERT: N 49 ARG cc_start: 0.8400 (mtm110) cc_final: 0.8019 (mtm-85) outliers start: 19 outliers final: 11 residues processed: 184 average time/residue: 1.9376 time to fit residues: 382.8372 Evaluate side-chains 187 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 222 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 38 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 143 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 M 31 HIS M 152 GLN N 31 HIS N 96 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.116219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.076987 restraints weight = 24031.611| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.52 r_work: 0.2905 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17080 Z= 0.161 Angle : 0.568 11.663 24436 Z= 0.333 Chirality : 0.035 0.171 2752 Planarity : 0.004 0.060 1988 Dihedral : 29.422 179.815 4890 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.54 % Allowed : 14.55 % Favored : 83.91 % 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: 2.29 (0.24), residues: 1198 helix: 2.71 (0.22), residues: 546 sheet: 1.07 (0.34), residues: 238 loop : 0.21 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 259 HIS 0.003 0.001 HIS F 75 PHE 0.010 0.001 PHE E 67 TYR 0.013 0.001 TYR M 199 ARG 0.013 0.001 ARG M 191 Details of bonding type rmsd hydrogen bonds : bond 0.03519 ( 939) hydrogen bonds : angle 3.17979 ( 2358) SS BOND : bond 0.00405 ( 4) SS BOND : angle 1.09338 ( 8) covalent geometry : bond 0.00363 (17076) covalent geometry : angle 0.56758 (24428) ********************** 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 190 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 1.444 Fit side-chains REVERT: B 24 ASP cc_start: 0.8031 (t0) cc_final: 0.7736 (t0) REVERT: B 79 LYS cc_start: 0.9085 (mtmm) cc_final: 0.8809 (mtpt) REVERT: C 91 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8728 (tp30) REVERT: E 122 LYS cc_start: 0.9031 (pttt) cc_final: 0.8798 (pttt) REVERT: G 36 LYS cc_start: 0.9142 (mmtm) cc_final: 0.8910 (mptt) REVERT: G 91 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8241 (tt0) REVERT: H 34 LYS cc_start: 0.8650 (mtpp) cc_final: 0.8236 (mttp) REVERT: H 36 SER cc_start: 0.9211 (p) cc_final: 0.8968 (p) REVERT: H 68 ASP cc_start: 0.9306 (t70) cc_final: 0.8705 (t0) REVERT: M 23 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8196 (mmm) REVERT: M 37 ARG cc_start: 0.8499 (ttm-80) cc_final: 0.7836 (ttm-80) REVERT: M 222 ASP cc_start: 0.8883 (t0) cc_final: 0.8465 (t0) REVERT: M 230 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.7639 (tmm) REVERT: N 19 MET cc_start: 0.7389 (tpp) cc_final: 0.7014 (pmt) REVERT: N 37 ARG cc_start: 0.8607 (ttm-80) cc_final: 0.7792 (ttm-80) REVERT: N 49 ARG cc_start: 0.8392 (mtm110) cc_final: 0.8028 (mtm-85) outliers start: 16 outliers final: 10 residues processed: 180 average time/residue: 1.9650 time to fit residues: 380.2793 Evaluate side-chains 185 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 171 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 222 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 24 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 72 optimal weight: 0.3980 chunk 0 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN M 31 HIS N 31 HIS N 96 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.112056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.070265 restraints weight = 24375.879| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.60 r_work: 0.2753 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 17080 Z= 0.248 Angle : 0.607 11.527 24436 Z= 0.352 Chirality : 0.038 0.185 2752 Planarity : 0.004 0.050 1988 Dihedral : 29.660 179.481 4890 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.45 % Allowed : 14.84 % Favored : 83.72 % 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: 2.50 (0.22), residues: 546 sheet: 0.98 (0.34), residues: 238 loop : 0.06 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 259 HIS 0.006 0.001 HIS F 75 PHE 0.010 0.001 PHE M 117 TYR 0.015 0.002 TYR M 199 ARG 0.012 0.001 ARG M 49 Details of bonding type rmsd hydrogen bonds : bond 0.04225 ( 939) hydrogen bonds : angle 3.33558 ( 2358) SS BOND : bond 0.00492 ( 4) SS BOND : angle 1.39181 ( 8) covalent geometry : bond 0.00574 (17076) covalent geometry : angle 0.60692 (24428) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15205.78 seconds wall clock time: 261 minutes 47.03 seconds (15707.03 seconds total)