Starting phenix.real_space_refine on Mon Jan 20 22:31:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vfx_43193/01_2025/8vfx_43193.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vfx_43193/01_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_43193/01_2025/8vfx_43193.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vfx_43193/01_2025/8vfx_43193.map" model { file = "/net/cci-nas-00/data/ceres_data/8vfx_43193/01_2025/8vfx_43193.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vfx_43193/01_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-5571/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: 9.30, per 1000 atoms: 0.58 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: 4.01 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: 8.27 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: 7.24 Time building geometry restraints manager: 4.67 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: 2.100 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: 0.660 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 43.530 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.130 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:13.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.360 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 4 poor density : 247 time to evaluate : 1.402 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: 2.0520 time to fit residues: 547.6034 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 : 1.475 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- 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 = 43)----------------| | 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: 0.2888 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 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 to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 1.553 Fit side-chains REVERT: A 64 LYS cc_start: 0.8941 (mmtm) cc_final: 0.8687 (mtmt) REVERT: B 24 ASP cc_start: 0.8076 (t0) cc_final: 0.7826 (t0) REVERT: B 79 LYS cc_start: 0.9023 (mtmm) cc_final: 0.8818 (mtpt) REVERT: B 88 TYR cc_start: 0.9117 (m-10) cc_final: 0.8917 (m-80) REVERT: C 91 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8721 (tp30) REVERT: D 33 ARG cc_start: 0.8557 (ptp-170) cc_final: 0.8082 (ptm-80) REVERT: D 76 GLU cc_start: 0.8969 (tp30) cc_final: 0.8740 (tp30) REVERT: E 122 LYS cc_start: 0.9027 (pttt) cc_final: 0.8785 (pttt) REVERT: G 36 LYS cc_start: 0.9101 (mmtm) cc_final: 0.8874 (mptt) REVERT: H 34 LYS cc_start: 0.8685 (mtpp) cc_final: 0.8237 (mttp) REVERT: H 36 SER cc_start: 0.9225 (p) cc_final: 0.8941 (p) REVERT: H 68 ASP cc_start: 0.9336 (t70) cc_final: 0.8742 (t0) REVERT: H 71 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8357 (mt-10) REVERT: M 30 MET cc_start: 0.8661 (ptp) cc_final: 0.7936 (ptm) REVERT: M 31 HIS cc_start: 0.8397 (m90) cc_final: 0.7550 (m-70) REVERT: M 33 SER cc_start: 0.8803 (m) cc_final: 0.8562 (p) REVERT: M 46 GLN cc_start: 0.8070 (tt0) cc_final: 0.7785 (mt0) REVERT: M 100 ASP cc_start: 0.9009 (p0) cc_final: 0.8791 (p0) REVERT: M 102 THR cc_start: 0.9517 (OUTLIER) cc_final: 0.9273 (t) REVERT: M 222 ASP cc_start: 0.8971 (t0) cc_final: 0.8459 (t0) REVERT: N 19 MET cc_start: 0.7220 (tpp) cc_final: 0.6807 (pmt) REVERT: N 20 ASP cc_start: 0.8815 (m-30) cc_final: 0.8573 (m-30) REVERT: N 49 ARG cc_start: 0.8046 (mtm110) cc_final: 0.7811 (mtm-85) REVERT: N 191 ARG cc_start: 0.8760 (ttp-170) cc_final: 0.8474 (ttp80) outliers start: 18 outliers final: 7 residues processed: 188 average time/residue: 2.0024 time to fit residues: 403.8196 Evaluate side-chains 182 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 172 time to evaluate : 1.414 ------------------------------------------------------------------------------- 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: 2.9990 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: 2.1588 ------------------------------------------------------------------------------- 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 N 57 GLN N 188 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.111430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.069657 restraints weight = 24230.404| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 1.62 r_work: 0.2742 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 17076 Z= 0.377 Angle : 0.620 8.207 24428 Z= 0.362 Chirality : 0.040 0.139 2752 Planarity : 0.005 0.037 1988 Dihedral : 29.765 179.802 4892 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.31 % Allowed : 10.69 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.24), residues: 1198 helix: 2.34 (0.22), residues: 544 sheet: 0.95 (0.34), residues: 230 loop : -0.08 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 259 HIS 0.006 0.002 HIS F 75 PHE 0.010 0.002 PHE M 117 TYR 0.015 0.002 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 194 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 1.332 Fit side-chains REVERT: A 64 LYS cc_start: 0.8875 (mmtm) cc_final: 0.8567 (mtmt) REVERT: B 79 LYS cc_start: 0.8941 (mtmm) cc_final: 0.8631 (mtpt) REVERT: B 88 TYR cc_start: 0.8974 (m-10) cc_final: 0.8759 (m-80) REVERT: C 71 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8130 (mtm-85) REVERT: D 33 ARG cc_start: 0.8568 (ptp-170) cc_final: 0.8179 (ptp-170) REVERT: E 122 LYS cc_start: 0.8909 (pttt) cc_final: 0.8627 (pttt) REVERT: G 13 LYS cc_start: 0.8752 (tppp) cc_final: 0.8549 (tppp) REVERT: G 36 LYS cc_start: 0.9033 (mmtm) cc_final: 0.8742 (mptt) REVERT: G 91 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8177 (tt0) REVERT: H 34 LYS cc_start: 0.8609 (mtpp) cc_final: 0.8120 (mttp) REVERT: H 36 SER cc_start: 0.9260 (p) cc_final: 0.8929 (p) REVERT: H 68 ASP cc_start: 0.9304 (t70) cc_final: 0.8575 (t0) REVERT: H 71 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8284 (mt-10) REVERT: M 30 MET cc_start: 0.8782 (ptp) cc_final: 0.8562 (ptm) REVERT: M 46 GLN cc_start: 0.8120 (tt0) cc_final: 0.7675 (mt0) REVERT: M 102 THR cc_start: 0.9440 (OUTLIER) cc_final: 0.9156 (t) REVERT: M 222 ASP cc_start: 0.8736 (t0) cc_final: 0.8221 (t0) REVERT: N 19 MET cc_start: 0.7361 (tpp) cc_final: 0.6974 (pmt) REVERT: N 49 ARG cc_start: 0.8202 (mtm110) cc_final: 0.7860 (mtm-85) REVERT: N 191 ARG cc_start: 0.8848 (ttp-170) cc_final: 0.8536 (ttp80) outliers start: 24 outliers final: 11 residues processed: 181 average time/residue: 1.9454 time to fit residues: 377.2033 Evaluate side-chains 180 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 165 time to evaluate : 1.427 ------------------------------------------------------------------------------- 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 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 221 SER 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 28 SER 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: 0.7980 chunk 17 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 63 optimal weight: 0.0870 chunk 21 optimal weight: 0.5980 chunk 144 optimal weight: 5.9990 chunk 110 optimal weight: 0.4980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN M 152 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.115807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.076605 restraints weight = 23952.193| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.52 r_work: 0.2897 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17076 Z= 0.185 Angle : 0.565 7.991 24428 Z= 0.335 Chirality : 0.035 0.133 2752 Planarity : 0.004 0.053 1988 Dihedral : 29.624 178.958 4890 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.73 % Allowed : 11.95 % Favored : 86.32 % 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: 2.15 (0.24), residues: 1198 helix: 2.63 (0.22), residues: 544 sheet: 1.17 (0.36), residues: 218 loop : 0.03 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 259 HIS 0.003 0.001 HIS F 75 PHE 0.011 0.001 PHE E 67 TYR 0.009 0.001 TYR M 199 ARG 0.008 0.001 ARG M 191 *********************** 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 194 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 1.492 Fit side-chains REVERT: B 24 ASP cc_start: 0.7999 (t0) cc_final: 0.7754 (t0) REVERT: B 79 LYS cc_start: 0.9009 (mtmm) cc_final: 0.8791 (mtpt) REVERT: C 71 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8242 (mtm-85) REVERT: C 91 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8738 (tp30) REVERT: C 110 ASN cc_start: 0.9301 (t0) cc_final: 0.9084 (t0) REVERT: D 33 ARG cc_start: 0.8595 (ptp-170) cc_final: 0.8166 (ptp-170) REVERT: E 122 LYS cc_start: 0.9026 (pttt) cc_final: 0.8795 (pttt) REVERT: G 36 LYS cc_start: 0.9139 (mmtm) cc_final: 0.8920 (mptt) REVERT: H 34 LYS cc_start: 0.8693 (mtpp) cc_final: 0.8294 (mttp) REVERT: H 36 SER cc_start: 0.9268 (p) cc_final: 0.8980 (p) REVERT: H 68 ASP cc_start: 0.9311 (t70) cc_final: 0.8751 (t0) REVERT: H 71 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8345 (mt-10) REVERT: M 46 GLN cc_start: 0.8031 (tt0) cc_final: 0.7735 (mt0) REVERT: M 102 THR cc_start: 0.9502 (OUTLIER) cc_final: 0.9240 (t) REVERT: M 222 ASP cc_start: 0.8800 (t0) cc_final: 0.8298 (t0) REVERT: N 19 MET cc_start: 0.7371 (tpp) cc_final: 0.7013 (pmt) REVERT: N 20 ASP cc_start: 0.8841 (m-30) cc_final: 0.8601 (m-30) REVERT: N 49 ARG cc_start: 0.8159 (mtm110) cc_final: 0.7923 (mtm-85) REVERT: N 191 ARG cc_start: 0.8767 (ttp-170) cc_final: 0.8524 (ttp80) REVERT: N 235 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8668 (mm) outliers start: 18 outliers final: 5 residues processed: 186 average time/residue: 1.9772 time to fit residues: 393.9802 Evaluate side-chains 179 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 169 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 152 GLN Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain N residue 22 LYS 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: 1.9990 chunk 121 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 12 optimal weight: 0.1980 chunk 16 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 84 GLN H 63 ASN M 152 GLN N 31 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.115846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.077005 restraints weight = 24229.969| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.53 r_work: 0.2904 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17076 Z= 0.212 Angle : 0.564 9.657 24428 Z= 0.333 Chirality : 0.035 0.131 2752 Planarity : 0.004 0.036 1988 Dihedral : 29.394 178.108 4890 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.64 % Allowed : 13.49 % 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: 2.29 (0.24), residues: 1198 helix: 2.71 (0.22), residues: 546 sheet: 1.10 (0.35), residues: 228 loop : 0.19 (0.29), residues: 424 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 0.011 0.001 TYR M 199 ARG 0.011 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 195 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 1.546 Fit side-chains REVERT: B 24 ASP cc_start: 0.8117 (t0) cc_final: 0.7770 (t0) REVERT: B 79 LYS cc_start: 0.9048 (mtmm) cc_final: 0.8771 (mtpt) REVERT: C 110 ASN cc_start: 0.9323 (t0) cc_final: 0.9096 (t0) REVERT: E 122 LYS cc_start: 0.9015 (pttt) cc_final: 0.8776 (pttt) REVERT: G 36 LYS cc_start: 0.9138 (mmtm) cc_final: 0.8899 (mptt) REVERT: H 34 LYS cc_start: 0.8681 (mtpp) cc_final: 0.8276 (mttp) REVERT: H 36 SER cc_start: 0.9197 (p) cc_final: 0.8964 (p) REVERT: H 68 ASP cc_start: 0.9317 (t70) cc_final: 0.8697 (t0) REVERT: H 71 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8359 (mt-10) REVERT: M 46 GLN cc_start: 0.7998 (tt0) cc_final: 0.7775 (mt0) REVERT: M 102 THR cc_start: 0.9497 (OUTLIER) cc_final: 0.9251 (t) REVERT: M 222 ASP cc_start: 0.8842 (t0) cc_final: 0.8357 (t0) REVERT: N 19 MET cc_start: 0.7331 (tpp) cc_final: 0.6958 (pmt) REVERT: N 20 ASP cc_start: 0.8785 (m-30) cc_final: 0.8546 (m-30) REVERT: N 49 ARG cc_start: 0.8320 (mtm110) cc_final: 0.7979 (mtm-85) REVERT: N 191 ARG cc_start: 0.8775 (ttp-170) cc_final: 0.8559 (ttp80) REVERT: N 235 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8573 (mm) outliers start: 17 outliers final: 7 residues processed: 187 average time/residue: 1.9479 time to fit residues: 391.4827 Evaluate side-chains 179 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 169 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain H residue 71 GLU 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 222 ASP Chi-restraints excluded: chain N residue 235 LEU 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: 0.0030 chunk 96 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 overall best weight: 1.1394 ------------------------------------------------------------------------------- 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 M 31 HIS M 152 GLN N 31 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.115776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.076467 restraints weight = 24101.986| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.52 r_work: 0.2896 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2106 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= 0.237 Angle : 0.565 10.308 24428 Z= 0.333 Chirality : 0.035 0.130 2752 Planarity : 0.004 0.035 1988 Dihedral : 29.387 178.488 4890 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.93 % Allowed : 13.87 % Favored : 84.20 % 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: 2.69 (0.22), residues: 546 sheet: 0.95 (0.34), residues: 240 loop : 0.24 (0.29), residues: 412 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 0.009 0.001 ARG M 191 *********************** 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 196 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 1.485 Fit side-chains REVERT: B 79 LYS cc_start: 0.9070 (mtmm) cc_final: 0.8799 (mtpt) REVERT: C 91 GLU cc_start: 0.8977 (tp30) cc_final: 0.8713 (tp30) REVERT: E 122 LYS cc_start: 0.9027 (pttt) cc_final: 0.8796 (pttt) REVERT: G 36 LYS cc_start: 0.9143 (mmtm) cc_final: 0.8908 (mptt) REVERT: H 34 LYS cc_start: 0.8715 (mtpp) cc_final: 0.8284 (mttp) REVERT: H 36 SER cc_start: 0.9256 (p) cc_final: 0.8992 (p) REVERT: H 68 ASP cc_start: 0.9310 (t70) cc_final: 0.8773 (t0) REVERT: M 46 GLN cc_start: 0.7991 (tt0) cc_final: 0.7725 (mt0) REVERT: M 102 THR cc_start: 0.9471 (OUTLIER) cc_final: 0.9222 (t) REVERT: M 123 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8584 (tt) REVERT: M 222 ASP cc_start: 0.8856 (t0) cc_final: 0.8381 (t0) REVERT: N 19 MET cc_start: 0.7373 (tpp) cc_final: 0.6992 (pmt) REVERT: N 49 ARG cc_start: 0.8334 (mtm110) cc_final: 0.7996 (mtm-85) REVERT: N 89 ASP cc_start: 0.8354 (m-30) cc_final: 0.7990 (p0) REVERT: N 191 ARG cc_start: 0.8810 (ttp-170) cc_final: 0.8602 (ttp80) outliers start: 20 outliers final: 7 residues processed: 188 average time/residue: 1.9475 time to fit residues: 392.9267 Evaluate side-chains 177 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 168 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 123 LEU 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 38 VAL 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: 1.9990 chunk 23 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 56 optimal weight: 0.2980 chunk 12 optimal weight: 0.0670 chunk 89 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 overall best weight: 0.6724 ------------------------------------------------------------------------------- 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 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 = 0.3722 r_free = 0.3722 target = 0.116324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.077138 restraints weight = 24012.202| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.51 r_work: 0.2911 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17076 Z= 0.186 Angle : 0.563 11.219 24428 Z= 0.331 Chirality : 0.035 0.134 2752 Planarity : 0.004 0.051 1988 Dihedral : 29.385 178.977 4890 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.22 % Allowed : 13.49 % 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: 2.33 (0.24), residues: 1198 helix: 2.74 (0.22), residues: 546 sheet: 1.01 (0.34), residues: 240 loop : 0.28 (0.30), residues: 412 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 0.009 0.001 PHE E 67 TYR 0.010 0.001 TYR D 83 ARG 0.010 0.000 ARG M 191 *********************** 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 196 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 1.395 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9074 (mtmm) cc_final: 0.8814 (mtpt) REVERT: C 91 GLU cc_start: 0.8983 (tp30) cc_final: 0.8732 (tp30) REVERT: E 122 LYS cc_start: 0.9022 (pttt) cc_final: 0.8800 (pttt) REVERT: G 36 LYS cc_start: 0.9130 (mmtm) cc_final: 0.8899 (mptt) REVERT: G 91 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8235 (tt0) REVERT: H 34 LYS cc_start: 0.8708 (mtpp) cc_final: 0.8288 (mttp) REVERT: H 36 SER cc_start: 0.9238 (p) cc_final: 0.8978 (p) REVERT: H 68 ASP cc_start: 0.9304 (t70) cc_final: 0.8715 (t0) REVERT: M 46 GLN cc_start: 0.7969 (tt0) cc_final: 0.7727 (mt0) REVERT: M 102 THR cc_start: 0.9476 (OUTLIER) cc_final: 0.9234 (t) REVERT: M 123 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8602 (tt) REVERT: M 222 ASP cc_start: 0.8844 (t0) cc_final: 0.8380 (t0) REVERT: M 230 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.7570 (tmm) REVERT: N 19 MET cc_start: 0.7362 (tpp) cc_final: 0.6993 (pmt) REVERT: N 20 ASP cc_start: 0.8735 (m-30) cc_final: 0.8501 (m-30) REVERT: N 37 ARG cc_start: 0.8568 (ttm-80) cc_final: 0.7814 (ttm-80) REVERT: N 49 ARG cc_start: 0.8316 (mtm110) cc_final: 0.7990 (mtm-85) REVERT: N 89 ASP cc_start: 0.8363 (m-30) cc_final: 0.8015 (p0) REVERT: N 192 GLN cc_start: 0.8620 (mt0) cc_final: 0.8179 (mm-40) outliers start: 23 outliers final: 12 residues processed: 184 average time/residue: 1.9462 time to fit residues: 383.3007 Evaluate side-chains 186 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 74 LYS 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 123 LEU 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 95 ASN Chi-restraints excluded: chain N residue 222 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 68 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 116 optimal weight: 40.0000 chunk 12 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN G 73 ASN M 152 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.116653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.077351 restraints weight = 23873.960| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.53 r_work: 0.2912 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17076 Z= 0.203 Angle : 0.559 11.358 24428 Z= 0.328 Chirality : 0.035 0.130 2752 Planarity : 0.004 0.049 1988 Dihedral : 29.314 179.852 4890 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.02 % Allowed : 14.07 % 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: 2.38 (0.24), residues: 1198 helix: 2.77 (0.22), residues: 546 sheet: 1.06 (0.34), residues: 240 loop : 0.31 (0.30), 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 0.009 0.001 PHE E 67 TYR 0.011 0.001 TYR M 199 ARG 0.012 0.001 ARG M 191 *********************** 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 196 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 1.398 Fit side-chains REVERT: B 79 LYS cc_start: 0.9071 (mtmm) cc_final: 0.8779 (mtpt) REVERT: C 91 GLU cc_start: 0.8987 (tp30) cc_final: 0.8742 (tp30) REVERT: E 122 LYS cc_start: 0.8998 (pttt) cc_final: 0.8758 (pttt) REVERT: G 36 LYS cc_start: 0.9140 (mmtm) cc_final: 0.8901 (mptt) REVERT: G 91 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8222 (tt0) REVERT: H 34 LYS cc_start: 0.8686 (mtpp) cc_final: 0.8234 (mttp) REVERT: H 36 SER cc_start: 0.9211 (p) cc_final: 0.8950 (p) REVERT: H 68 ASP cc_start: 0.9324 (t70) cc_final: 0.8754 (t0) REVERT: H 86 ARG cc_start: 0.8451 (mtp85) cc_final: 0.7972 (mtp-110) REVERT: M 23 MET cc_start: 0.9079 (OUTLIER) cc_final: 0.8246 (mmm) REVERT: M 46 GLN cc_start: 0.7970 (tt0) cc_final: 0.7685 (mt0) REVERT: M 102 THR cc_start: 0.9435 (OUTLIER) cc_final: 0.9211 (t) REVERT: M 222 ASP cc_start: 0.8849 (t0) cc_final: 0.8354 (t0) REVERT: M 230 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.7561 (tmm) REVERT: N 19 MET cc_start: 0.7364 (tpp) cc_final: 0.6991 (pmt) REVERT: N 49 ARG cc_start: 0.8325 (mtm110) cc_final: 0.7978 (mtm-85) REVERT: N 89 ASP cc_start: 0.8373 (m-30) cc_final: 0.7980 (p0) outliers start: 21 outliers final: 10 residues processed: 183 average time/residue: 1.9719 time to fit residues: 388.2882 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 : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 74 LYS 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 129 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 117 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN M 152 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.116945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.077999 restraints weight = 24102.864| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.50 r_work: 0.2927 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17076 Z= 0.199 Angle : 0.557 11.516 24428 Z= 0.326 Chirality : 0.035 0.130 2752 Planarity : 0.004 0.051 1988 Dihedral : 29.265 179.746 4890 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.54 % Allowed : 15.13 % Favored : 83.33 % 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: 2.43 (0.24), residues: 1198 helix: 2.80 (0.22), residues: 546 sheet: 1.11 (0.34), residues: 240 loop : 0.34 (0.30), 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 0.009 0.001 PHE E 67 TYR 0.012 0.001 TYR M 199 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 189 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 173 time to evaluate : 1.501 Fit side-chains REVERT: B 79 LYS cc_start: 0.9083 (mtmm) cc_final: 0.8806 (mtpt) REVERT: C 91 GLU cc_start: 0.8960 (tp30) cc_final: 0.8718 (tp30) REVERT: E 122 LYS cc_start: 0.9008 (pttt) cc_final: 0.8783 (pttt) REVERT: G 36 LYS cc_start: 0.9132 (mmtm) cc_final: 0.8898 (mptt) REVERT: G 91 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8225 (tt0) REVERT: H 34 LYS cc_start: 0.8645 (mtpp) cc_final: 0.8208 (mttp) REVERT: H 36 SER cc_start: 0.9217 (p) cc_final: 0.8967 (p) REVERT: H 68 ASP cc_start: 0.9307 (t70) cc_final: 0.8775 (t0) REVERT: H 86 ARG cc_start: 0.8436 (mtp85) cc_final: 0.7976 (mtp-110) REVERT: M 46 GLN cc_start: 0.7997 (tt0) cc_final: 0.7756 (mt0) REVERT: M 102 THR cc_start: 0.9442 (OUTLIER) cc_final: 0.9236 (t) REVERT: M 222 ASP cc_start: 0.8835 (t0) cc_final: 0.8365 (t0) REVERT: M 230 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.7619 (tmm) REVERT: N 19 MET cc_start: 0.7380 (tpp) cc_final: 0.6992 (pmt) REVERT: N 37 ARG cc_start: 0.8552 (ttm-80) cc_final: 0.8332 (ttm-80) REVERT: N 49 ARG cc_start: 0.8315 (mtm110) cc_final: 0.7986 (mtm-85) REVERT: N 89 ASP cc_start: 0.8368 (m-30) cc_final: 0.8008 (p0) outliers start: 16 outliers final: 10 residues processed: 179 average time/residue: 1.9497 time to fit residues: 374.8546 Evaluate side-chains 182 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 169 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 76 GLN 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 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 222 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 38 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.115758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.076590 restraints weight = 24040.924| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.50 r_work: 0.2898 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17076 Z= 0.258 Angle : 0.576 11.684 24428 Z= 0.336 Chirality : 0.036 0.130 2752 Planarity : 0.004 0.041 1988 Dihedral : 29.388 178.456 4890 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.25 % Allowed : 15.41 % Favored : 83.33 % 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: 2.30 (0.24), residues: 1198 helix: 2.67 (0.22), residues: 546 sheet: 1.09 (0.34), residues: 240 loop : 0.27 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 0.010 0.001 ARG M 49 ********************** 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 184 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 1.484 Fit side-chains REVERT: B 79 LYS cc_start: 0.9075 (mtmm) cc_final: 0.8794 (mtpt) REVERT: C 91 GLU cc_start: 0.8955 (tp30) cc_final: 0.8673 (tp30) REVERT: E 122 LYS cc_start: 0.9020 (pttt) cc_final: 0.8780 (pttt) REVERT: G 36 LYS cc_start: 0.9127 (mmtm) cc_final: 0.8884 (mptt) REVERT: G 91 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8212 (tt0) REVERT: H 34 LYS cc_start: 0.8652 (mtpp) cc_final: 0.8223 (mttp) REVERT: H 36 SER cc_start: 0.9249 (p) cc_final: 0.8984 (p) REVERT: H 68 ASP cc_start: 0.9311 (t70) cc_final: 0.8739 (t0) REVERT: H 86 ARG cc_start: 0.8468 (mtp85) cc_final: 0.7990 (mtp-110) REVERT: M 37 ARG cc_start: 0.8694 (ttm-80) cc_final: 0.7996 (ttm-80) REVERT: M 46 GLN cc_start: 0.8011 (tt0) cc_final: 0.7752 (mt0) REVERT: M 102 THR cc_start: 0.9450 (OUTLIER) cc_final: 0.9237 (t) REVERT: M 222 ASP cc_start: 0.8892 (t0) cc_final: 0.8450 (t0) REVERT: M 230 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.7764 (tmm) REVERT: N 19 MET cc_start: 0.7384 (tpp) cc_final: 0.6994 (pmt) REVERT: N 37 ARG cc_start: 0.8556 (ttm-80) cc_final: 0.8351 (ttm-80) REVERT: N 49 ARG cc_start: 0.8334 (mtm110) cc_final: 0.8059 (mtm-85) outliers start: 13 outliers final: 8 residues processed: 177 average time/residue: 2.0400 time to fit residues: 387.5880 Evaluate side-chains 180 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 169 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 24 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 31 HIS N 192 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.113237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.071464 restraints weight = 24369.656| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.61 r_work: 0.2778 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17076 Z= 0.271 Angle : 0.583 11.752 24428 Z= 0.339 Chirality : 0.036 0.129 2752 Planarity : 0.004 0.052 1988 Dihedral : 29.499 178.635 4890 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.25 % Allowed : 15.61 % Favored : 83.14 % 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: 2.60 (0.22), residues: 546 sheet: 1.04 (0.34), residues: 240 loop : 0.22 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 259 HIS 0.005 0.001 HIS F 75 PHE 0.008 0.001 PHE E 67 TYR 0.014 0.002 TYR M 199 ARG 0.014 0.001 ARG M 191 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13983.86 seconds wall clock time: 250 minutes 50.39 seconds (15050.39 seconds total)